Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname

Abstract

The arthropod-borne Zika virus (ZIKV) is currently causing a major international public health threat in the Americas. This study describes the isolation of ZIKV from the plasma of a 29-year-old female traveler that developed typical symptoms, like rash, fever and headache upon return from Suriname. The complete genome sequence including the 5' and 3' untranslated regions was determined and phylogenetic analysis showed the isolate clustering within the Asian lineage, close to other viruses that have recently been isolated in the Americas. In addition, the viral quasispecies composition was analyzed by single molecule real time sequencing, which suggested a mutation frequency of 1.4 × 10^-4 for this ZIKV isolate. Continued passaging of the virus in cell culture led to the selection of variants with mutations in NS1 and the E protein. The latter might influence virus binding to cell surface heparan sulfate.

Figure 1

Photographs of (A) erythema in the face and slightly engorged blood vessels in the eyes, and (B) non-itching maculopapular rash on the abdomen of the patient from which ZIKV SL1602 was isolated.

Figure 2

Phylogenetic tree for ZIKV SL1602 and 12 selected ZIKV isolates that represent the recognized diversity. A maximum likelihood phylogenetic tree inferred from the nucleotide sequences of full-length ZIKV genomes is shown. The country of isolation and GenBank accession numbers of the isolates that were used are: Uganda MR 766 (NC012532), Brazil-Natal (KU527068), Thailand (KU681081), Philippines (KU681082), Brazil-Paraiba (KX280026), Colombia (KX247646), Brazil-Recife (KX197192), Haiti (KX051563), Senegal (KU955591), Cambodia (KU955593), Federated States of Micronesia (EU545988) and French Polynesia (KJ776791.2). Spondweni virus (NC029055, not shown) was used as the outgroup. Bootstrap values above 70 are shown. The scale bar represents the number of nucleotide substitutions per site.

Figure 3

Quasispecies population of ZIKV SL1602. Synonymous substitutions are indicated by dots and nonsynonymous substitutions by squares. Red squares indicate SNVs that became dominant (fixed) when the virus was passaged 9 more times on Vero cells.