Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity

Natalie D. Collins, Steven Widen, Li Li, Daniele M. Swetnam, Pei-Yong Shi, Robert B. Tesh, Vanessa Sarathy

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Zika virus (ZIKV) strains belong to the East African, West African, and Asian/American phylogenetic lineages. RNA viruses, like ZIKV, exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. Genetic diversity of representative ZIKVs from each lineage was examined using next generation sequencing (NGS) paired with downstream entropy and single nucleotide variant (SNV) analysis. Comparisons showed that inter-lineage diversity was statistically supported, while intra-lineage diversity. Intra-lineage diversity was significant for East but not West Africa strains. Furthermore, intra-lineage diversity for the Asian/American lineage was not supported for human serum isolates; however, a placenta isolate differed significantly. Relative in the pre-membrane/membrane (prM/M) gene of several ZIKV strains. Additionally, the East African lineage contained a greater number of synonymous SNVs, while a greater number of non-synonymous SNVs were identified for American strains. Further, inter-lineage SNVs were dispersed throughout the genome, whereas intra-lineage non-synonymous SNVs for Asian/American strains clustered within prM/M and NS1 gene. This comprehensive analysis of ZIKV genetic diversity provides a repository of SNV positions across lineages. We posit that increased non-synonymous SNV populations and increased relative genetic diversity of the prM/M and NS1 proteins provides more evidence for their role in ZIKV virulence and fitness.

Original languageEnglish (US)
Pages (from-to)1126-1138
Number of pages13
JournalEmerging Microbes and Infections
Volume8
Issue number1
DOIs
StatePublished - Jan 1 2019

Fingerprint

Nucleotides
Asian Americans
Membranes
Virulence
Western Africa
RNA Viruses
Entropy
African Americans
Placenta
Population
Genes
Membrane Proteins
Zika Virus
Genome
Serum

Keywords

  • genetic diversity
  • Next generation sequencing
  • Shannon entropy
  • Zika lineage
  • Zika virus

ASJC Scopus subject areas

  • Epidemiology
  • Parasitology
  • Microbiology
  • Immunology
  • Drug Discovery
  • Infectious Diseases
  • Virology

Cite this

Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity. / Collins, Natalie D.; Widen, Steven; Li, Li; Swetnam, Daniele M.; Shi, Pei-Yong; Tesh, Robert B.; Sarathy, Vanessa.

In: Emerging Microbes and Infections, Vol. 8, No. 1, 01.01.2019, p. 1126-1138.

Research output: Contribution to journalArticle

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