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New Zika Genomes From African, Asian Lineages Document Virus' Population Diversity

NEW YORK (GenomeWeb) – A team led by researchers at the J. Craig Venter Institute has produced high-quality genome sequences for more than a dozen Zika viruses (ZIKV) from African and Asian lineages, identifying variant and phylogenetic patterns that are intended to aid in future analyses of strains behind the recent outbreak in South America, Central America, the Caribbean, and the Southern US.

The researchers focused on 16 ZIKV strains obtained from the American Type Culture Collection BEI Resources, a collection developed with support from the National Institute of Allergy and Infectious Diseases. Using a combination of sequencing, 3' rapid amplification of complementary DNA ends (RACE), and comparisons with 90 publicly available ZIKV sequences from strains sequenced in the past, they annotated the new genomes and came up with consensus sequences spanning multiple viral lineages.

"The purpose of this work is to authenticate the coding region sequence of ZIKV strains commonly used by the scientific community," senior author Brett Pickett, a JCVI researcher, and his colleagues wrote, noting that "[w]e have generated [a] consensus sequence and identified minor variants through deep sequencing on the ZIKV strains stored at BEI Resources."

The team's results, published online today in Scientific Reports, also made it possible to pick up more subtle changes and evidence of selection pressures in the virus, while retracing historical relationships between strains from different parts of the world.

For example, the authors noted that "[r]ecombination does not appear to play a significant role in the evolution of ZIKV, while evidence of selection is present across viral proteins that are exposed to the host immune system."

For their analyses, the researchers used reverse transcription to produce complementary DNA from 16 samples with ZIKV RNA content that was verified through quantitative real-time PCR testing — a set that included four isolates from an African ZIKV lineage and 12 samples from an Asian lineage, including samples collected in the current outbreak.

From there, they targeted consensus ZIKV sequences with several sets of custom PCR primers and sequenced the resulting amplicons with Illumina MiSeq and Sanger sequencing.

Together with 3' RACE data and sequences from 90 previously sequenced ZIKVs, the newly sequenced, assembled, and annotated genomes proved useful for uncovering minor variants, small insertions and deletions, and past recombination events in the viruses, they reported.

When the team considered ZIKV phylogenetics, based on polyprotein coding sequences in the complete collection of sequenced ZIKVs, it identified distinct lineages representing strains from East and West Africa, along with an Asian lineage that split from the line leading to these African lineages in around the 17th century.

Within the Asian lineage, which appeared to share a common ancestor going back to the 19th century, the group uncovered a set of closely clustered strains implicated in the ongoing outbreak. 

Although the authors did not see ZIKV clusters corresponding to the host species involved, they noted that "[i]n almost all cases, the sequences cluster together with the geographic origin of the virus."