Close to 200 new Zika virus genome sequences are reported in three papers published in Nature this week. The genomes, which were obtained from infected patients and Aedes aegypti mosquitoes, provide detailed insights into the emergence and spread of the current epidemic in the Americas.
Although the recent Zika virus (ZIKV) outbreak in the Americas has attracted a great deal of attention, the epidemiology and evolution of the virus are still poorly understood - thanks, in part, to limited genomic data. ZIKV genomes are technically challenging to sequence because clinical samples contain low viral loads.
To better understand how and when ZIKV was introduced into the continental United States, Kristian Andersen and colleagues sequenced 39 new ZIKV genomes from infected patients and mosquitoes. They tracked occurrences of the virus from its first detection in Miami, Florida, and their phylogenetic analyses show that ZIKV was introduced to Florida at least four times and that most of these introductions were linked to travel from the Caribbean. The authors also describe the areas in southern Florida that are particularly vulnerable to ZIKV introductions.
In two further papers, Oliver Pybus and co-workers and Pardis Sabeti and colleagues reconstruct the spread of ZIKV in Brazil and the Americas, suggesting that the virus was circulating in northeast Brazil by late 2013 or early 2014. In one paper, Pybus and co-authors report 54 new ZIKV genomes, mostly from northeast Brazil and several of which were sequenced in real time using portable DNA sequencers and a mobile genomics lab. They find that northeast Brazil had a crucial role in the establishment of the epidemic and spread of the virus throughout the Americas. In the other paper, Sabeti and co-authors sequenced 110 ZIKV genomes collected from 10 countries. They too observe rapid expansion of the epidemic within Brazil and multiple introductions to other geographic regions. The authors also describe the ongoing evolution of ZIKV and discuss the implications of the accumulation of mutations on the likely future performance of diagnostic tests.
All three papers show that ZIKV circulated undetected for many months before transmission was detected. “These papers, along with a report this year on Ebola, set a new standard for what can be achieved by studying disease outbreaks in tantalizingly close to real time, using rapidly obtained genome sequences analysed in a powerful computational framework,” concludes Michael Worobey in an accompanying News & Views article.
Finally, in a Nature Protocols paper, Nicholas Loman and colleagues describe one of the methods used for sequencing the ZIKV genome directly from clinical samples, without the need for isolation and culture, which is suitable for sequencing either RNA or DNA viruses derived from outbreaks in the field using a portable sequencing platform, or as an inexpensive, convenient method for use in the lab.