Virus Genes

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Genome sequence and phylogenetic analysis of a novel comovirus from tabasco pepper (Capsicum frutescens)

  • Ricardo Iván Alcalá-Briseño
  • Pongtharin Lotrakul
  • Rodrigo A. ValverdeEmail author
Short Report


A virus isolate from tabasco pepper (Capsicum frutescens) has been reported as a strain of the comovirus Andean potato mottle virus (APMoV). Using the replicative intermediate viral dsRNA, the pepper virus strain was sequenced by Illumina MiSeq. The viral genome was de novo assembled resulting in two RNAs with lengths of 6028 and 3646 nt. Nucleotide sequence analysis indicated that they corresponded to the RNA-1 and RNA-2 of a novel comovirus which we tentatively named pepper mild mosaic virus (PepMMV). Predictions of the open reading frame (ORF) of RNA-1 resulted in a single ORF of 5871 nt with five cistrons typical of comoviruses, cofactor proteinase, helicase, viral protein genome-linked, 3C-like proteinase (Pro), and RNA-dependent RNA polymerase (RdRP). Similarly, sequence analysis of RNA-2 resulted in a single ORF of 3009 nt with two cistrons typical of comoviruses: movement protein and coat protein (large coat protein and small coat proteins). In pairwise amino acid sequence alignments using the Pro-Pol protein, PepMMV shared the closest identities with broad bean true mosaic virus and cowpea mosaic virus, 56% and 53.9% respectively. In contrast, in alignments of the amino acid sequence of the coat protein (small and large coat proteins) PepMMV shared the closest identities to APMoV and red clover mottle virus, 54% and 40.9% respectively. A phylogenetic tree constructed using the conserved domains for the Pro-Pol from all members of the family Secoviridae confirmed the comovirus nature of the virus. Phylogenetic and sequence analyses supports proposing PepMMV as a new species of the genus Comovirus.


Capsicum annuum dsRNA Next generation sequencing Replicative intermediate dsRNA Secoviridae 



We wish to thank Andrea Hebert, Middleton Library, Louisiana State University, for proof reading the manuscript.

Author contributions

RIA-B conducted the phylogenetic and sequence analyses. PL conducted preliminary RT-PCR experiments and analyses of sequences of PCR products. RAV planned the experiments, conducted dsRNA purifications, and wrote the manuscript.


Partial support for this investigation was provided by the National Institute of Food and Agriculture, USDA.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary file5 (PDF 260 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Dept. of Plant PathologyUniversity of FloridaGainesvilleUSA
  2. 2.Dept. of Botany, Faculty of ScienceChulalongkorn UniversityBangkokThailand
  3. 3.Dept. of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeUSA

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