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Archives of Virology

, Volume 160, Issue 6, pp 1593–1619 | Cite as

Revision of Begomovirus taxonomy based on pairwise sequence comparisons

  • Judith K. BrownEmail author
  • F. Murilo ZerbiniEmail author
  • Jesús Navas-Castillo
  • Enrique Moriones
  • Roberto Ramos-Sobrinho
  • José C. F. Silva
  • Elvira Fiallo-Olivé
  • Rob W. Briddon
  • Cecilia Hernández-Zepeda
  • Ali Idris
  • V. G. Malathi
  • Darren P. Martin
  • Rafael Rivera-Bustamante
  • Shigenori Ueda
  • Arvind Varsani
Virology Division News

Abstract

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Keywords

Geminiviridae Nomenclature Sequence Demarcation Tool Single-stranded DNA virus Species demarcation Taxonomy Whitefly-transmitted viruses 

Introduction

The genus Begomovirus (family Geminiviridae) is the largest genus of plant viruses with respect to the number of species that it includes. In fact, with 288 species currently recognized by the International Committee on Taxonomy of Viruses (ICTV) (http://www.ictvonline.org/virusTaxonomy.asp), it is the largest genus of all viral taxonomy. Begomoviruses infect a wide range of dicotyledonous plants, mostly in tropical and subtropical regions of the world. Their circular, single-stranded DNA genomes can be either monopartite or bipartite (with genomic components known as DNA-A and DNA-B), with the two components of bipartite genomes sharing a common region of approximately 200 nucleotides that includes the origin of replication [1]. In the Old World (OW; Africa, Asia, Australasia and Europe), most begomoviruses are monopartite, with a few having a bipartite genome. Begomoviruses native to the New World (NW; the Americas) are almost exclusively bipartite, with only a single monopartite virus having been identified so far [2, 3]. However, a number of monopartite begomoviruses occur in the NW as a result of their recent introduction from the OW [4, 5].

Geminiviruses have characteristically twinned or “geminate” particle morphology. The capsid consists of two joined, incomplete T = 1 icosahedral heads, with 110 molecules of the capsid protein organized as 22 pentameric capsomers [6]. Geminate particles contain a single molecule of circular ssDNA that ranges from 2.5 to 3.0 kilobases (kb) [1]. Therefore, for viruses having a bipartite genome, two particles, each containing a different genomic component (DNA-A and DNA-B), are required to establish infection.

Due to their economic importance as plant pathogens and their small genomes, begomoviruses were among the first plant viruses whose complete genomes were cloned and sequenced [7, 8]. By January 2014, more than 3500 full-length begomovirus sequences had been deposited in public databases. Even during the early days of full-genome sequencing, the increasingly large numbers of begomovirus sequences being determined worldwide made it clear that these viruses are abundant and widespread, and that they display a significant degree of genetic diversity [9]. Also, it created the opportunity for the development of a sequence-based taxonomy that relied primarily on pairwise sequence comparisons [10]. Such a system has been in place for the Geminiviridae since the mid-1990s, and it has been remarkably stable. It was also widely embraced by the begomovirus community, mostly due to its simplicity and ease of use. Similar classification systems have been adopted by a number of ICTV study groups, including those concerned with the Anelloviridae and the Circoviridae.

As useful as it has been to establish and streamline taxonomic communications, begomovirus taxonomy is not without controversy. Several criticisms have been voiced in the literature (one recent example being ref. [11]) and by the ICTV Executive Committee (EC), which rejected the Geminiviridae Study Group’s taxonomic proposals for creating new begomovirus species in 2010 and 2011. The main points of contention can be summarized as follows: (i) the creation of “too many” species in the genus; (ii) the recognition of new species based solely on sequence comparisons of members, without taking into consideration the biological properties of the viruses; and (iii) the establishment of species demarcation criteria that were “too relaxed” compared to those for other genera in the family, thus leading to point i. Moreover, and as pointed out by the Geminiviridae Study Group (SG) itself in the recent Mastrevirus and Curtovirus taxonomy revisions [12, 13], pairwise sequence identities for any particular pair of sequences may be calculated in different ways and therefore can result in differences in identity scores depending on the algorithm employed. Such discrepancies have made it highly desirable to establish a standard procedure to perform pairwise alignments and to calculate identity scores in order to eliminate (or at least minimize) taxonomic uncertainties and/or misplacements.

The concerns raised by the ICTV EC regarding begomovirus taxonomy encouraged the Geminiviridae SG to perform a comprehensive re-evaluation of the species demarcation criteria for the genus Begomovirus. The results of this re-evaluation have demonstrated that the current pairwise-identity-based taxonomy is sound, that it accurately reflects the biology of begomoviruses, that it will be stable, and that it will be easy to understand and to be adopted by geminivirologists worldwide. Here, we present the specific guidelines for the classification of begomoviruses, following those recently published for the genera Mastrevirus [12] and Curtovirus [13] of the family Geminiviridae.

A comprehensive analysis of the species demarcation criteria for the begomoviruses

Since a significant proportion of begomoviruses do not have a cognate DNA-B component, this component is not considered for species demarcation. A total of 3,123 full-length begomovirus genomic sequences (or DNA-A sequences) were downloaded from the NCBI-GenBank database on 31 Dec 2012. They corresponded to viruses belonging to 283 species according to the currently accepted 89 % species demarcation criterion (for comparison, see the 9th Report of the ICTV, which lists 192 species in the genus [1]). To reduce computing time, only the oldest sequences (full-length genomes or DNA-A components) from groups of sequences that shared >99.5 % genome-wide nucleotide (nt) sequence identity were included in the analysis. To the best of our knowledge, the analysis included sequences of members of all ICTV-recognized species and unclassified begomoviruses for which at least one full-length sequence was available in GenBank at that time (for many, there were multiple sequences per virus/strain). Using this data set (1,826 sequences), a preliminary phylogeny using the neighbor-joining (NJ) method was constructed (data not shown). The purpose of the NJ phylogenetic analysis was not to construct a definitive phylogeny but rather to identify groups of most closely related sequences that could be combined for pairwise sequence comparisons and maximum-likelihood (ML) phylogenetic analyses.

Based on the NJ phylogenetic tree, 38 groups were identified, each of which contained sequences that did not obviously correspond to the same viral species but also did not obviously correspond to distinct species. This approach was employed to more easily delineate distinct groups. Some groups consisted of as few as 2-3 sequences, whereas, others were represented by >30 sequences (Supplementary File S1). Pairwise sequence comparisons were carried out separately for each one of the 38 groups, using Sequence Demarcation Tool (SDT) v. 1.0 [14] with the MUSCLE [15] alignment option. Also, ML phylogenetic trees were predicted for each group using the PHYML3.0 method implemented in MEGA 5.2 [16] with the GTR+I+G nucleotide (nt) substitution model and branch support being tested with 3,000 bootstrap iterations.

Simulations were performed based on the results of pairwise sequence comparisons, using different cutoff values (rounded to the nearest full percentile) to delineate potential species so as to determine which sequences corresponded to virus isolates belonging to the same species, and which were isolates of distinct species. For this, we looked for the optimum cutoff value that placed each sequence into a given species without “outliers” (sequences that displayed identity levels above the cutoff value with two or more species).

Analysis of all 38 groups indicated that the best nt sequence identity cutoff value to separate isolates from different species was 91 %. This value is proposed here as the new species demarcation criterion for viruses of the genus Begomovirus using the outlined methodology. Implementing this value yielded the lowest number of outlier sequences compared to any other value within the range of 86 % to 94 % nt sequence identity. The cutoff for strain demarcation is 94 %. Parameters used for comparison are crucial. It is important to note that percent nt sequence identities must be calculated from true pairwise sequence alignments, with the exclusion of sites with gap characters. Ideally, the SDT software that is freely available [14] (http://web.cbio.uct.ac.za/SDT) should be used, as it was developed specifically for this purpose.

Phylogenetic support was found to be robust for all new species analyzed across the 38 groups. The 91 % cutoff value is actually quite conservative, as is indicated by the trees for groups 3, 5, 7, 11, 16, 30 and 33 (Supplementary File S1). However, several groups (1, 2, 6, 27, 34 and 36; Supplementary File S1) required additional consideration because the pairwise sequence comparisons and phylogenetic results are conflicting, possibly due to recombination.

Dealing with outliers

The resulting taxonomic framework resulted in the delineation of a small number of outliers. Nevertheless, as the number of sequenced begomoviral genomes continues to increase, additional “conflicting” sequences will become evident. To address this problem, we propose the adoption of the approach described for viruses of the genera Mastrevirus [12] and Curtovirus [13]. In this light, the four possible conflicts are as follows:
  1. 1.

    An isolate having ≥91 % identity (full-length genome or DNA-A component) to isolates assigned to two (or more) species.

     
  2. 2.

    An isolate having ≥91 % identity to one or a few isolates from a particular species, even though it shares <91 % identity with the majority of isolates in that species.

     
  3. 3.

    An isolate having ≥94 % identity to isolates of two (or more) strains of a given species.

     
  4. 4.

    An isolate having ≥94 % identity to one or a few isolates from a particular strain, even though it shares <94 % identity with the majority of isolates from that strain.

     
The corresponding conflict-resolution criteria are as follows:
  1. 1.

    The new isolate should be considered to belong to the species that includes the isolate with which it shares the highest percentage of pairwise identity (full-length genome or DNA-A component).

     
  2. 2.

    The new isolate should be classified as belonging to the species with which it shares ≥91 % nt sequence identity with any one isolate from that species, even if it is <91 % identical to all other isolates from that species.

     
  3. 3.

    The new isolate should be considered to belong to the strain that includes the isolate with which it shares the highest percent identity.

     
  4. 4.

    The new isolate should be classified as belonging to the strain with which it shares ≥94 % nt sequence identity with any one isolate from that strain, even if it has <94 % identity to all other isolates from that strain.

     

Naturally, any working cutoff value established for viruses, particularly when rapid divergence is occurring (as appears to be the case for begomoviruses), will yield a number of outliers. By adopting these four conflict-resolution criteria, all outliers identified so far could be readily placed into an extant species group.

Exceptions to these rules can include recombinant viruses such as tomato yellow leaf curl Malaga virus (TYLCMaV) and tomato yellow leaf curl Axarquia virus (TYLCAxV), which have ≥91 % identity to both parental viruses (tomato yellow leaf curl virus, TYLCV, and tomato yellow leaf curl Sardinia virus, TYLCSV), thus leading to conflict #1 and causing the two parental species to merge into a single species, even though all isolates of the parental viruses have <91 % identity. Such recombinant viruses will have to be examined on a case-by-case basis for species assignment.

The new species demarcation criterion of <91 % nt sequence identity (for full-length genomes or DNA-A components) is more stringent than the previously used 89 %

At first, the higher value, at 91 %, compared to the previously implemented working cutoff of 89 %, may give the impression of a more relaxed species demarcation scenario that might delineate an even greater number of begomovirus species. However, this is not the case. Rather, the pairwise cutoff value at 91 % is a consequence of the implementation of a more robust approach (now standardized for the entire family Geminiviridae) for calculating pairwise identities: true pairwise alignments (compared to global alignment-based pairwise identities) without gaps. This proved to be more stringent than previous approaches based on multiple sequence alignments with gaps treated as a fifth character, which yielded a working cutoff of 89 %.

One group of begomoviruses that has been affected the most by applying the revised analysis is the “sweepovirus” group, a divergent clade of whitefly-transmitted geminiviruses that infect sweet potato and wild species in the Convolvulaceae. Previously, the group was proposed to include 17 species [17]. The new system reduces the number of species by more than half, delineating 8 species (Table 1; Fig. 1).
Fig. 1

(A) Pairwise sequence comparisons and (B) maximum-likelihood phylogenetic tree of sequences comprising the “sweepovirus” group. Sequences corresponding to the same species based on a 91 % cutoff (using the parameters described in the main text) are highlighted in the same color

Table 1

List of begomovirus species, as of January 2015. Species names are shown in bold italics, and isolate names are given in regular font. For species that do not have any known strains, only one isolate is listed, and that isolate is recognized as the “type” isolate. For species that have known strains, one isolate from each strain is shown, and the type isolate is the first one listed. Sequence accession numbers and assigned abbreviations are also listed. An expanded table including all begomovirus isolates in GenBank is available for download at the ICTV website (talk.ictvonline.org/ictv_wikis/m/files_begomo/default.aspx)

Abutilon golden mosaic Yucatan virus

   

Abutilon golden mosaic Yucatan virus - [Mexico-Yucatan-2007]

AbGMYV-[MX-Yuc-2007]

KC430935

 

Abutilon mosaic Bolivia virus

   

Abutilon mosaic Bolivia virus - [Bolivia-2007]

AbMBoV-[BO-07]

HM585445

HM585446

Abutilon mosaic Brazil virus

   

Abutilon mosaic Brazil virus - [Brazil-BgV01A.1.C21]

AbMBV-[BR-BgV01A.1.C21]

JF694480

JF694483

Abutilon mosaic virus

   

Abutilon mosaic virus - [Germany]

AbMV-[DE]

X15983

X15984

African cassava mosaic virus

   

African cassava mosaic virus - [Cameroon-1998]

ACMV-[CM-98]

AF112352

AF112353

Ageratum enation virus

   

Ageratum enation virus - Nepal [Nepal-1999]

AEV-NP[NP-99]

AJ437618

 

Ageratum enation virus - India [India-Kangra-2008]

AEV-IN[IN-Kan-08]

FN543099

 

Ageratum enation virus - Uttar Pradesh [India-Uttar Pradesh-SKS-P-2010]

AEV-UP[IN-UP-Ag10-10]

HM149260

 

Ageratum leaf curl virus

   

Ageratum leaf curl virus - [China-Guangxi 52-2003]

ALCuV-[CN-Gx52-03]

AJ851005

 

Ageratum yellow vein Sri Lanka virus

   

Ageratum yellow vein Sri Lanka virus - [Sri Lanka-1999]

AYVSLV-[LK-99]

AF314144

 

Ageratum yellow vein virus

   

Ageratum yellow vein virus - Guangxi [China-Guangxi 129-2005]

AYVV-Gx[CN-Gx129-05]

AM940137

 

Ageratum yellow vein virus - [Japan-Soybean crinkle leaf]

AYVV-[JP-Soy]

AB050781

 

Ageratum yellow vein virus - China [China-Tomato-2012]

AYVV-CN[CN-Tom-12]

KC172826

 

Ageratum yellow vein virus - Hsinchu [Taiwan-Hsinchu-Tom-2003]

AYVV-Hsi[TW-Hsi-Tom-03]

DQ866124

 

Ageratum yellow vein virus - Hualian [Taiwan-Hualian 4-2000]

AYVV-Hua[TW-Hua4-00]

DQ866132

 

Ageratum yellow vein virus - Indonesia [Indonesia-Tomato]

AYVV-ID[ID-Tom]

AB100305

 

Ageratum yellow vein virus - Kamphaengsaen [Thailand-Kamphaengsaen-AFSP3d-2010]

AYVV-Ka[TH-Ka-AFSP3d-10]

JN809816

 

Ageratum yellow vein virus - Nanning [China-Nanning-NN1-2009]

AYVV-NN[CN-Nan-NN1-09]

JQ804985

 

Ageratum yellow vein virus - Philippines [Philippines-Mindanao-2007]

AYVV-PH[PH-Min-07]

EU487045

 

Ageratum yellow vein virus - Singapore [Japan-Ishigaki-2005]

AYVV-SG[JR-Ish-05]

AB306314

 

Ageratum yellow vein virus - Taiwan [Taiwan-Tainan-1999]

AYVV-TW[TW-Tai-99]

AF307861

 

Ageratum yellow vein virus - Thailand [Thailand-Kamphaengsaen-AFSP6b-2010]

AYVV-TH[TH-Ka-AFSP6b-10]

JN809820

 

Allamanda leaf curl virus

   

Allamanda leaf curl virus - [China-Guangdong 10-2006]

AllLCV-A[CN-Gd10-06]

EF602306

 

Alternanthera yellow vein virus

   

Alternanthera yellow vein virus - A [China-Fujian 22-2006]

AlYVV-A[CN-Fj22-06]

EF544604

 

Alternanthera yellow vein virus - B [China-Fujian-PT1-2006]

AlYVV-B[CN-Fj-PT1-06]

EF544602

 

Bean calico mosaic virus

   

Bean calico mosaic virus - [Mexico-Sonora-1986]

BCaMV-[MX-Son-86]

AF110189

AF110190

Bean chlorosis virus

   

Bean chlorosis virus - [Venezuela-LaBarinesa459-2006]

BChV-[VE-LaB459-06]

JN848770

JN848771

Bean chlorotic mosaic virus

   

Bean chlorotic mosaic virus - [Venezuela-Rubio932-2007]

BChMV-[VE-Rub932-07]

JN848772

JN848773

Bean dwarf mosaic virus

   

Bean dwarf mosaic virus - [Colombia-1987]

BDMV-[CO-87]

M88179

M88180

Bean golden mosaic virus

   

Bean golden mosaic virus - [Brazil-Campinas 1-1978]

BGMV-[BR-Cam1-78]

M88686

M88687

Bean golden mosaic virus - Alagoas [Brazil-Mac2-2010]

BGMV-Ala[Brazil-Mac2-2010]

JN419006

 

Bean golden yellow mosaic virus

   

Bean golden yellow mosaic virus - [Dominican Republic-1987]

BGYMV-[DO-87]

L01635

L01636

Bean yellow mosaic Mexico virus

   

Bean yellow mosaic Mexico virus - [Mexico-Mac2-2011]

BYMMxV-[MX-Mac2-11]

FJ944023

 

Bhendi yellow vein Bhubhaneswar virus

   

Bhendi yellow vein Bhubhaneswar virus - [India-Orissa-2003]

BYVBhV-[IN-Ori-03]

FJ589571

 

Bhendi yellow vein mosaic virus

   

Bhendi yellow vein mosaic virus - India [India-Madurai]

BYVMV-IN[IN-Mad]

AF241479

 

Bhendi yellow vein mosaic virus - [India-Maharashtra-NOL751]

BYVMV-[IN-Mah-NOL751]

EU589392

 

Bhendi yellow vein mosaic virus - Haryana [India-Haryana-2007]

BYVMV-Har[IN-Har-07]

FN645923

 

Bhendi yellow vein mosaic virus - Pakistan [Pakistan-Faisalabad 201-1995]

BYVMV-[PK-Fai201-95]

AJ002451

 

Bhendi yellow vein mosaic virus - Tamil Nadu [India-Coimbatore 4-2004]

BYVMV-TN[IN-Coi4-04]

FJ179372

 

Bhendi yellow vein mosaic virus - Thanagan [India-Thanagan-2005]

BYVMV-Tha[IN-Tha-05]

FJ176235

 

Blainvillea yellow spot virus

   

Blainvillea yellow spot virus - [Brazil-Coi25-2007]

BlYSV-[BR-Coi25-07]

EU710756

EU710757

Blechum interveinal chlorosis virus

   

Blechum interveinal chlorosis virus - [Mexico-Campeche-2011]

BleICV-[MX-Cam-11]

JX827487

JX827488

Boerhavia yellow spot virus

   

Boerhavia yellow spot virus - [Mexico-Yucatan-2005]

BoYSV-[MX-Yuc-05]

EF121755

 

Cabbage leaf curl Jamaica virus

   

Cabbage leaf curl Jamaica virus - [Jamaica-CUc3-2005]

CabLCJV-[JM-CUc3-05]

DQ178608

DQ178609

Cabbage leaf curl virus

   

Cabbage leaf curl virus - [United States-Florida-1996]

CabLCV-[US-Flo-96]

U65529

U65530

Capraria yellow spot Yucatan virus

   

Capraria yellow spot Yucatan virus - [Mexico-Yucatan-Conkal-2007]

CarYSYV-[MX-Yuc-Con-07]

KC426927

KC426928

Cassava mosaic Madagascar virus

   

Cassava mosaic Madagascar virus - [Madagascar-Toliary-2006]

CMMGV-[MG-Tol-06]

HE617299

HE617300

Catharanthus yellow mosaic virus

   

Catharanthus yellow mosaic virus - [Pakistan-Lahore-KN4]

CaYMV-[PK-Lah-KN4]

HE580234

 

Centrosema yellow spot virus

   

Centrosema yellow spot virus - [Brazil-Car1-2009]

CeYSV - [BR-Car1-09]

JN419002

 

Chayote yellow mosaic virus

   

Chayote yellow mosaic virus - [Nigeria-Ibadan]

ChaYMV-[NG-Iba]

AJ223191

 

Chenopodium leaf curl virus

   

Chenopodium leaf curl virus - [USA-Florida-Citra-2007]

ChLCV-[[USA-FL-Cit-07]

HM626515

 

Cherry tomato leaf curl virus

   

Cherry tomato leaf curl virus - [India-CTM-2005]

CToLCV-[IN-CTM-06]

DQ629102

 

Chilli leaf curl Pakistan virus

   

Chilli leaf curl Pakistan virus - Pakistan [Pakistan-Shorkot-2004]

ChiLCPKV-PK[PK-Sho-04]

DQ114477

 

Chilli leaf curl Pakistan virus - China [China-Yunnan 1045-2009]

ChiLCPKV-CN[CN-Yn1045-09]

HM587709

 

Chilli leaf curl India virus

   

Chilli leaf curl India virus - [India-2008]

ChiLCINV-[IN-08]

FM877858

 

Chilli leaf curl Kanpur virus

   

Chilli leaf curl Kanpur virus [India-Kanpur-2008]

ChiLCKV-[IN-Kan-08]

HM007106

 

Chilli leaf curl Vellanad virus

   

Chilli leaf curl Vellanad virus - [India-Vellanad-2008]

ChiLCVV-[IN-Vel-08]

HM007121

 

Chilli leaf curl virus

   

Chilli leaf curl virus - India [India-Amritsar-Papaya-2009]

ChiLCV-IN[IN-Amr-Pap-09]

GU136803

 

Chilli leaf curl virus - [Bangladesh-Gazipur]

ChiLCV-[BD-Gaz]

AJ875159

 

Chilli leaf curl virus - Chilli [India-Chilli-2005]

ChiLCV-Chi[IN-Chi-05]

DQ673859

 

Chilli leaf curl virus - Joydebpur [India-Pondalu-Hibiscus-2007]

ChiLCV-JO[IN-Pon-Hib-07]

FJ345402

 

Chilli leaf curl virus - Khanewal [Pakistan-Khanewal-2004]

ChiLCV-Kha[PK-Kha-04]

DQ116878

 

Chilli leaf curl virus - Pakistan [Pakistan-Multan-1998]

ChiLCV-PK[PK-Mul-98]

AF336806

 

Chino del tomate Amazonas virus

   

Chino del tomate Amazonas virus - [Brazil-AM10-2007]

CdTAV-[BR-AM10-07]

HM357461

 

Chino del tomate virus

   

Chino del tomate virus - Tomato [Mexico-Sinaloa IC-1983]

CdTV-To[MX-SinIC-83]

AF101476

AF101478

Chino del tomate virus - [Mexico-Iguala]

CdTV-[MX-Igu]

AY751753

 

Chino del tomate virus - Soybean [Mexico-Sinaloa-2005]

CdTV-Sb[MX-Sin-05]

DQ347945

 

Cleome golden mosaic virus

   

Cleome golden mosaic virus - [Brazil-BA 05-2007]

CleGMV-[BR-BA05-07]

HQ396465

 

Cleome leaf crumple virus

   

Cleome leaf crumple virus - [Brazil-BgV05A.1.C75]

CleLCrV-[BR-BgV051C75]

JF694461

JF694465

Clerodendron yellow mosaic virus

   

Clerodendron yellow mosaic virus - [India-Iari-2006]

ClYMV-[IN-Iari-06]

EF408037

 

Clerodendrum golden mosaic China virus

   

Clerodendron golden mosaic China virus - Fuzon [China-Fuzhou 7-2007]

ClGMCNV-Fu[CN-Fz7-07]

FJ011668

FJ011669

Clerodendron golden mosaic China virus - Jiangsu [China-Jiangsu XY1-2008]

ClGMCNV-Ji[CN-JsXY1-08]

FN396962

FN396963

Clerodendrum golden mosaic Jiangsu virus

   

Clerodendron golden mosaic Jiangsu virus - [China-Jiangsu XY2-2008]

ClGMJsV-[CN-JsXY2-08]

FN396966

 

Clerodendrum golden mosaic virus

   

Clerodendron golden mosaic virus - [Vietnam-Sonla-2005]

ClGMV-[VN-Son-05]

DQ641692

DQ641693

Corchorus golden mosaic virus

   

Corchorus golden mosaic virus - India [India-Bahraich-2008]

CoGMV-Ba[IN-Bah-08]

FJ463902

FJ463901

Corchorus golden mosaic virus - Hanoi [Vietnam-Hanoi-2005]

CoGMV-Ha[VN-Han-05]

DQ641688

DQ641689

Corchorus yellow spot virus

   

Corchorus yellow spot virus - [Mexico-Yucatan-2005]

CoYSV-[MX-Yuc-05]

DQ875868

DQ875869

Corchorus yellow vein mosaic virus

   

Corchorus yellow vein mosaic virus - [India-Maharashtra-2011]

CoYV-[IN-Mah-11]

KC196077

 

Corchorus yellow vein Vietnam virus

   

Corchorus yellow vein Vietnam virus - [Vietnam-Hoa Binh-2000]

CoYVV-[VN-Hoa-00]

AY727903

AY727904

Cotton chlorotic spot virus

   

Cotton chlorotic spot virus - [Brazil-CampinaGrandeB012-2009]

CoChSpV-[BR-Cam-09]

KF358470

 

Cotton leaf crumple virus

   

Cotton leaf crumple virus - Arizona [Mexico-Sonora-1991]

CLCrV-AZ[MX-Son-91]

AF480940

AF480941

Cotton leaf crumple virus - Texas [United States-Texas-1991]

CLCrV-TX[US-Tex-91]

AY083351

 

Cotton leaf curl Alabad virus

   

Cotton leaf curl Alabad virus - Alabad [Pakistan-Alabad 804a-1996]

CLCuAlV-Al[PK-Ala804a-96]

AJ002452

 

Cotton leaf curl Alabad virus - Haryana [India-Karnal-OY77-Okra-2005]

CLCuAlV-Ha[IN-Kar-OY77-Okr-05]

GU112081

 

Cotton leaf curl Alabad virus - Karnal [India-Karnal-OY81B-Okra-2005]

CLCuAlV-Ka[IN-Kar-OY81B-Okr-05]

GU112004

 

Cotton leaf curl Alabad virus - Lobatum [Pakistan-Multan-Lobatum-2006]

CLCuAlV-Lo[PK-Mul-Lob-06]

FJ210467

FJ218488

Cotton leaf curl Alabad virus - Multan [Pakistan-Multan-Punctatum-2006]

CLCuAlV-Mu[PK-Mul-Pun-06]

EU384575

EU384578

Cotton leaf curl Bangalore virus

   

Cotton leaf curl Bangalore virus - [India-Bangalore-2004]

CLCuBaV-[IN-Ban-04]

AY705380

 

Cotton leaf curl Gezira virus

   

Cotton leaf curl Gezira virus - Sudan [Sudan-Gezira-1996]

CLCuGeV-SD[SD-Gez-96]

AF260241

 

Cotton leaf curl Gezira virus - Burkina Faso [Burkina Faso-Bazega-Okra-2009]

CLCuGeV-BF[BF-Baz-Okr-09]

FN554540

 

Cotton leaf curl Gezira virus - Cairo [Egypt-Cairo-Hollyhock]

CLCuGeV-Ca[EG-Cai-Hol]

AJ542539

 

Cotton leaf curl Gezira virus - Cameroon [Cameroon-Muea-Okra-2008]

CLCuGeV-CM[CM-Mue-Okr-08]

FM210276

 

Cotton leaf curl Gezira virus - Egypt [Egypt-Aswan-Okra]

CLCuGeV-EG[EG-Asw-Okr]

AF155064

 

Cotton leaf curl Gezira virus - Hollyhock [Egypt-Giza-Hollyhock]

CLCuGeV-Ho[EG-Giz-Hol]

AF014881

 

Cotton leaf curl Gezira virus - Lysoka [Cameroon-Lysoka11-Okra-2008]

CLCuGeV-Ly[CM-Lys11-Okr08]

FM164726

 

Cotton leaf curl Gezira virus - Madagascar [Madagascar-Fort Dauphin-bean-2001]

CLCuGeV-MG[MG-FtD-Bea-01]

AM701757

 

Cotton leaf curl Gezira virus - Mali [Mali-Bamako-Okra-2006]

CLCuGeV-ML[ML-Bam-Okr-06]

EU024120

 

Cotton leaf curl Gezira virus - Niger [Niger-Niamey2-Okra-2007]

CLCuGeV-NENE-Nia2-Okr-07]

EU432373

 

Cotton leaf curl Gezira virus - Okra [Sudan-Okra-2007]

CLCuGeV-Ok[SD-Okr-07]

FJ868828

 

Cotton leaf curl Kokhran virus

   

Cotton leaf curl Kokhran virus - Kokhran [Pakistan-Faisalabad 1]

CLCuKoV-Ko[PK-Fai1]

AJ496286

 

Cotton leaf curl Kokhran virus - Burewala [Pakistan-Vehari-2006]

CLCuKoV-Bu[PK-Veh-06]

AM421522

 

Cotton leaf curl Kokhran virus - Layyah [Pakistan-Layyah-2011]

CLCuKoV-La[PK-Lay-11]

HF549182

 

Cotton leaf curl Kokhran virus - Lucknow [India-Lucknow-Cyamopsis tetragonoloba-Bean-2010]

CLCuKoV-Lu[IN-Luc-Ct-Bea10]

GU385879

 

Cotton leaf curl Kokhran virus - Shadadpur [Pakistan-Shadadpur-2005]

CLCuKoV-Sha[PK-Sha-05]

FN552001

 

Cotton leaf curl Multan virus

   

Cotton leaf curl Multan virus - Darwinii [Pakistan-Multan-Darwinii 1-2006]

CLCuMuV-Dar[PK-Mul-Dar1-06]

EU365613

 

Cotton leaf curl Multan virus - Faisalabad [Pakistan-Yazman 62-1995]

CLCuMuV-Fai[PK-Yaz62-95]

AJ002447

 

Cotton leaf curl Multan virus - Hibiscus [India-Hibiscus1-2011]

CLCuMuV-Hib[IN-Hib1-11]

JN807763

 

Cotton leaf curl Multan virus - Hisar [Pakistan-Multan-H65-1-1997]

CLCuMuV-His[PK-Mul-H65-1-97]

AJ132430

 

Cotton leaf curl Multan virus - Pakistan [Pakistan-Multan-Davidsonii-2006]

CLCuMuV-PK[PK-Mul-06]

EU365616

 

Cotton leaf curl Multan virus - Rajasthan [India-Sriganganagar-1994]

CLCuMuV-Ra[IN-Sri-94]

AF363011

 

Cowpea golden mosaic virus

   

Cowpea golden mosaic virus - [Nigeria-Nsukka-1990]

CPGMV-[NG-Nsu-90]

AF029217

 

Crassocephalum yellow vein virus

   

Crassocephalum yellow vein virus - [China-Jinhong-2005]

CraYVV-[CN-Jin-05]

EF165536

 

Cucurbit leaf curl virus

   

Cucurbit leaf curl virus - [United States-Arizona-1991]

CuLCuV-[US-Ari-91]

AF256200

AF327559

Dalechampia chlorotic mosaic virus

   

Dalechampia chlorotic mosaic virus - [Venezuela-Albarico1020-2007]

DaChMV-[VE-Alb1020-07]

JN848775

JN848776

Datura leaf distortion virus

   

Datura leaf distortion virus - [Venezuela-Rubio 933-2007]

DaLDV-[VE-Rub933-07]

JN848773

JN848774

Desmodium leaf distortion virus

   

Desmodium leaf distortion virus - [Mexico-Yucatan-2005]

DesLDV-[MX-Yuc-05]

DQ875870

DQ875871

Dicliptera yellow mottle virus

   

Dicliptera yellow mottle virus - [United States-Florida-1998]

DiYMoV-[US-Flo-98]

AF139168

AF170101

Dolichos yellow mosaic virus

   

Dolichos yellow mosaic virus - [Bangladesh-Gazipur]

DoYMV-[BD-Gaz]

AY271891

 

East African cassava mosaic virus

   

East African cassava mosaic virus - Kenya [Kenya-Boa-K48-2001]

EACMV-KE[KE-Boa-K48-01]

AJ717542

AJ704949

East African cassava mosaic virus - [Malawi-8N-2007]

EACMV-[MW-8N-07]

JX473582

 

East African cassava mosaic virus - Cameroon [Cameroon-1998]

EACMV-CM[CM-98]

AF112354

AF112355

East African cassava mosaic virus - Tanzania [Tanzania-1-2001]

EACMV-TZ[TZ-1-01]

AY795983

AY795989

East African cassava mosaic virus - Uganda [Uganda-Mild2-1997]

EACMV-UG[UG-Mld2-97]

AF126804

 

East African cassava mosaic Kenya virus

   

East African cassava mosaic Kenya virus - [Kenya-Kathiana-K300-2002]

EACMKV-[KE-Kat-K300-02]

AJ717580

AJ704965

East African cassava mosaic Malawi virus

   

East African cassava mosaic Malawi virus - [Malawi-K-1996]

EACMMV-[MW-K-96]

AJ006460

 

East African cassava mosaic Zanzibar virus

   

East African cassava mosaic Zanzibar virus - [Kenya-Felunzi-K19-2001]

EACMZV-[KE-Fel-K19-01]

AJ717562

AJ704942

Emilia yellow vein virus

   

Emilia yellow vein virus - [China-Fuzhou 1-2007]

EYVV-[CN-Fz1-07]

U377539

 

Erectites yellow mosaic virus

   

Erectites yellow mosaic virus - [Vietnam-Hoabinh-2005]

ErYMV-[VN-Hoa-05]

DQ641698

 

Eupatorium yellow vein virus

   

Eupatorium yellow vein virus - A [Japan-Kumamoto]

EpYVV-A[JR-Kum]

AB007990

 

Eupatorium yellow vein virus - [Japan-SOJ3-2000]

EpYVV-[JR-SOJ3-00]

AJ438937

 

Eupatorium yellow vein virus - B [Japan-MNS2-2000]

EpYVV-B[JR-MNS2-00]

AJ438936

 

Eupatorium yellow vein virus - C [Japan-Yamaguchi]

EpYVV-C[JR-Yam]

AB079766

 

Eupatorium yellow vein virus - D [Japan-Suya-2007]

EpYVV-D[JR-Suy-07]

AB300463

 

Eupatorium yellow vein virus - E [Japan-Kagawa-Tomato-1997]

EpYVV-E[JR-Kag-97]

AB433979

 

Euphorbia leaf curl Guangxi virus

   

Euphorbia leaf curl Guangxi virus - A [China-Guangxi 35-1-2002]

EuLCGxV-A[CN-Gx35-1-02]

AM411424

 

Euphorbia leaf curl virus

   

Euphorbia leaf curl virus - [China-Fujian-2006]

EuLCuV-[CN-Fuj-06]

FJ487911

 

Euphorbia mosaic virus

   

Euphorbia mosaic virus - [Cuba-Tobacco-2007]

EuMV-[CU-Tb-07]

FJ807782

FJ807783

Euphorbia yellow mosaic virus

   

Euphorbia yellow mosaic virus - [Brazil-2008]

EuMV-[BZ-08]

FJ619507

FJ619508

Euphorbia yellow mosaic virus - Goias [Brazil-GO-Luziania 8675-2009]

EuYMV-GO[BR-GO-Luz 8675-09]

JF756676

 

French bean leaf curl virus

   

French bean leaf curl virus - [India-Kanpur-2011]

FbLCV-[IN-Kan-11]

JQ866297

 

Hedyotis uncinella yellow mosaic virus

   

Hedyotis uncinella yellow mosaic virus - [Vietnam-VN1]

HeuYMV-[VN-VN1]

KF429251

 

Hemidesmus yellow mosaic virus

   

Hemidesmus yellow mosaic virus - [India-Tirupati-H1-2012]

HemYMV-[IN-Tir-H1-12]

KC898543

 

Hollyhock leaf curl virus

   

Hollyhock leaf curl virus - [Pakistan-Faisalabad-20-4-06]

HoLCV-[PK-Fai-20-4-06]

FR772082

 

Honeysuckle yellow vein virus

   

Honeysuckle yellow vein virus - Japan [Japan-Sapporo 1-2000]

HYVV-JR[JR-SP1-00]

AB182261

 

Honeysuckle yellow vein virus - [Australia-Ayr-BRIP57501-1983]

HYVV-[AU-Ayr-BRIP57501-83]

JX416174

 

Honeysuckle yellow vein virus - A [Japan-Fukuoka 1]

HYVV-A[JR-Fuk1]

AB178945

 

Honeysuckle yellow vein virus - B [Japan]

HYVV-B[JR]

AB020781

 

Honeysuckle yellow vein virus - C [Japan-Yamaguchi]

HYVV-C[JR-Yam]

AB079765

 

Honeysuckle yellow vein virus - D [Japan-Nara 2-2006]

HYVV-D[JR-Nar2-06]

AB287441

 

Honeysuckle yellow vein virus - E [Japan-Nara 1-2006]

HYVV-E[JR-Nar1-06]

AB287440

 

Honeysuckle yellow vein virus - Ibaraki [Japan-Ibaraki-Honeysuckle-2006]

HYVV-Iba[JR-Iba-06]

AB287439

 

Honeysuckle yellow vein virus - Jeju [South Korea-Jeju 138-Tomato-2008]

HYVV-Je[KR-Jeju138-To-08]

HM164545

 

Honeysuckle yellow vein virus - Kobe [Japan-Hyogo 12-2000]

HYVV-Kob[JR-Hyo12-00]

AB178946

 

Honeysuckle yellow vein virus - Kochi [Japan-Kochi-Tomato-2000]

HYVV-Koc[JR-Koc-Tom-00]

AB055009

 

Honeysuckle yellow vein virus - Mas [Japan-Masuda-2006]

HYVV-Mas[JR-Mas-06]

AB236325

 

Honeysuckle yellow vein virus - Nara [Japan-Nara3-2001]

HYVV-Nar[JR-Nar3-01]

AB079689

 

Honeysuckle yellow vein virus - South Korea 1 [South Korea-2007]

HYVV-KR1[KR-07]

FJ434943

 

Honeysuckle yellow vein virus - South Korea 2 [South Korea-KJ-Tomato-2007]

HYVV-KR2[KR-KJ-To-07]

HM164547

 

Honeysuckle yellow vein virus - UK [Japan-Fukui-2006]

HYVV-UK[JR-Fuk-06]

AB236321

 

Horsegram yellow mosaic virus

   

Horsegram yellow mosaic virus - [India-Bangalore-2004]

HgYMV-[IN-Ban-04]

AM932427

AM932428

Indian cassava mosaic virus

   

Indian cassava mosaic virus - India [India-Maharashtra 2-1988]

ICMV-IN[IN-Mah2-88]

AY730035

AY730036

Indian cassava mosaic virus - [India-Maharashtra-2009]

ICMV-[IN-Mah-09]

JF496657

 

Indian cassava mosaic virus - Jatropha [India-Dhawad-2008]

ICMV-Jat[IN-Dha-08]

GQ924760

GQ924761

Indian cassava mosaic virus - Kerala [India-Kerala 2-2002]

ICMV-Ker[IN-Ker2-02]

AJ575819

 

Jacquemontia mosaic Yucatan virus

   

Jacquemontia mosaic Yucatan virus - [Mexico-Yucatan-2007]

JacMYuV-[MX-Yuc-07]

JQ821386

JQ821387

Jatropha leaf curl virus

   

Jatropha leaf curl virus - New Delhi [India-New Delhi-2007]

JLCuV-ND[IN-ND-07]

EU798996

 

Jatropha leaf curl virus - [India-Gujarat-2009]

JLCuV-Gu[IN-Guj-09]

GU451249

 

Jatropha mosaic India virus

   

Jatropha mosaic India virus - [India-Lucknow-2009]

JMINV-[IN-Luc-09]

HM230683

 

Jatropha mosaic Nigerian virus

   

Jatropha mosaic Nigerian virus - [Nigeria-2-2011]

JMNV-[NG-2-11]

JX025358

 

Jatropha mosaic virus

   

Jatropha mosaic virus - [Jamaica-Spanish Town 1-2004]

JMV-[JM-ST1-04]

KF723258

KF723261

Jatropha yellow mosaic India virus

   

Jatropha yellow mosaic India virus - [India-Kathaupahadi-2008]

JYMINV-[IN-Kat-08]

FJ177030

 

Kudzu mosaic virus

   

Kudzu mosaic virus - [China-Fujian-2008]

KuMV-[CN-Fuj-08]

FJ539014

FJ539015

Lindernia anagallis yellow vein virus

   

Lindernia anagallis yellow vein virus - [China-Hainan-2004]

LaYVV-[CN-Hn-04]

AY795900

 

Ludwigia yellow vein virus

   

Ludwigia yellow vein virus - [China-Guangxi 37-2003]

LuYVV-[CN-Gx37-03]

AJ965539

 

Luffa yellow mosaic virus

   

Luffa yellow mosaic virus - [Vietnam]

LYMV-[VN]

AF509739

AF509740

Macroptilium golden mosaic virus

   

Macroptilium golden mosaic virus - [Jamaica- Augusta Town-2004]

MacGMV-[JM-StT-04]

EU158096

EU158097

Macroptilium mosaic Puerto Rico virus

   

Macroptilium mosaic Puerto Rico virus - [Puerto Rico-Bean-1998]

MacMPRV-[PR-Bea-98]

AF449192

AF449193

Macroptilium yellow mosaic Florida virus

   

Macroptilium yellow mosaic Florida virus - [United States-Florida-1985]

MacYMFV-[US-Flo-85]

AY044135

AY044136

Macroptilium yellow mosaic virus

   

Macroptilium yellow mosaic virus - Cuba [Cuba]

MacYMV-CU[CU]

AJ344452

 

Macroptilium yellow mosaic virus - Jamaica [Jamaica-Mona-2006]

MacYMV-JM[JM-Mon-06]

EF582840

EF582841

Macroptilium yellow spot virus

   

Macroptilium yellow spot virus - [Brazil-Agua das Flores 1-2010]

MaYSV-[BR-Agf1-10]

JN419013

 

Macroptilium yellow vein virus

   

Macroptilium yellow vein virus - [Brazil-Maceio 4-2010]

MaYVV-[BR-Mac4-10]

JN419021

 

Malvastrum leaf curl Philippines virus

   

Malvastrum leaf curl Philippines virus - [Philippines-Mc1-2012]

MaLCPHV-[PH-Mc1-12]

KC577540

 

Malvastrum leaf curl virus

   

Malvastrum leaf curl virus - [China-Guangxi 100 -Papaya-2005]

MaLCuV-[CN-Gx100-Pap-05]

AM260699

 

Malvastrum yellow mosaic Helshire virus

   

Malvastrum yellow mosaic Helshire virus - [Jamaica–2005]

MaYMHeV-[JM–05]

FJ600483

 

Malvastrum yellow mosaic Jamaica virus

   

Malvastrum yellow mosaic Jamaica virus - [Jamaica-179A73-2003]

MaYMJV-[JM-179A73-03]

FJ601917

FJ600485

Malvastrum yellow mosaic virus

   

Malvastrum yellow mosaic virus - [China-Hainan 36-2004]

MaYMV-[CN-Hn36-04]

AM236755

 

Malvastrum yellow vein virus

   

Malvastrum yellow vein virus - [China-Yunnan 206-Ageratum-2003]

MaYVV-[CN-Yn206-Age-03]

AJ744881

 

Malvastrum yellow vein virus - A [China-Yunnan 278-2004]

MaYVV-A[CN-Yn278-04]

FN386459

 

Malvastrum yellow vein virus - B [China-Yunnan 340-Sida-2008]

MaYVV-C[CN-Yn340-Sid-08]

FN806779

 

Malvastrum yellow vein Yunnan virus

   

Malvastrum yellow vein Yunnan virus - [China-Yunnan 160-2003]

MaYVYnV-[CN-Yn160-03]

AJ786711

 

Melon chlorotic leaf curl virus

   

Melon chlorotic leaf curl virus - Costa Rica [Costa Rica-Guanacaste-1998]

MCLCuV-CR[CR-Gua-98]

AY064391

AF440790

Melon chlorotic leaf curl virus - [Costa Rica-Cucurbita-2A-2003]

MCLCuV-[CR-Cuc-2A-03]

KC153490

 

Melon chlorotic leaf curl virus - Guatemala [Guatemala-2000]

MCLCuV-GT[GT-00]

AF325497

AF325498

Melon chlorotic mosaic virus

   

Melon chlorotic mosaic virus - [Venezuela-Watermelon-2009]

MClMV-[VN-Wat-09]

HM163576

HM163577

Merremia leaf curl virus

   

Merremia leaf curl virus - [Puerto Rico-N1-2006]

MerLCV-[PR-N1-06]

DQ644561

 

Merremia mosaic virus

   

Merremia mosaic virus - Venezuela [Venezuela-Trujillo]

MerMV-VE[VE-Tru]

AY508991

AY508992

Merremia mosaic virus - Puerto Rico [Puerto Rico-]

MerMV-PR[PR]

AF068636

AY965899

Merremia mosaic Puerto Rico virus

   

Merremia mosaic Puerto Rico virus - [Puerto Rico-89-1998]

MerMPRV-[PR-PR89-98]

FJ944021

FJ944022

Mesta yellow vein mosaic Bahraich virus

   

Mesta yellow vein mosaic Bahraich virus - [India-Bahraich-2007]

MeYVMBaV-[IN-Bah-07]

EU360303

 

Mesta yellow vein mosaic virus

   

Mesta yellow vein mosaic virus - Andhra Pradesh [India-Amadalavalasa 27-2008]

MeYVMV-And[IN-Ama27-08]

FJ159269

 

Mesta yellow vein mosaic virus - [Pakistan-Changa Manga-2009]

MeYVMV-[PK-CM-09]

FR715681

 

Mesta yellow vein mosaic virus - Bengal [India-Bongaon-Leaf curl-2007]

MeYVMV-Ben[IN-Bon-LC-07]

FJ345400

 

Mimosa yellow leaf curl virus

   

Mimosa yellow leaf curl virus - [Vietnam-Binhduong-2005]

MiYLCV-[VN-Bin-05]

DQ641695

 

Mungbean yellow mosaic India virus

   

Mungbean yellow mosaic India virus - [India- Sriganganagar-Mungbean 1-1996]

MYMIV-[IN-Sri-Mg1-96]

AF416742

AF416741

Mungbean yellow mosaic virus

   

Mungbean yellow mosaic virus - [India-Madurai-Soybean]

MYMV-[IN-Mad-Sb]

AJ421642

AJ867554

Okra enation leaf curl virus

   

Okra enation leaf curl virus - [India-Sonipat EL10-2006]

OELCuV-[IN-SonEL10-06]

GU111996

 

Okra mottle virus

   

Okra mottle virus - [Brazil-6319-2008]

OMoV-[BR-6319-08]

EU914817

EU914818

Okra yellow crinkle virus

   

Okra yellow crinkle virus - Cameroon [Cameroon-Muea-2008]

OYCrV-CM[CM-Mue-08]

FM210275

 

Okra yellow crinkle virus - [Cameroon-Njombe 5-2007]

OYCrV-[CM-Njo5-07]

HE793424

 

Okra yellow crinkle virus - Mali [Mali-Bamako 4-2006]

OYCrV-ML[ML-Bam4-06]

EU024119

 

Okra yellow mosaic Mexico virus

   

Okra yellow mosaic Mexico virus - [Mexico-Mazatepec 3-2004]

OYMV-[MX-Maz3-04]

DQ022611

GU972604

Papaya leaf crumple virus

   

Papaya leaf crumple virus - [India-Nirulas-2007]

PaLCrV-[IN-Nir-07]

HM140368

 

Papaya leaf curl China virus

   

Papaya leaf curl China virus - Ageratum [China-Guangxi 10-Ageratum-2002]

PaLCuCNV-Age[CN-Gx10-02]

AJ558125

 

Papaya leaf curl China virus - [China-Hainan-HK7-2008]

PaLCuCNV-[CN-Hn-HK7-08]

FN256261

 

Papaya leaf curl China virus - Guangxi [China-Guangxi 4-Tomato-2008]

PaLCuCNV-Gx[CN-Gx8-To-08]

FN297834

 

Papaya leaf curl China virus - Papaya [China-Guangxi 30-Tomato-2002]

PaLCuCNV-Pap[CN-Gx30-Tom-02]

AJ558117

 

Papaya leaf curl China virus - Tomato [China-Guangxi 12-Tomato-2002]

PaLCuCNV-To[CN-Gx12-02]

AJ558116

 

Papaya leaf curl China virus - Vietnam [Vietnam-Hanoi 112-2007]

PaLCuCNV-VN[VN-Han112-07]

GQ373254

 

Papaya leaf curl Guang dong virus

   

Papaya leaf curl Guangdong virus - [China-Fujian-Euphorbia-2006]

PaLCuGdV-[CN-Fuj-Eu-06]

FJ495184

 

Papaya leaf curl virus

   

Papaya leaf curl virus - Lucknow [India-Lucknow]

PaLCuV-Luc[IN-Luc]

Y15934

 

Papaya leaf curl virus - A [India-WB-Cr-Croton-2008]

PaLCuV-A[IN-WB-Cr-Cro-08]

JN817517

 

Papaya leaf curl virus - Amaranthus [India-Lucknow-Amaranthus-2011]

PaLCuV-Ama[PK-Luc-Am-11]

JN135233

 

Papaya leaf curl virus - Aster [India-Lucknow-Aster-2011]

PaLCuV-Ast[PK-Luc-As-11]

JQ954859

 

Papaya leaf curl virus - Cirica [India-PaND13-2012]

PaLCuV-Cir[IN-PaND13-12]

KF307208

 

Papaya leaf curl virus - Croton[India-Croton]

PaLCuV-Cro[IN-Cro]

AJ507777

 

Papaya leaf curl virus - India [India-Pataudi-Radish-2009]

PaLCuV-IN[IN-Pat-Rad-09]

FJ593629

 

Papaya leaf curl virus - Lahore [Pakistan-Lahore-HYDNA-Alcea rosea-2006]

PaLCuV-Lah[PK-Lah-HYDNA-Alc-06] FN678906

  

Papaya leaf curl virus - Pakistan [Pakistan-Cotton-2002]

PaLCuV-PK[PK-Cot-02]

AJ436992

 

Papaya leaf curl virus - Punjab [Pakistan-Punjab-Cro-2006]

PaLCuV-Pun[PK-Pun-Cro-06]

FN543112

 

Papaya leaf curl virus - Rhynchosia [Pakistan-Mianwali-Rhynchosia capitata-2007]

PaLCuV-Rh[PK-Mia-Rc-07]

FM955601

 

Papaya leaf curl virus - Sikar [India-Sikar-Calotropis procera-2010]

PaLCuV-Sik[In-Sik-Cal-10]

JQ407224

 

Papaya leaf curl virus - Soybean [India-Lucknow-Soybean-2011]

PaLCuV-Soy[IN-Luc-Soy-11]

JN807765

 

Papaya leaf curl virus - Tobacco[India-Lucknow-Nicotiana glutinosa-2010]

PaLCuV-Tob[IN-Luc-Nic-10]

HM143914

 

Papaya leaf curl virus - Tomato [India-CTM-Tomato-2005]

PaLCuV-Tom[IN-CTM-Tom-06]

DQ629102

 

Passionfruit severe leaf distortion virus

   

Passionfruit severe leaf distortion virus - [Brazil-LSN 2-2001]

PSLDV-[BR-LSN2-01]

FJ972767

FJ972768

Pedilanthus leaf curl virus

   

Pedilanthus leaf curl virus - [Pakistan-Multan-2006]

PeLCV-[PK-Mul-06]

AM712436

 

Pedilanthus leaf curl virus - Euphorbia [Pakistan-Rahim Yar Khan 1-Tomato-2004]

PeLCV-Eu[PK-RYK1-To-04]

DQ116884

 

Pedilanthus leaf curl virus - Soybean [Pakistan-Nawab Shah-Soybean-2009]

PeLCV-Sb[PK-NS-Sb-09]

AM948961

 

Pepper golden mosaic virus

   

Pepper golden mosaic virus - United States [United States-Mosaic-1987]

PepGMV-US[US-Mos-87]

AY928512

AY928513

Pepper golden mosaic virus - Costa Rica [Costa Rica]

PepGMV-CR[CR]

AF149227

 

Pepper golden mosaic virus - [Costa Rica-Llano Grande-2008]

PepGMV-[CR-LG-08]

JQ743486

 

Pepper huasteco yellow vein virus

   

Pepper huasteco yellow vein virus - [Mexico-Tamaulipas]

PHYVV-[MX-Tam]

X70418

X70419

Pepper leaf curl Bangladesh virus

   

Pepper leaf curl Bangladesh virus - Bangladesh [Bangladesh-Bogra-1999]

PepLCBV-BD[BD-Bog-99]

AF314531

 

Pepper leaf curl Bangladesh virus - [Pakistan-Lahore-2004]

PepLCBV-[PK-Lah-04]

AM404179

 

Pepper leaf curl Bangladesh virus - India [India-Coimbatore-2008]

PepLCBV-IN[IN-Coi-08]

HM007096

 

Pepper leaf curl Bangladesh virus - Pakistan [Pakistan-Khanewal-2004]

PepLCBV-PK[PK-Kha-04]

DQ116881

 

Pepper leaf curl Lahore virus

   

Pepper leaf curl Lahore virus - [India-Lucknow-2011]

PepLCLaV-[IN-Luc-11]

JN135234

 

Pepper leaf curl virus

   

Pepper leaf curl virus - Malaysia [Malaysia-Klang-1997]

PepLCV-MY[MY-Kla-97]

AF414287

 

Pepper leaf curl virus - Thailand [Thailand]

PepLCV-TH[TH]

AF134484

 

Pepper leaf curl Yunnan virus

   

Pepper leaf curl Yunnan virus - [China-Yunnan323-2007]

PepLCYnV-[CN-Yn323-07]

EU585781

 

Pepper yellow leaf curl China virus

   

Pepper yellow leaf curl China virus - [China-YN65-1-2010]

PepYLCCNV-[CN-YN65-1-10]

KC149938

 

Pepper yellow leaf curl Indonesia virus

   

Pepper yellow leaf curl Indonesia virus - [Indonesia-2005]

PepYLCIV-[ID-05]

AB267834

AB267835

Pepper yellow vein Mali virus

   

Pepper yellow vein Mali virus - [Burkina Faso-Banfora-hot pepper1-2009]

PepYVMLV-[BF-Ban-Hpe1-09]

FN555172

 

Potato yellow mosaic virus

   

Potato yellow mosaic virus - Potato [Venezuela-1991]

PYMV-Po[VE-91]

D00940

D00941

Potato yellow mosaic virus - [Trinidad and Tobago-Tomato-1996]

PYMV-[TT-Tom-96]

AF039031

AF039032

Potato yellow mosaic virus - Colombia [Colombia-Valle del Cauca-Tomato-2007]

PYMV-Co[CO-VdC-Tom-07]

EU518935

 

Potato yellow mosaic virus - Tomato [Puerto Rico-Tomato-2004]

PYMV-To[PR-Tom-04]

AY965897

AY965898

Pouzolzia golden mosaic virus

   

Pouzolzia golden mosaic virus - [China-TY01-2012]

PouGMV-[CN-TY01-12]

JX183732

 

Pouzolzia mosaic Guangdong virus

   

Pouzolzia mosaic Guangdong virus - [Taiwan-Miaoli-ML13W1-2013]

PouMGDV-[TW-Mia-ML13W1-13]

KF414123

 

Premna leaf curl virus

   

Premna leaf curl virus - [Vietnam-VN7-2011]

PreLCV-[VN-VN7-11]

JQ793786

 

Pumpkin yellow mosaic Malaysia virus

   

Pumpkin yellow mosaic Malaysia virus - [Malaysia-Negeri Sambilan-2001]

PuYMV-[MY-Neg-01]

EF197941

 

Radish leaf curl virus

   

Radish leaf curl virus - [India-Varanasi-2005]

RaLCuV-[IN-Var-03]

EF175733

 

Radish leaf curl virus - Tomato [Pakistan-Bihar-Tomato-2009]

RaLCuV-To[PK-Bih-To-09]

GU732204

 

Rhynchosia golden mosaic Havana virus

   

Rhynchosia golden mosaic Havana virus - [Cuba-Havana-2007]

RhGMHaV-[CU-Hav-07]

HM236368

HM236369

Rhynchosia golden mosaic virus

   

Rhynchosia golden mosaic virus - Mexico [Mexico-Sinaloa-2005]

RhGMV-MX[MX-Sin-05]

DQ347950

DQ356429

Rhynchosia golden mosaic virus - Honduras [Mexico-Chiapas-Tobacco]

RhGMV-HN[MX-Chi-Tob]

AF408199

 

Rhynchosia golden mosaic virus - Soybean [Mexico-Sinaloa 4-Soybean-2007]

RhGMV-Sb[MX-Sin4-Sb-07]

EU339936

EU339937

Rhynchosia mild mosaic virus

   

Rhynchosia mild mosaic virus - [Puerto Rico-PR79-1997]

RhMMV-[PR-PR79-97]

FJ944019

 

Rhynchosia rugose golden mosaic virus

   

Rhynchosia rugose golden mosaic virus - [Cuba-Camaguey-2009]

RhRGMV-[CU-Cam-09]

HM236370

HM236371

Rhynchosia yellow mosaic India virus

   

Rhynchosia yellow mosaic India virus - [India-Thiruvananthapuram-JRH1-2009]

RhYMIV-[IN-Thi-JRH1-09]

HM777508

HM777510

Rhynchosia yellow mosaic virus

   

Rhynchosia yellow mosaic virus - [Pakistan-Lahore33-2007]

RhYMV-[PK-Lah33-07]

AM999981

AM999982

Rose leaf curl virus

   

Rose leaf curl virus - [Pakistan-Faisalabad-2006]

RoLCuV-[PK-Fai-06]

GQ478342

 

Sauropus leaf curl virus

   

Sauropus leaf curl virus - [Thailand-Kamphaengsaen-AFSP5e-2010]

SauLCuV-[TH-Kam-AFSP5e-10]

JN809820

 

Senecio yellow mosaic virus

   

Senecio yellow mosaic virus - [China-Guangxi 46-2003]

SeYMV-[CN-Gx46-03]

AJ876550

 

Sida ciliaris golden mosaic virus

   

Sida ciliaris golden mosaic virus - [Venezuela-Lara-M3-2009]

SicGMV-[VE-Lar-M3-09]

JX857691

 

Sida common mosaic virus

   

Sida common mosaic virus - [Brazil-Coimbra 4-2007]

SiCMV-[BR-Coi4-07]

EU710751

 

Sida golden mosaic Braco virus

   

Sida golden mosaic Braco virus - [Jamaica-Liguanea-A4-2008]

SiGMBcV-[JM-Lin-A4-08]

JX162595

 

Sida golden mosaic Brazil virus

   

Sida golden mosaic Brazil virus - [Brazil-Mato Grosso do Sul-2007]

SiGMBRV-[BR-MS-07]

FN436001

 

Sida golden mosaic Buckup virus

   

Sida golden mosaic Buckup virus - [Jamaica-St Elizabeth 1-2004]

SiGMBuV-[JM-SE1-04]

HQ008338

HQ009518

Sida golden mosaic Costa Rica virus

   

Sida golden mosaic Costa Rica virus - [Costa Rica]

SiGMCRV-[CR]

X99550

X99551

Sida golden mosaic Florida virus

   

Sida golden mosaic Florida virus - Malvastrum [Cuba-Havana-Malvastrum-111-2009]

SiGMFlV-Malv[CU-Hav-Mal-111-09]

HM003779

HM003778

Sida golden mosaic Florida virus - [United States-Homestead-A1]

SiGMFlV-[US-Hom-A1]

U77963

 

Sida golden mosaic Lara virus

   

Sida golden mosaic Lara virus - [Venezuela-Lara-M1-2009]

SiGMLaV-[VE-Lar-M1-09]

JX857693

 

Sida golden mosaic virus

   

Sida golden mosaic virus - [United States-Florida]

SiGMV-[US-Flo]

AF049336

AF039841

Sida golden mottle virus

   

Sida golden mottle virus - [United States-Florida-Bradenton-1997]

SiGMoV-[US-Flo-Bra-97]

GU997691

GU997692

Sida golden yellow vein virus

   

Sida golden yellow vein virus - [Cuba-Havana]

SiGYVV-[CU-Hav]

AJ577395

 

Sida leaf curl virus

   

Sida leaf curl virus - [China-Hainan 57-2004]

SiLCuV-[CN-Hn57-04]

AM050730

 

Sida micrantha mosaic virus

   

Sida micrantha mosaic virus - [Brazil-A2B2]

SiMMV-[BR-A2B2]

AJ557451

AJ557453

Sida micrantha mosaic virus - Rhombifolia [Bolivia-Cerro Fraile 2-2007]

SiMMV-Rho[Bo-CF2-07]

HM585439

 

Sida micrantha mosaic virus - Santaremensi [BR-GO-Luziania 780-2003]

SiMMV-San[BR-GO-Luz780-03]

JX415187

 

Sida mosaic Bolivia virus 1

   

Sida mosaic Bolivia virus 1 - [Bolivia-Sida micrantha-2007]

SiMBoV1-[BO-mic-07]

HM585441

 

Sida mosaic Bolivia virus 2

   

Sida mosaic Bolivia virus 2 - [Bolivia-Sida micrantha-2007]

SiMBoV2-[BO-mic-07]

HM585443

 

Sida mosaic Sinaloa virus

   

Sida mosaic Sinaloa virus - [Mexico-Guasave-2006]

SiMSiV-[MX-Gua-06]

DQ520944

DQ356428

Sida mottle Alagoas virus

   

Sida mottle Alagoas virus - [BR-Alagoas-Vicosa 2-2010]

SiMoAV-[BR-AL-Vsa2-10]

JX871385

 

Sida mottle virus

   

Sida mottle virus - Micrantha [Brazil-A1B3]

SiMoV-Mic[BR-A1B3]

AJ557450

AJ557454

Sida mottle virus - Rhombifolia [Brazil-Vicosa 1-1999]

SiMoV-Rho[BR-Vic1-99]

AY090555

 

Sida yellow blotch virus

   

Sida yellow blotch virus - [Brazil-Rio Largo 1-2010]

SiYBV-[BR-Rla1-10]

JX871380

 

Sida yellow leaf curl virus

   

Sida yellow leaf curl virus - [Brazil-Coimbra3-2007]

SiYLCV-[BR-Coi3-07]

EU710750

 

Sida yellow mosaic Alagoas virus

   

Sida yellow mosaic Alagoas virus - [Brazil-Alagoas-Vicosa 3-2010]

SiYMAV-[BR-AL-Vsa3-10]

JX871383

 

Sida yellow mosaic China virus

   

Sida yellow mosaic China virus - [China-Hainan 7-Ageratum-2003]

SiYMCNV-[CN-Hn7-Age-03]

AM048837

 

Sida yellow mosaic virus

   

Sida yellow mosaic virus - [Brazil-Vicosa 2-1999]

SiYMV-[BR-Vic2-99]

AY090558

 

Sida yellow mosaic Yucatan virus

   

Sida yellow mosaic Yucatan virus - [Mexico-Yucatan-2005]

SiYMYuV-[MX-Yuc-05]

DQ875872

DQ875873

Sida yellow mottle virus

   

Sida yellow mottle virus - [Cuba-Sancti Spiritus159-1-2009]

SiYMoV-[CU-SSp159-1-09]

JN411687

JN411688

Sida yellow vein Vietnam virus

   

Sida yellow vein Vietnam virus - [Vietnam-Hanoi-2005]

SiYVVV-[VN-Han-05]

DQ641696

 

Sida yellow vein virus

   

Sida yellow vein virus - [Honduras-yellow vein]

SiYVV-[HN-yv]

Y11099

Y11100

Sidastrum golden leaf spot virus

   

Sidastrum golden leaf spot virus - [Brazil-DF334-2010]

SidGLSV-[BR-DF334-10]

HM357458

 

Siegesbeckia yellow vein Guangxi virus

   

Siegesbeckia yellow vein Guangxi virus - [China-Guangxi 111-2005]

SgYVGxV-[CN-Gx111-05]

AM238692

 

Siegesbeckia yellow vein virus

   

Siegesbeckia yellow vein virus - [China-Guangdong 13-2004]

SgYVV-[CN-Gd13-04]

AM183224

 

Solanum mosaic Bolivia virus

   

Solanum mosaic Bolivia virus - [Bolivia-2007]

SoMBoV-[BO-07]

HM585435

 

South African cassava mosaic virus

   

South African cassava mosaic virus - [Madagascar-12]

SACMV-[MG-12]

AJ422132

 

Soybean blistering mosaic virus

   

Soybean blistering mosaic virus - [Argentina-NOA-2005]

SbBMV-[AR-NOA-05]

EF016486

 

Soybean chlorotic blotch virus

   

Soybean chlorotic blotch virus - [Nigeria-Soybean 19-2007]

SbCBV-[NG-Sb19-07]

GQ472985

GQ472986

Soybean mild mottle virus

   

Soybean mild mottle virus - [Nigeria-Soybean 17-2007]

SbMMoV-[NG-Sb17-07]

GQ472984

 

Spilanthes yellow vein virus

   

Spilanthes yellow vein virus - [Vietnam-Dalat-2005]

SpYVV-[VN-Dal-05]

DQ641694

 

Spinach yellow vein Sikar virus

   

Spinach yellow vein Sikar virus - [India-Sikar-AS22]

SpiYVSKV-[IN-Sik-AS22]

KF660223

 

Squash leaf curl China virus

   

Squash leaf curl China virus - China [China-Guangxi25-2005]

SLCCNV-CN[CN-Gx25-05]

AM260206

AM260208

Squash leaf curl China virus - [Philippines-Benguet-P54]

SLCCNV-[PH-Ben-P54]

EU487031

 

Squash leaf curl China virus - India [Pakistan-Lahore-2004]

SLCCNV-IN[PK-Lah-04]

AM286794

AM778959

Squash leaf curl China virus - Thailand [Thailand-Nakhon Pathom-Wax Gourd-2007]

SLCCNV-TH[TH-NP-WG-07]

EU543562

 

Squash leaf curl Philippines virus

   

Squash leaf curl Philippines virus - [Philippines-Batangas P133-Pumpkin-2007]

SLCuPV-[PH-BatP133-Pum-07]

EU487041

 

Squash leaf curl virus

   

Squash leaf curl virus - [Jordan-Malva-2006]

SLCuV-[JD-Mal-06]

EF532620

EF532621

Squash leaf curl Yunnan virus

   

Squash leaf curl Yunnan virus- [China-Yunnan-Y23]

SLCuYV-[CN-Yun-Y23]

AJ420319

 

Squash mild leaf curl virus

   

Squash mild leaf curl virus - [United States-Imperial Valley-1979]

SMLCuV-[US-IV-79]

AF421552

AF421553

Sri Lankan cassava mosaic virus

   

Sri Lankan cassava mosaic virus - India [India-Adivaram-2003]

SLCMV-IN[IN-Adi-03]

AJ579307

AJ579308

Sri Lankan cassava mosaic virus - Sri Lanka [Sri Lanka-Colombo-1998]

SLCMV-LK[LK-Col-98]

AJ314737

AJ314738

Stachytarpheta leaf curl virus

   

Stachytarpheta leaf curl virus - [China-Hainan 30-2004]

StaLCuV-[CN-Hn30-04]

AJ810156

 

Sunn hemp leaf distortion virus

   

Sunn hemp leaf distortion virus - [India-Barrackpore 1-2008]

SHLDV-[IN-Bar-08]

FJ455449

 

Sweet potato leaf curl Canary virus

   

Sweet potato leaf curl Canary virus - [Spain-Canary Islands-BG4-2002]

SPLCCV-[ES-CI-BG4-02]

EF456742

 

Sweet potato leaf curl China virus

   

Sweet potato leaf curl China virus - [China-2005]

SPLCCNV-[CN-05]

DQ512731

 

Sweet potato leaf curl Georgia virus

   

Sweet potato leaf curl Georgia virus - [United States-Georgia-16]

SPLCGV-[US-Geo-16]

AF326775

 

Sweet potato leaf curl Henan virus

   

Sweet potato leaf curl Henan virus - [China-Henan 10-2012]

SPLCHnV-[CN-Hn10-12]

KC907406

 

Sweet potato leaf curl Sao Paulo virus

   

Sweet potato leaf curl Sao Paulo virus - [Brazil-Sao Paulo-Alvares Machado-2009]

SPLCSPV-[BR-SP-AlvM-09]

HQ393477

 

Sweet potato leaf curl Sichuan virus 1

   

Sweet potato leaf curl Sichuan virus 1 - [China-Sichuan 15-2012]

SPLCSiV-1-[CN-Sc15-12]

KC488316

 

Sweet potato leaf curl Sichuan virus 2

   

Sweet potato leaf curl Sichuan virus 2 - [China-Sichuan 14-2012]

SPLCSiV-2-[CN-Sc14-12]

KF156759

 

Sweet potato leaf curl South Carolina virus

   

Sweet potato leaf curl South Carolina virus - [United States-South Carolina-648-B9-2006]

SPLCSCV-[US-SC-648-B9-06]

HQ333144

 

Sweet potato leaf curl Uganda virus

   

Sweet potato leaf curl Uganda virus - [Uganda-Kampala-2008]

SPLCUV-[UG-KAMP-08]

FR751068

 

Sweet potato leaf curl virus

   

Sweet potato leaf curl virus - China [China-Yunnan-RL31-2006]

SPLCV-CN[CN-Yn-RL31-06]

EU253456

 

Sweet potato leaf curl virus - [Spain-1998]

SPLCV-[ES-98]

AJ132548

 

Sweet potato leaf curl virus - Brazil [Brazil-Para-Belem1-2008]

SPLCV-BR[BR-PA-Bel1-08]

FJ969829

 

Sweet potato leaf curl virus - Fujian [China-Jujian-Fp3-2007]

SPLCV-Fu[CN-Fuj-Ip3-07]

FJ515898

 

Sweet potato leaf curl virus - Italy [Italy-Sicily-2002]

SPLCV-IT[IT-Sic-02]

AJ586885

 

Sweet potato leaf curl virus - Japan [Japan-Miyazaki-1996]

SPLCV-JP[JR-Miy-96]

AB433786

 

Sweet potato leaf curl virus - Paraiba [Brazil-Paraiba-Souza1-2008]

SPLCV-PB[BR-PB-Sou1-08]

FJ969830

 

Sweet potato leaf curl virus - Pernambuco [Brazil-Rondonia-Porto Velho-2008]

SPLCV-PE[BR-RO-PV-08]

HQ393456

 

Sweet potato leaf curl virus - Puerto Rico [Puerto Rico-80-N2-2006]

SPLCV-PR[PR-80-N2-06]

DQ644562

 

Sweet potato leaf curl virus - Rondonia [Brazil-Bahia-Utinga-2008]

SPLCV-RO[BR-BA-Uti-08]

HQ393447

 

Sweet potato leaf curl virus - Sao Paulo [Brazil-Sao Paulo-Alvares Machado-2009]

SPLCV-SP[BR-SP-AlvM-09]

HQ393473

 

Sweet potato leaf curl virus - South Carolina [United States-South Carolina-646-B11-2006]

SPLCV-SC[US-SC-646-B11-06]

HQ333138

 

Sweet potato leaf curl virus - Spain [Spain-Canary Islands-BG6-2002]

SPLCV-ES[ES-CI-BG6-02]

EF456744

 

Sweet potato leaf curl virus - United States [United States- Louisiana-1994]

SPLCV-US[US-Lou-94]

AF104036

 

Sweet potato mosaic virus

   

Sweet potato mosaic virus - [Brazil-Brasilia1-2008]

SPMV-[BR-BSB1-08]

FJ969831

 

Tobacco curly shoot virus

   

Tobacco curly shoot virus - [China-Alternanthera-2008]

TbCSV-[CN-Alt-08]

GU199583

 

Tobacco leaf curl Comoros virus

   

Tobacco leaf curl Comoros virus - [Comoros-Simboussa-2004]

TbLCKMV-[KM-Sim-04]

AM701760

 

Tobacco leaf curl Cuba virus

   

Tobacco leaf curl Cuba virus - [Cuba-Taguasco-2005]

TbLCuCV-[CU-Tag-05]

AM050143

 

Tobacco leaf curl Pusa virus

   

Tobacco leaf curl Pusa virus - [India-Pusa-2009]

TbLCPuV-To[IN-Pus-09]

HQ180391

 

Tobacco leaf curl Thailand virus

   

Tobacco leaf curl Thailand virus - [Thailand-Tomato-2005]

TbLCTHV-[TH-To-05]

DQ871221

 

Tobacco leaf curl Yunnan virus

   

Tobacco leaf curl Yunnan virus - China [China-Yunnan 136-2002]

TbLCYnV-CN[CN-Yn136-02]

AJ512761

 

Tobacco leaf curl Zimbabwe virus

   

Tobacco leaf curl Zimbabwe virus - [Comoros-Foumboudziouni-2005]

TbLCZV-[KM-Fou-05]

AM701756

 

Tobacco leaf rugose virus

   

Tobacco leaf rugose virus - [Cuba-Havana-2001]

TbLRV-[CU-Hav-01]

AJ488768

 

Tobacco mottle leaf curl virus

   

Tobacco mottle leaf curl virus - [Cuba-Sanci Spiritus-2003]

TbMoLCV-[CU-SS-03]

FM160943

 

Tobacco yellow crinkle virus

   

Tobacco yellow crinckle virus - [Cuba–2007]

TbYCV-[CU–07]

FJ213931

HQ896204

Tomato bright yellow mosaic virus

   

Tomato bright yellow mosaic virus - [Brazil-BA167-2012]

ToBYMV-[BR-BA167-12]

KC791690

 

Tomato bright yellow mottle virus

   

Tomato bright yellow mottle virus - [Brazil-TO167-2008]

ToBYMoV-[BR-TO167-08]

KC791691

 

Tomato chino La Paz virus

   

Tomato chino La Paz virus - A [Mexico-Baja La Paz-2002]

ToChLPV-A[MX-BLP-02

AY339618

 

Tomato Chino La Paz virus - [Mexico-SLP4-2011]

ToChLPV-[MX-SLP4-11]

JN676150

 

Tomato chino La Paz virus - B [Mexico-Baja El Carrizal-2002]

ToChLPV-A[MX-BEC-02]

AY339619

 

Tomato chlorotic leaf distortion virus

   

Tomato chlorotic leaf distortion virus - [Venezuela-Zulia-2004]

ToClLDV-[VE-Zul-04]

HQ201952

 

Tomato chlorotic mottle virus

   

Tomato chlorotic mottle virus - Bahia [Brazil-Seabra 1-1996]

ToCMoV-BA[BR-Sea1-96]

AF490004

AF491306

Tomato chlorotic mottle virus - [Brazil-Florestal 211-2008]

ToCMoV-[BR-Flo211-08]

KC706561

 

Tomato chlorotic mottle virus - Minas Gerais [Brazil-Betim 1-1996]

ToCMoV-MG[BR-Bet1-96]

AY090557

 

Tomato common mosaic virus

   

Tomato common mosaic virus - [Brazil-Coimbra 22-2007]

ToCmMV-[BR-Coi22-07]

EU710754

EU710755

Tomato curly stunt virus

   

Tomato curly stunt virus - [South Africa-Onderberg-1998]

ToCSV-[ZA-Ond-98]

AF261885

 

Tomato dwarf leaf virus

   

Tomato dwarf leaf virus - [Argentin-Pichanal 397-2008]

ToDfLV-[AR-Pic397-08]

JN564749

 

Tomato golden leaf distortion virus

   

Tomato golden leaf distortion virus - [Brazil-TO45-2007]

ToGLDV-[BR-TO45-07]

HM357456

 

Tomato golden leaf spot virus

   

Tomato golden leaf spot virus - [Brazil-Araguaina-TO83-2013]

ToGLSV-[BR-Ara-TO83-13]

KC626021

 

Tomato golden mottle virus

   

Tomato golden mottle virus - [Mexico-San Luiz Potosi-2005]

ToGMoV-[MX-SLP-05]

DQ520943

DQ406674

Tomato golden mosaic virus

   

Tomato golden mosaic virus - [Brazil-Common-1984]

TGMV-[BR-Com-84]

K02029

K02030

Tomato golden vein virus

   

Tomato golden vein virus - [Brazil-Ita1220-2003]

TGVV-[BR-Ita1220-03]

JF803254

 

Tomato interveinal chlorosis virus

   

Tomato interveinal chlorosis virus - [Brazil-Pernambuco-Mdc2681-2004]

ToICV-[BR-PE-Mdc2681-04]

JF803252

 

Tomato leaf curl Anjouan virus

   

Tomato leaf curl Anjouan virus - [Comoros-Ouani-2004]

ToLCAnV-[KM-Oua-04]

AM701758

 

Tomato leaf curl Arusha virus

   

Tomato leaf curl Arusha virus - [Tanzania-Kilimandjaro-2005]

ToLCArV-[TZ-Kil-05]

EF194760

 

Tomato leaf curl Bangalore virus

   

Tomato leaf curl Bangalore virus - A [India-Bangalore 1]

ToLCBaV-A[IN-Ban1]

Z48182

 

Tomato leaf curl Bangalore virus - [India-Hessaraghatta-TC265-2010]

ToLCBaV-[IN-Hes-TC265-10]

KF663698

 

Tomato leaf curl Bangalore virus - B [India-Bangalore 5]

ToLCBaV-B[IN-Ban5]

AF295401

 

Tomato leaf curl Bangalore virus - C [India-Bangalore 4-1997]

ToLCBaV-C[IN-Ban4-97]

AF165098

 

Tomato leaf curl Bangalore virus - D [India-Kerala II-2005]

ToLCBaV-D[IN-KerII-05]

DQ852623

 

Tomato leaf curl Bangladesh virus

   

Tomato leaf curl Bangladesh virus - [Bangladesh-BD2]

ToLCBV-[BD-BD2]

AF188481

 

Tomato leaf curl Cebu virus

   

Tomato leaf curl Cebu virus - [Philippines-Nueva Ecita P2-1-2007]

ToLCCeV-[PH-NuEP2-1-07]

EU487025

 

Tomato leaf curl China virus

   

Tomato leaf curl China virus - Baise [China-Guangxi 32-2002]

ToLCCNV-BS[CN-Gx32-02]

AJ558118

 

Tomato leaf curl China virus - [China-Guangxi-Tobacco-JX-2-2010]

ToLCCNV-[CN-Gx-Tob-JX-2-10]

JF681158

 

Tomato leaf curl China virus – Nanning1 [China-Guangxi 18-2002]

ToLCCNV-NN1[CN-Gx18-02]

AJ558119

 

Tomato leaf curl China virus – Nanning2 [China-Guangxi 63-2003]

ToLCCNV-NN2[CN-Gx63-03]

AJ704603

 

Tomato leaf curl Diana virus

   

Tomato leaf curl Diana virus - [Madagascar-Namakely-2001]

ToLCDiV-[MG-Nam-01]

AM701765

 

Tomato leaf curl Ghana virus

   

Tomato leaf curl Ghana virus - [Ghana-Akumadan-2006]

ToLCGV-[GH-Aku-06]

EU350585

 

Tomato leaf curl Ghana virus - Ageratum [Cameroon-AGFG24-2009]

ToLCGV-Ag[CM-AGFG24-09]

FR873228

 

Tomato leaf curl Guangdong virus

   

Tomato leaf curl Guangdong virus - [China-Guangzhou 2-2003]

ToLCGdV-[CN-Gz2-03]

AY602165

 

Tomato leaf curl Guangxi virus

   

Tomato leaf curl Guangxi virus - [China-Guangxi 1-2003]

ToLCGxV-[CN-Gx1-03]

AM236784

 

Tomato leaf curl Hainan virus

   

Tomato leaf curl Hainan virus - [China-FQ12-2012]

ToLCHaiV-[CN-FQ12-12]

KF150142

 

Tomato leaf curl Hanoi virus

   

Tomato leaf curl Hanoi virus - [Vietnam-Hanoi-Tomato-2010]

ToLCHaV-[VN-Han-tom-10]

HQ162270

 

Tomato leaf curl Hsinchu virus

   

Tomato leaf curl Hsinchu virus - [China-Hainan-Ramie-2007]

ToLCHsV-[CN-Hn-Ram-07]

EU596959

EU596960

Tomato leaf curl Java virus

   

Tomato leaf curl Java virus - A [Indonesia]

ToLCJaV-A[ID]

AB100304

 

Tomato leaf curl Java virus - B [Indonesia-Ageratum]

ToLCJaV-B[ID-Age]

AB162141

 

Tomato leaf curl Joydebpur virus

   

Tomato leaf curl Joydebpur virus - [India-Varanasi-Capsicum annuum-2010]

ToLCJV-[IN-Var-Caa-10]

HM991146

 

Tomato leaf curl Kerala virus

   

Tomato leaf curl Kerala virus - [India-Kerala 3-2007]

ToLCKeV-[IN-Ker3-07]

EU910141

 

Tomato leaf curl Laos virus

   

Tomato leaf curl Laos virus - [Laos]

ToLCLV-[LA]

AF195782

 

Tomato leaf curl Liwa virus

   

Tomato leaf curl Liwa virus - [Oman-Liwa-LW1-2012]

ToLCLwV-[OM-Liw-LW1-12]

HF912280

 

Tomato leaf curl Madagascar

   

Tomato leaf curl Madagascar virus - Atsimo [Madagascar-Toliary-2001]

ToLCMGV-Ats[MG-Tol-01]

AJ865339

 

Tomato leaf curl Madagascar virus - Menabe [Madagascar-Morondova-2001]

ToLCMGV-Men[MG-Mor-01]

AJ865338

 

Tomato leaf curl Malaysia virus

   

Tomato leaf curl Malaysia virus - Malaysia [Malaysia-Klang-1997]

ToLCMYV-MY[MY-Kla-97]

AF327436

 

Tomato leaf curl Mali virus

   

Tomato leaf curl Mali virus - [Mali]

ToLCMLV-[ML]

AY502936

 

Tomato leaf curl Mayotte virus

   

Tomato leaf curl Mayotte virus - [Mayotte-Kahani-2003]

ToLCYTV-[YT-Kah-03]

AJ865340

 

Tomato leaf curl Mayotte virus - Madagascar [Madagascar-Dimadjou-2006]

ToLCYTV-MG[MG-Dim-06]

AM701761

 

Tomato leaf curl Mindanao virus

   

Tomato leaf curl Mindanao virus – [Philippines-Mindanao P162-2007]

ToLCMiV-[PH-MinP162-07]

EU487046

 

Tomato leaf curl New Delhi virus

   

Tomato leaf curl New Delhi virus - [Bangladesh-Jessore- Severe-2005]

ToLCNDV-[BG-Jes-Svr -05]

AJ875157

AJ875158

Tomato leaf curl New Delhi virus 2

   

Tomato leaf curl New Delhi virus 2 - [India-IANDS1-2011]

ToLCNDV2-[IN-IANDS1-11]

JQ897969

 

Tomato leaf curl New Delhi virus 3

   

Tomato leaf curl New Delhi virus 3 - [India-Bijnor-Chilli-2012]

ToLCNDV3-[IN-Bij-Chi-12]

KC465466

 

Tomato leaf curl New Delhi virus 4

   

Tomato leaf curl New Delhi virus 4 - [India-Junagad-TC306-2011]

ToLCNDV4-[IN-Jun-TC306-11]

KF551592

 

Tomato leaf curl Palampur virus

   

Tomato leaf curl Palampur virus - [India-Palampur-2007]

ToLCPalV-[IN-Pal-047]

AM884015

AM992534

Tomato leaf curl Patna virus

   

Tomato leaf curl Patna virus - [India-Patna-2008]

ToLCPatV-[IN-Pat-08]

EU862323

 

Tomato leaf curl Philippines virus

   

Tomato leaf curl Philippines virus - A [Philippines-Laguna-2006]

ToLCPV-A[PH-Lag-06]

AB377113

 

Tomato leaf curl Philippines virus - B [Philippines-Laguna 1-2006]

ToLCPV-B[PH-Lag1-06]

AB377111

 

Tomato leaf curl Philippines virus - C [Philippines-Laguna-2006]

ToLCPV-C[PH-Lag-06]

AB307731

 

Tomato leaf curl Pune virus

   

Tomato leaf curl Pune virus - [India-Pune-2005]

ToLCPuV-[IN-Pun-05]

AY754814

 

Tomato leaf curl Rajasthan virus

   

Tomato leaf curl Rajasthan virus - [India-Rajasthan-2005]

ToLCRaV-[IN-Raj-05]

DQ339117

 

Tomato leaf curl Seychelles virus

   

Tomato leaf curl Seychelles virus - [Seychelles-Val d’Endor-2004]

ToLCSCV-[SC-VE-04]

AM491778

 

Tomato leaf curl Sinaloa virus

   

Tomato leaf curl Sinaloa virus - [Nicaragua-Santa Lucia-NI2]

ToLCSiV-[NI-SL]

AJ608286

AJ508783

Tomato leaf curl Sri Lanka virus

   

Tomato leaf curl Sri Lanka virus - [Sri Lanka-Bandarawela-1997]

ToLCLKV-[LK-Ban-97]

AF274349

 

Tomato leaf curl Sudan virus

   

Tomato leaf curl Sudan virus - Gezira [Sudan-Gezira-1996]

ToLCSDV-Gez[SD-Gez-96]

AY044137

 

Tomato leaf curl Sudan virus - [Sudan-WM-2011]

ToLCSDV-[SD-WM-11]

KC763630

 

Tomato leaf curl Sudan virus - Shambat [Sudan-Shambat-1996]

ToLCSDV-Sha[SD-Sha-96]

AY044139

 

Tomato leaf curl Sudan virus - Yemen [Yemen-2005]

ToLCSDV-YE[YE-05]

EF110891

 

Tomato leaf curl Sulawesi virus

   

Tomato leaf curl Sulawesi virus - [Indonesia-Sulawesi-Langowan F101-2006]

ToLCSuV-[ID-Sul-LanF101-06]

FJ237614

 

Tomato leaf curl Taiwan virus

   

Tomato leaf curl Taiwan virus - A [China-Hong Kong T1-2007]

ToLCTV-A[CN-HKT1-07]

EU624503

 

Tomato leaf curl Taiwan virus - [China-NS1-2011]

ToLCTV-[CN-NS1-11]

JQ867093

 

Tomato leaf curl Taiwan virus - B [Taiwan-Luye 2-4-2009]

ToLCTV-B[TW-Luy2-4-09]

GU723730

 

Tomato leaf curl Taiwan virus - C [Taiwan-Chiayi-LJC14-2005]

ToLCTV-C[TW-Cy-LJC14-05]

DQ866128

 

Tomato leaf curl Toliara virus

   

Tomato leaf curl Toliara virus - [Madagascar-Miandrivazo-2001]

ToLCToV-[MG-Mia-01]

AM701768

 

Tomato leaf curl Uganda virus

   

Tomato leaf curl Uganda virus - [Uganda-Iganga-2005]

ToLCUV-[UG-Iga-05]

DQ127170

 

Tomato leaf curl Vietnam virus

   

Tomato leaf curl Vietnam virus - [Vietnam-Dan Xa 2-2007]

ToLCVV-[VN-DX1-07]

EU189149

 

Tomato leaf curl virus

   

Tomato leaf curl virus - Solanum [Australia-Solanum-D1]

ToLCV-Sol[AU-Sol-D1]

AF084006

 

Tomato leaf curl virus - [India-New Delhi-CTS-2006]

ToLCV-[IN-ND-06]

DQ629101

 

Tomato leaf curl virus - Bangalore [India-Punjab-Mentha-2007]

ToLCV-Ban[IN-Pun-Me-07]

FJ514798

 

Tomato leaf curl virus - Janti [India-Janti-2005]

ToLCV-Jan[IN-Jan-05]

AY754812

 

Tomato leaf curl virus - Tomato [Australia]

ToLCV-To[AU]

S53251

 

Tomato leaf deformation virus

   

Tomato leaf deformation virus - [Peru-Tomato-1-2003]

ToLDeV-[PE-tom-1-03]

GQ334472

 

Tomato leaf distortion virus

   

Tomato leaf distortion virus - [Brazil-Paty do Alferes 4-2005]

ToLDV-[BR-Pda4-05]

EU710749

 

Tomato mild mosaic virus

   

Tomato mild mosaic virus - [Brazil-Paty do Alferes 58-2005]

ToMMV-[BR-Pda58-05]

EU710752

EU710753

Tomato mild yellow leaf curl Aragua virus

   

Tomato mild yellow leaf curl Aragua virus - [Venezuela-10-2003]

ToMYLCV-[VE-10-03]

AY927277

EF547938

Tomato mosaic Havana virus

   

Tomato mosaic Havana virus - [Cuba-Quivican]

ToMHaV-[CU-Qui]

Y14874

Y14875

Tomato mottle leaf curl virus

   

Tomato mottle leaf curl virus - [Brazil-Jaiba 13-2008]

ToMoLCV-[BR-Jai13-08]

KC706615

 

Tomato mottle Taino virus

   

Tomato mottle Taino virus - [Cuba]

ToMoTaV-[CU]

AF012300

AF012301

Tomato mottle virus

   

Tomato mottle virus - [United States-Florida-1989]

ToMoV-[US-Flo-89]

L14460

L14461

Tomato mottle wrinkle virus

   

Tomato mottle wrinkle virus - [Argentina-Pichanal-400-2008]

ToMoWV-[AR-Pic-400-08]

JQ714137

 

Tomato rugose mosaic virus

   

Tomato rugose mosaic virus - [Brazil-Uberlandia 1-1996]

ToRMV-[BR-Ube1-96]

AF291705

AF291706

Tomato rugose yellow leaf curl virus

   

Tomato rugose yellow leaf curl virus - [Uruguay-Salto Grande-U2-2009]

TRYLCV-[UY-SG-U2-09]

JN381819

 

Tomato severe leaf curl virus

   

Tomato severe leaf curl virus - Guatemala [Guatemala-Sansirisay-1996]

ToSLCV-GT[GT-San-96]

AF130415

 

Tomato severe leaf curl virus - [Mexico-Huasteca-2011]

ToSLCV-[MX-Hua-11]

JN680352

 

Tomato severe leaf curl virus - Nicaragua [Nicaragua-Condega]

ToSLCV-NI[NI-Con]

AJ508784

 

Tomato severe rugose virus

   

Tomato severe rugose virus - [Brazil-Petrolina de Goias 1-Capsicum-2003]

ToSRV-[BR-PG1-Cap-03]

DQ207749

 

Tomato yellow leaf curl Axarquia virus

   

Tomato yellow leaf curl Axarquia virus - [Spain-Algarrobo-ES-mh800-2000]

TYLCAxV-[ES-Alg-ES-mh800-00]

AY227892

 

Tomato yellow leaf curl China virus

   

Tomato yellow leaf curl China virus - Baoshan1 [China-Yunnan 10-Tobacco-2000]

TYLCCNV-BS1[CN-Yn10-Tob -00]

AJ319675

 

Tomato yellow leaf curl China virus - [China-Yunnan 25-Tomato-2000]

TYLCCNV-[CN-Yn25-Tom-00]

AJ457985

 

Tomato yellow leaf curl China virus - Baoshan3 [China-Yunnan 278-Malvastrum-2007]

TYLCCNV-BS3[CN-Yn278-Mal-07]

AM980509

 

Tomato yellow leaf curl China virus - Bean [China-Yunnan-Bean-2004]

TYLCCNV-Bea[CN-Yn-Bea-04]

DQ256460

 

Tomato yellow leaf curl China virus - Dali [China-Yunnan 5-Tobacco-1999]

TYLCCNV-DL[CN-Yn5-Tob-99]

AJ319674

 

Tomato yellow leaf curl China virus - Datura [China-Yunnan 72- Datura -2005]

TYLCCNV-Dat[CN-Yn72-Dat-05]

EF011559

 

Tomato yellow leaf curl China virus - Honghe [China-Guangxi]

TYLCCNV-HH[CN-Gx]

AF311734

 

Tomato yellow leaf curl Indonesia virus

   

Tomato yellow leaf curl Indonesia virus - [Indonesia-Lembang-2005]

TYLCIDV-[ID-Lem-05]

AF189018

 

Tomato yellow leaf curl Kanchanaburi virus

   

Tomato yellow leaf curl Kanchanaburi virus - [Thailand-Kanchanaburi 1-2001]

TYLCKaV-[TH-Kan1-01]

AF511529

AF511528

Tomato yellow leaf curl Malaga virus

   

Tomato yellow leaf curl Malaga virus - [Spain-421-1999]

TYLCMaV-[ES-421-99]

AF271234

 

Tomato yellow leaf curl Mali virus

   

Tomato yellow leaf curl Mali virus - Ethiopia [Ethiopia-Melkassa-2005]

TYLCMLV-ET[ET-Mel-05]

DQ358913

 

Tomato yellow leaf curl Mali virus - Mali [Mali -2003]

TYLCMLV-ML[ML-03]

AY502934

 

Tomato yellow leaf curl Sardinia virus

   

Tomato yellow leaf curl Sardinia virus - [Italy-Sardinia-1988]

TYLCSV-[IT-Sar-88]

X61153

 

Tomato yellow leaf curl Thailand virus

   

Tomato yellow leaf curl Thailand virus - A [Thailand-1]

TYLCTHV-A[TH-1]

X63015

X63016

Tomato yellow leaf curl Thailand virus - B [Thailand-Chiang Mai]

TYLCTHV-B[TH-ChMai]

AY514630

AY514633

Tomato yellow leaf curl Thailand virus - C [China-Yunnan 72-2002]

TYLCTHV-C[CN-Yn72-02]

AJ495812

 

Tomato yellow leaf curl Thailand virus - D [Myanmar-Yangon-1999]

TYLCTHV-D[MY-Yan-99]

AF206674

 

Tomato yellow leaf curl Thailand virus - E [Thailand-Sakon Nakhon]

TYLCTHV-E[TH-SaNa]

AY514632

AY514635

Tomato yellow leaf curl virus

   

Tomato yellow leaf curl virus - [Israel-Rehovot-1986]

TYLCV-[IL-Reo-86]

X15656

 

Tomato yellow leaf curl virus - Boushehr [Iran- Genaveh 29-2006]

TYLCV-Bou[IR-Gen29-06]

GU076454

 

Tomato yellow leaf curl virus - Iran [Iran-Iranshahr-1998]

TYLCV-IR[IR-Ira-98]

AJ132711

 

Tomato yellow leaf curl virus - Kahnoo [Iran-Kahnooj-2007]

TYLCV-Kah[IR-Kah-07]

EU635776

 

Tomato yellow leaf curl virus - Kerman [Iran-Hormozgan 32-2006]

TYLCV-Ker[IR-Hor32-06]

GU076442

 

Tomato yellow leaf curl virus - Mild [Israel-1993]

TYLCV-Mld[IL-93]

X76319

 

Tomato yellow leaf curl virus - Oman [Oman-Al-batinah 22-2005]

TYLCV-OM[OM-Alb22-05]

FJ956700

 

Tomato yellow leaf curl Yunnan virus

   

Tomato yellow leaf curl Yunnan virus - [China-YN2013-2011]

TYLCYnV-[CN-YN2013-11]

KC686705

 

Tomato yellow leaf distortion virus

   

Tomato yellow leaf distortion virus - [Cuba-5E17-2007]

ToYLDV-[CU-5E17-07]

FJ174698

 

Tomato yellow margin leaf curl virus

   

Tomato yellow margin leaf curl virus - [Venezuela-Merida-57]

ToYMLCV-[VE-Mer-57]

AY508993

 

Tomato yellow mottle virus

   

Tomato yellow mottle virus - [Costa Rica-2003]

ToYMoV-[CR-03]

KC176780

 

Tomato yellow spot virus

   

Tomato yellow spot virus - [Brazil-Bicas 2-1999]

ToYSV-[BR-Bic2-99]

DQ336350

DQ336351

Tomato yellow spot virus - Leonurus [Brazil-PR49-2007]

ToYSV-Le[BR-PR49-07]

JX863081

 

Tomato yellow vein streak virus

   

Tomato yellow vein streak virus - [Brazil-Potato-1983]

ToYVSV-[BR-Pot-83]

EF417915

EF417916

Velvet bean severe mosaic virus

   

Velvet bean severe mosaic virus - [India-Lucknow-2008]

VBSMV-[IN-Luc-08]

FN543425

FN543426

Vernonia yellow vein Fujian virus

   

Vernonia yellow vein Fujian virus - [China-Fujian-2009]

VeYVFV-[CN-Fj-09]

JF265670

 

Vernonia yellow vein virus

   

Vernonia yellow vein virus - [India-Madurai-2005]

VeYVV-[IN-Mad-05]

AM182232

 

Vigna yellow mosaic virus

   

Vigna yellow mosaic virus - [Mexico-Morelos-Yautepec-2007]

ViYMV-[MX-Mor-Yau-07]

KC430936

 

Watermelon chlorotic stunt virus

   

Watermelon chlorotic stunt virus - [Iran-1997]

WmCSV-[IR-97]

AJ245652

AJ245653

West African Asystasia virus 1

   

West African Asystasia virus 1 - [West Africa-Asystasia1-2011]

WAAV1-[WA-Asy1-11]

JF694486

 

West African Asystasia virus 2

   

West African Asystasia virus 2 - [West Africa-Asystasia2-2011]

WAAV2-[WA-Asy2-11]

JF694484

 

Wissadula golden mosaic virus

   

Wissadula golden mosaic virus - [Jamaica-St Thomas-2005]

WGMV-[JM-StT-05]

DQ395343

EU158095

Results of pairwise sequence comparisons accurately reflect the biology of begomoviruses

It has been claimed that begomoviral species are artificial because they are arbitrarily defined based on sequence alone, and therefore their biological characteristics have been ignored [11]. This is a misconception. Sequence-based taxonomy is possible only because it relies on the knowledge of the biological properties of these well-studied viruses. Therefore, sequence comparisons among related begomovirus isolates can accurately reflect differences in their biology. Several examples can be drawn upon to argue this point. One well-known example involves bean golden mosaic disease, an important disease of bean crops in Latin America. The disease is caused by at least two distinct, well-characterized begomoviruses, bean golden mosaic virus (BGMV), which occurs in Brazil and Argentina, and bean golden yellow mosaic virus (BGYMV), which occurs in Central/North America and the Caribbean Basin [18]. The symptoms of the disease are nearly indistinguishable, the whitefly vector species is the same for both pathogens, and the economic importance with respect to crop loss is comparable as well. In fact, initially, the same begomoviral etiology was suspected for the disease occurring in the two regions. However, when the causal agents from plants collected in Puerto Rico (USA) and Brazil were sequenced, the results indicated that they had substantially different genome sequences [19, 20]. Later, it was demonstrated that the two agents differed in at least one relevant biological property: tissue tropism. BGMV is phloem-restricted in beans, while BGYMV is not [20, 21]. Thus, the species cutoff based on sequence alone was accurate and reflected the biological differences between the viruses belonging to these two species.

The most obvious benefit to using the SDT-based pairwise identity analysis is that there are fewer species and strains at the interface between the cutoff and the next lower or higher percent nt sequence identity. As such, applying the proposed 91 % cutoff increases reliability owing to the robust stringency.

Why so many begomoviruses?

As noted above, the genus Begomovirus includes the largest number of species of all currently established genera, with 288 species currently recognized by the ICTV. Why so many begomoviruses? Are these species “artificial”, the result of flawed taxonomic demarcation criteria? The existence of this large number of species can be explained by natural order relationships based on the characteristics of this genus that set it apart from many other viral genera.

Begomoviruses are transmitted by members of a cryptic species complex, Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae), which is distributed worldwide and colonize a wide array of plants belonging to species in many families [22, 23, 24, 25]. B. tabaci has emerged as a major threat to agricultural systems in many regions of the world since the 1970s and 1980s [26, 27]. Reports of unprecedented B. tabaci infestations have characteristically resulted in outbreaks of previously undescribed begomoviruses and the apparent disappearance of others from cultivated plants [28]. Because B. tabaci colonizes so many plant species [25], it potentiates the transfer of begomoviruses between non-cultivated and cultivated hosts (which are most studied by plant virologists). While it is beyond the scope of this proposal to fully explore the hypothesis that most begomoviruses isolated from cultivated hosts likely evolved from viruses originally adapted to infecting non-cultivated hosts, this hypothesis could explain, at least in part, why there are so many more begomovirus species than are found for other virus genera where virus-host-vector interactions are more evolutionarily ancient.

Another consideration is that virologists working with ssDNA viruses have gained a powerful new tool in the form of rolling circle-amplification (RCA), a method that allows for rapid, sequence-independent sampling of virus populations. The impact of RCA in the field of geminivirology cannot be overstated (for example, see ref. [29]). Using RCA, it is possible to amplify and recover the complete genome of almost any begomovirus from minute amounts of total plant DNA extracted under suboptimal conditions [30]. Presently, tissue samples can be collected, dried, and stored for months or years at room temperature, and thousands of complete begomovirus genomes will be readily amplified using RCA following a quick DNA extraction [31, 32]. In the 1990s it would take months to clone one full-length begomovirus genome, whereas hundreds of genomes can now be cloned in a matter of weeks. Furthermore (and equally relevant), because RCA uses random primers, it reduces sequence amplification biases and enables the detection of most or all unique genome molecules present in a sample. As a result, new begomoviruses and other, often highly divergent, geminiviruses have been discovered that will probably lead to the recognition of additional genera in the family (and perhaps new families as well) [33, 34, 35, 36]. Also, this new technology has prompted a significant increase in the numbers of novel begomoviruses that are being sought, and found, in non-cultivated plants.

Finally, it should be pointed out that the extent of diversity currently recognized within this genus (and possibly for all viruses) represents only the tip of the iceberg. Metagenomic approaches are rapidly becoming affordable and will probably lead to the discovery of viruses belonging to hundreds of new genera and families, not to mention species [37]. Its impact on geminivirus discovery has already been felt [38, 39, 40, 41, 42].

Different cutoff values must be used for the different genera in the family Geminiviridae

The approach implemented herein to demarcate species in the genus Begomovirus is identical to that used and approved by the ICTV for the other genera in the family [12, 13, 36]. However, for each genus, the working cutoff for species demarcation differs, even though the method applied to determine these cutoffs has been the same. For example, mastrevirus species are demarcated using a 78% cutoff. The 78% species cutoff value for the mastreviruses is demonstrated by the pairwise distance distribution plot (Fig. 2A), in which a clear valley is apparent at 78%. Such a valley is not readily evident in the equivalent plot for the begomoviruses (Fig. 2B and C), leading us to analyze this genus using groups of sequences. The analysis reported herein supported a 91% cutoff value for begomoviruses as that which best separates the species in the genus, and this is well supported by the SDT analysis.
Fig. 2

Distribution of the full-genome pairwise sequence identity scores for members of the genera (A) Mastrevirus and (B, C) Begomovirus (C corresponds to a higher resolution of the shaded region in B). Note the valley (or gap) corresponding to the 72–78 % frequencies in the Mastrevirus plot and the absence of significant valleys in the Begomovirus plot

Several other families and genera have species demarcation thresholds similar to that of the begomoviruses, including Parvovirus (95 %), Microviridae (80–85 %) and Sobemovirus (60–85 %). It is perhaps troubling that a uniform approach for computing species thresholds does not exist across all of viral taxonomy at this time. Currently, various study groups use different algorithms for specific genes, sets of genes, or complete genomes. Further, complete genome sequences are lacking for viruses of many species, particularly those with large genomes. In those instances, the trees represent a gene tree instead of a virus tree, which can create misconceptions about viral genome structure and lead to incorrect evolutionary inferences. It will be interesting to see if our approach may be useful for other viral families.

A step-by-step guide for classifying new begomovirus isolates as members of species or strains

To facilitate the taxonomic placement of newly discovered begomoviruses and to assist in the standardization of this procedure, the following guidelines are proposed for classification into species and strains:
  1. 1.

    A BLASTn analysis of the “non-redundant nucleotide” database should be performed to identify the species whose members have sequences most similar to the new sequence. The nucleotide sequence database at the NCBI website (http://www.ncbi.nlm.nih.gov/nuccore/) can also be searched using the search term “txid10814 [Organism: exp] AND 2500:3500[SLEN]”, which will return all begomovirus nucleotide sequences that are between 2500 and 3500 nucleotides long.

     
  2. 2.

    The new sequence should be added to a dataset of full-length genomes or DNA-A components created based on the BLAST results, and saved in FASTA format. All sequences must start at the same genomic coordinate (the first nucleotide after the nicking site within the conserved nonanucleotide at the origin of replication is the recommended standard).

     
  3. 3.

    The MUSCLE option in SDT v1.2 (freely available at http://www.cbio.uct.ac.za/SDT) or any other program that uses the MUSCLE alignment algorithm with pairwise deletion of gaps should be used to calculate identities between every pair of sequences in the dataset. If using SDT, these pairwise identities may be saved in either a column or matrix csv format that can then be viewed in a spreadsheet program such as Microsoft Excel. Percent identities must be rounded to the nearest full percentile.

     
  4. 4.

    If the new sequence shares <91 % genome-wide pairwise identity to any other known begomovirus sequence, appropriate species and virus names should then be proposed (see below for guidelines on doing so).

     
  5. 5.

    If the sequence shares <94 % genome-wide pairwise identity to all isolates described for that species, a strain name should then be proposed.

     

Guidelines for naming new species that include newly discovered begomoviruses

Virus species name

This is the ICTV-accepted name of a group of begomoviruses sharing ≥91 % pairwise sequence identity for the full-length genome or DNA-A component. If the sequence has <91 % sequence identity to all begomoviruses previously classified as members of distinct species, the virus should be considered a member of a new species, and a unique name that is not currently in use for any ICTV-recognized species should be assigned. This name should follow the template “Host symptom virus” (e.g., Bean golden mosaic virus). Although it was common practice for begomoviruses, the Geminiviridae SG recommends that country, city, town, village or province names not be used in naming new viruses and new viral species (e.g., Tomato yellow leaf curl Thailand virus), as this may cause misunderstandings when a virus named after a country or city is subsequently found in other locations within that country or in other countries. (Previously accepted names using this practice will not be changed to avoid conflicts in the literature.)

Strain name

Based on ICTV guidelines, there is no practical or standardized approach for differentiating or naming strains (or any other category below the species level). In fact, item 3.3 of the ICTV Statutes states that “The ICTV is not responsible for classification and nomenclature of virus taxa below the rank of species.” Nevertheless, the Geminiviridae Study Group has adopted its own guidelines for strain differentiation and nomenclature [43], although there is no formal requirement to do so. Our new analysis indicated a sequence identity threshold of 94 % for strain demarcation.

Ideally (when knowledge is available), strains should follow a nomenclature that reflects biological differences between the members of the same species. For example, if it is established that a number of BGMV isolates comprising a distinct strain are capable of infecting a host (e.g., lima bean) that other BGMV isolates do not normally infect, it would then be appropriate to name the strain BGMV-Lima bean. Likewise, symptom severity descriptors (e.g., Tomato golden mosaic virus-Yellow vein) could also be used. In either case, such strain names should be used only when the phenotype is observed in multiple isolates of the same strain. As recommended for species names, country, city, town, village or province names should not be used in naming new strains. Strain name follows species name separated by a hyphen (“-”).

Isolate descriptor

Following the species/strain name, and within square brackets (“[ ]”), the isolate descriptor may contain any number of sub-fields separated by hyphens. Although the 9th ICTV Report’s recommendations for geminivirus nomenclature [1] suggested the use of colons (“:”) to separate sub-fields in the isolate descriptor, this can cause problems in various phylogenetic-tree-drawing programs, which, when reading phylogenetic trees in Newick format, will misinterpret numbers after the colon as representing branch length information.

The first sub-field should always be the two-letter international code of the country/territory in which the isolate was sampled (Supplementary Table S2), whereas the last sub-field should always be the year in which the isolate was last present within living tissue. If the year in which the isolate was sampled differs from the date on which it was last present within living tissue (e.g., when isolates are propagated in the laboratory), the date when the isolate was sampled should then be included as an internal sub-field. Between the first and last sub-fields, any additional descriptors can be used (for example, the laboratory code of the sample from which the isolate was obtained, the city nearest to the place where the sample was obtained, the host species from which the virus was isolated).

Conclusions

Since the 1990s begomovirus taxonomy has been based primarily on sequence comparisons methods. In this regard, it was pioneering, helped by the large number of full-length sequences available, and allowed for a robust statistical treatment of the data. Although this approach has been criticized for not taking biology into account, a closer look into the recognized species will show that biology is accurately reflected in the taxonomy. This revision demonstrated the robustness and the reliability of a sequence-based taxonomy, and this was acknowledged by the ICTV with the positive outcome of the latest taxonomy proposal and the establishment of new begomovirus species (http://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/m/plant-official/4838.aspx). It should be noted, however, that the ICTV Geminiviridae SG has no ulterior motivation for continuing to propose new species. Rather, the number of new species proposed is a genuine reflection of our increasingly effective methods to conceptualize the natural genetic variability of this remarkable group of viruses. By establishing clear guidelines for the analysis of full-length genomic sequences, and following standardized nomenclature for the naming of newly established species and strains, the intention of the ICTV Geminiviridae SG is that these changes will improve taxonomic communications among users while also leaving open options for further improvements in the future that will serve the geminivirus community at large.

Notes

Acknowledgments

The analysis described in this manuscript was part of the taxonomic proposal 2013.015a,bP, approved by the Executive Committee of the ICTV in July 2013 and ratified in March 2014. JKB and FMZ are past and current chairs, respectively, of the Geminiviridae Study Group of the ICTV. JNC, EM, RWB, CHZ, AI, VGM, DPM, RRB, SU and AV were members of the Geminiviridae SG during 2012–2014, when the work was performed. JNC and EM are members of the Research Group AGR-214, partially funded by Consejería de Economía, Innovación y Ciencia, Junta de Andalucía, Spain, cofinanced by FEDER-FSE. DPM and AV are supported by the National Research Foundation of South Africa.

Supplementary material

705_2015_2398_MOESM1_ESM.xls (608 kb)
Supplementary File S1 Pairwise sequence identity analysis and maximum-likelihood phylogenetic trees of 38 groups of closely related viruses in the genus Begomovirus. For each group, sequences corresponding to the same species based on a 91% cutoff are shaded in the same color. As two examples, Group 1 has no sequences that conflict with the proposed threshold, while Group 6 has one that, according to the conflict-resolution criteria adopted (the isolate should be considered to belong to the species containing the isolate with which it shares the highest degree of sequence identity), corresponds to Honeysuckle yellow vein mosaic virus (xls 607 kb)
705_2015_2398_MOESM2_ESM.docx (29 kb)
Supplementary Table S2 Two-letter international country or territory codes (docx 28 kb)

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Copyright information

© Springer-Verlag Wien 2015

Authors and Affiliations

  • Judith K. Brown
    • 1
    Email author
  • F. Murilo Zerbini
    • 2
    • 3
    Email author
  • Jesús Navas-Castillo
    • 2
    • 3
    • 4
  • Enrique Moriones
    • 4
  • Roberto Ramos-Sobrinho
    • 2
    • 3
  • José C. F. Silva
    • 3
  • Elvira Fiallo-Olivé
    • 2
    • 3
    • 4
  • Rob W. Briddon
    • 5
  • Cecilia Hernández-Zepeda
    • 6
  • Ali Idris
    • 7
  • V. G. Malathi
    • 8
  • Darren P. Martin
    • 9
  • Rafael Rivera-Bustamante
    • 10
  • Shigenori Ueda
    • 11
  • Arvind Varsani
    • 12
    • 13
    • 14
  1. 1.School of Plant SciencesUniversity of ArizonaTucsonUSA
  2. 2.Dep. de Fitopatologia/BIOAGROUniversidade Federal de ViçosaViçosaBrazil
  3. 3.National Research Institute for Plant-Pest Interactions (INCT-IPP)Universidade Federal de ViçosaViçosaBrazil
  4. 4.Instituto de Hortofruticultura Subtropical y Mediterránea, “La Mayora”Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC)Algarrobo-CostaSpain
  5. 5.National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
  6. 6.Centro de Investigación Científica de YucatánUnidad de Ciencias del AguaCancúnMexico
  7. 7.Division of Biological and Environmental Sciences and Engineering, Center for Desert AgricultureKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
  8. 8.Department of Plant Pathology, Adjunct FacultyTamil Nadu Agricultural UniversityCoimbatoreIndia
  9. 9.Computational Biology Group, Institute of Infectious Diseases and Molecular MedicineUniversity of Cape TownCape TownSouth Africa
  10. 10.Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad IrapuatoIrapuatoMexico
  11. 11.Kurume Research Station, National Agricultural ResearchCenter for Kyushu Okinawa RegionKurumeJapan
  12. 12.Electron Microscope UnitUniversity of Cape TownCape TownSouth Africa
  13. 13.Department of Plant Pathology and Emerging Pathogens InstituteUniversity of FloridaGainesvilleUSA
  14. 14.School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand

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