Genome-wide diversity of Zika virus: exploring spatio-temporal dynamics to guide a new nomenclature proposal

Global Health and Tropical Medicine. Instituto de Higiene e Medicina Tropical. Universidade Nova de Lisboa. Lisboa, Portugal.
Department of Computer Science. Artificial Intelligence Lab. Vrije Universiteit Brussel. Brussels, Belgium / Department of Microbiology. Immunology and Transplantation. Rega Institute for Medical Research. Laboratory of Clinical and Epidemiological Virology. KU Leuven, Leuven, Belgium / Data Science Institute. I-Biostat. Hasselt University. Agoralaan Gebouw D, Diepenbeek, Belgium.
Department of Microbiology. Immunology and Transplantation. Rega Institute for Medical Research. Laboratory of Clinical and Epidemiological Virology. KU Leuven, Leuven, Belgium.
Institut Pasteur. Université Paris Cité. Unité Bioinformatique Evolutive. Paris, France / Institut Pasteur. Université Paris Cité. Bioinformatics and Biostatistics Hub. Paris, France
Department of Microbiology. Immunology and Transplantation. Rega Institute for Medical Research. Laboratory of Clinical and Epidemiological Virology. KU Leuven, Leuven, Belgium.
Global Health and Tropical Medicine. Instituto de Higiene e Medicina Tropical. Universidade Nova de Lisboa. Lisboa, Portugal.
Department of Medical Microbiology. Leiden University Medical Cente. Leiden, The Netherlands / Faculty of Bioengineering and Bioinformatics. Lomonosov Moscow State University. Moscow, Russia,
Department of Medical Microbiology. Leiden University Medical Cente. Leiden, The Netherlands.
Global Health and Tropical Medicine. Instituto de Higiene e Medicina Tropical. Universidade Nova de Lisboa. Lisboa, Portugal.
Global Health and Tropical Medicine. Instituto de Higiene e Medicina Tropical. Universidade Nova de Lisboa. Lisboa, Portugal.
National Laboratory for Scientific Computing. Petrópolis, RJ, Brasil.
Department of Microbiology. Immunology and Transplantation. Rega Institute for Medical Research. Laboratory of Clinical and Epidemiological Virology. KU Leuven, Leuven, Belgium / Spatial Epidemiology Lab (SpELL). Université Libre de Bruxelles. Roosevelt, Bruxelles, Belgium.
Department of Microbiology. Immunology and Transplantation. Rega Institute for Medical Research. Laboratory of Clinical and Epidemiological Virology. KU Leuven, Leuven, Belgium / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil.
Institut Pasteur. Université Paris Cité. Unite Bioinformatique Evolutive. Paris, France / Institut de Systématique, Evolution, Biodiversite. Muséum National d’Histoire Naturelle. Buffon, Paris, France.
Global Health and Tropical Medicine. Instituto de Higiene e Medicina Tropical. Universidade Nova de Lisboa. Lisboa, Portugal / Department of Microbiology. Immunology and Transplantation. Rega Institute for Medical Research. Laboratory of Clinical and Epidemiological Virology. KU Leuven, Leuven, Belgium.
Department of Microbiology. Immunology and Transplantation. Rega Institute for Medical Research. Laboratory of Clinical and Epidemiological Virology. KU Leuven, Leuven, Belgium.
Department of Laboratory Medicine. University Hospitals Leuven. Herestraat, Leuven, Belgium.
Global Health and Tropical Medicine. Instituto de Higiene e Medicina Tropical. Universidade Nova de Lisboa. Lisboa, Portugal.

Resumen en ingles

The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall num ber of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classifica tion system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolu tionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic dis tances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively.

Editor

Oxford University Press

Referencia

SEABRA, Sofia G et al. Genome-wide diversity of zika virus: exploring spatio-temporal dynamics to guide a new nomenclature proposal. Virus Evolution, v. 8, n. 1, p. 1–15, 2022.

DOI

10.1093/ve/veac029

ISSN

2057-1577

Por favor, use este identificador para citar o enlazar este ítem: https://www.arca.fiocruz.br/handle/icict/54928

Tipo

Derechos de autor

Acceso abierto

Colecciones

Compartir

Estadísticas

Metadatos

Autor

Afiliación

Resumen en ingles

Palabras clave en portugues

Palabras clave en ingles

DeCS

Editor

Oxford University Press

Referencia

DOI

ISSN