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Zika Genome Sequence of World Health Organization Reference Strain Will Aid Diagnostic Assays

NEW YORK (GenomeWeb) – An international team has sequenced and assembled the genome of a Zika virus reference strain that is intended for use in viral detection assays.

The researchers published the sequence in a study appearing online today in the American Society for Microbiology journal Genome Announcements.

The RNA genome, sequenced at the behest of the World Health Organization, spanned nearly 11,000 bases. When the researchers compared the genome sequence to partial or complete Zika virus genomes from other parts of the world, they found that it belonged to an American Zika virus clade and most closely resembled sequences from another isolate in French Polynesia.

Those involved in the study argued that the availability of a reference sequence may spur more effective nucleic acid amplification-based methods for diagnosing Zika virus infections. Though WHO experts plan to do a formal review of the reference strain next month, it is reportedly making the strain available to investigators developing diagnostic and treatment strategies.

"WHO's go-ahead before its expert committee meeting in October reflects the urgent need for researchers and companies to access valid reference material to diagnose Zika virus infection," senior author Sally Baylis, a virus safety researcher at Germany's Paul-Ehrlich-Institut, said in a statement.

The Zika virus has traditionally been associated with mild symptoms, if any. But an outbreak of infections that started last year, moving across South and Central America and into the southern US, has been linked to microcephaly and other central nervous system symptoms in infants born to women infected with the virus. A subset of infected adult and infants have also developed the immune condition Guillain-Barré syndrome, which can lead to peripheral nervous system problems.

Using a Zika virus strain called PF13/251013-18 that was isolated from the blood of a patient in French Polynesia in 2013 and grown in Vero E6 cells, researchers from Germany, French Polynesia, and the UK sequenced the viral genome with the Illumina MiSeq.

After filtering out low-quality reads, they assembled the Zika virus genome de novo with help from scaffolds that best matched the reads in their BLAST search. The resulting assembly contained 10,769 base pairs.

The team compared it to complete or partial sequences from Zika viruses with an Asian genotype. Its phylogenetic analysis suggested that the WHO reference strain is related to Zika viruses in South America, Central America, and parts of the Pacific. 

This relationship "is important, because the selection of viruses for the development of WHO reference materials has been based on strains representative of viruses that are clinically significant and have widespread distribution," Baylis and co-authors wrote.