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Hepatitis C virus genotype 3A in a population of injecting drug users in Montenegro: Bayesian and evolutionary analysis

Archives of Virology volume 162, pages 1549–1561 (2017)Cite this article

Abstract

Few reports are available on HCV molecular epidemiology among IDUs in Eastern Europe, and none in Montenegro. The aim of this study was to investigate the HCV genotype distribution in Montenegro among IDUs and to perform Bayesian and evolutionary analysis of the most prevalent HCV genotype circulating in this population. Sixty-four HCV-positive IDUs in Montenegro were enrolled between 2013 and 2014, and the NS5B gene was sequenced. The Bayesian analysis showed that the most prevalent subtype was HCV-3a. Phylogenetic data showed that HCV-3a reached Montenegro in the late 1990s, causing an epidemic that exponentially grew between the 1995 and 2005. In the dated tree, four different entries, from 1990 (clade D), 1994 (clade A) to 1999 (clade B) and 2001 (clade C), were identified. In the NS5B protein model, the amino acids variations were located mainly in the palm domain, which contains most of the conserved structural elements of the active site. This study provides an analysis of the virus transmission pathway and the evolution of HCV genotype 3a among IDUs in Montenegro. These data could represent the basis for further strategies aimed to improve disease management and surveillance program development in high-risk populations.

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Author information

Author notes

    Affiliations

    1. Institute of Public Health, Podgorica, Montenegro

      Boban Mugosa, Zoran Vratnica, Danijela Vujoševic & Dragan Lauševic

    2. Department of Infectious, Parasitic and Immunomediated Disease, National Institute of Health, Rome, Italy

      Eleonora Cella, Alessandra Lo Presti & Massimo Ciccozzi

    3. Public Health and Infectious Diseases, Sapienza University, Rome, Italy

      Eleonora Cella

    4. Department of Biomedical and Clinical Sciences “L. Sacco”, Infectious Diseases and Tropical Medicine Chair, University of Milan, Milan, Italy

      Alessia Lai, Erika Ebranati & Gianguglielmo Zehender

    5. Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico, Via Alvaro del Portillo 200, 00128, Rome, Italy

      Aletheia Blasi, Silvia Angeletti & Massimo Ciccozzi

    6. Department of Gastrointestinal Diseases, Campus Bio-Medico University, Rome, Italy

      Michele Guarino

    7. Department of Biochemical Science “A. Rossi Fanelli”, Sapienza University, Rome, Italy

      Teresa Milano & Stefano Pascarella

    8. Internal Medicine Department, University Hospital Campus Bio-Medico, Rome, Italy

      Silvia Spoto

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    1. Boban Mugosa
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    Correspondence to Silvia Angeletti.

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    All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standard.

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    B. Mugosa, E. Cella and A. Lai contributed equally.

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    705_2017_3224_MOESM1_ESM.tif

    Supplementary material 1 (TIFF 59 kb) Fig. S1 Likelihood mapping of the HCV-3a dataset of nucleotide sequences. The three corners represent fully resolved tree topologies, i.e., the presence of a tree-like phylogenetic signal, in the given dataset

    705_2017_3224_MOESM2_ESM.tif

    Supplementary material 2 (TIFF 367 kb) Fig. S2 Detail of the variant positions 250, 330 and 334. The protein is represented as a salmon- colored cartoon, while the side chain of the variable amino acids are shown by sticks. In A, reference amino acid Arg250 is shown, while the replacing Lys is represented in B. H-bonds between side chains of the residues in positions 250 and Gln241 are depicted by yellow dashed lines, and distances are shown. In C and D reference residues are shown with salmon-colored stick models, while the variant residues are represented by grey sticks

    705_2017_3224_MOESM3_ESM.tif

    Supplementary material 3 (TIFF 444 kb) Fig. S3 Detail of the variant positions 304, 305 and 307. The protein is represented as a cartoon, while the side chains of the variable amino acids are shown by sticks. In A, reference amino acids Lys304, Ala305, Asn307 are shown, while the variant amino acids are represented by grey sticks in B, C and D. In B, the interactions between residue side chains in position 304 and the residues Thr66 and Glu70 are indicated by yellow dashed lines, labeled with atomic distances

    705_2017_3224_MOESM4_ESM.tif

    Supplementary material 4 (TIFF 240 kb) Fig. S4 Residue conservation analysis. The residue conservation was analyzed using Consurf through the comparison of 250 NS5B protein sequences of different HCV genotypes obtained from the UniProt database. The reference sequence of the HCV-3a NS5B is displayed with the residue conservation score at each site color-coded into it. The conservation scale was defined from the most variable amino acid position (grade 1, colored turquoise) to the most conserves amino acid position (grade 9, colored maroon). Positions for which the inferred conservation level was assigned with low confidence are marked with light yellow. The first row below the sequence lists the predicted burial status of the site (i.e., ‘‘b’’– buried versus ‘‘e’’ – exposed). The second row indicates residues predicted to be structurally and functionally important: ‘‘s’’ and ‘‘f’’, respectively. Positions 219 and 221, marked by black arrows, are discussed in the text

    705_2017_3224_MOESM5_ESM.tif

    Supplementary material 5 (TIFF 678 kb) Fig. S5 Sequence alignment of HCV 3a NS5B protein sequences. Multiple sequence alignment of the NS5B sequences. Alignment was obtained with the program Clustal Omega and displayed with Jalview. Sequences are reported with the amino acid one-letter code; the last sequence is the HCV 3a NS5B reference sequence labeled with its RefSeq code. The black arrows indicate the 219, 221 and 307 positions (numbers are referred to the reference sequence), which have an high mutation frequency with respect to reference sequence. Residues are colored according to the ClustalX scheme, which for each alignment column, takes into account conservation and amino acid type

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    Mugosa, B., Cella, E., Lai, A. et al. Hepatitis C virus genotype 3A in a population of injecting drug users in Montenegro: Bayesian and evolutionary analysis. Arch Virol 162, 1549–1561 (2017). https://doi.org/10.1007/s00705-017-3224-5

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    • DOI: https://doi.org/10.1007/s00705-017-3224-5

    Keywords

    • Inject Drug User
    • Bayesian Skyline Plot
    • NS5B Protein
    • Likelihood Mapping Analysis
    • Selective Pressure Analysis