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Abstract

An approach is proposed for environmental surveillance of poliovirus by concentrating sewage samples with tangential flow filtration (TFF) followed by deep sequencing of viral RNA. Subsequent to testing the method with samples from Finland, samples from Pakistan, a country endemic for poliovirus, were investigated. Genomic sequencing was either performed directly, for unbiased identification of viruses regardless of their ability to grow in cell cultures, or after virus enrichment by cell culture or immunoprecipitation. Bioinformatics enabled separation and determination of individual consensus sequences. Overall, deep sequencing of the entire viral population identified polioviruses, non-polio enteroviruses, and other viruses. In Pakistani sewage samples, adeno-associated virus, unable to replicate autonomously in cell cultures, was the most abundant human virus. The presence of recombinants of wild polioviruses of serotype 1 (WPV1) was also inferred, whereby currently circulating WPV1 of south-Asian (SOAS) lineage comprised two sub-lineages depending on their non-capsid region origin. Complete genome analyses additionally identified point mutants and intertypic recombinants between attenuated Sabin strains in the Pakistani samples, and in one Finnish sample. The approach could allow rapid environmental surveillance of viruses causing human infections. It creates a permanent digital repository of the entire virome potentially useful for retrospective screening of future discovered viruses.

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/content/10.2807/1560-7917.ES.2016.21.15.30193
2016-04-14
2024-11-05
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2016.21.15.30193
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Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Vyacheslav+Furtak&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Furtak Vyacheslav</a>, <a href="/search?value1=Merja+Roivainen&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Roivainen Merja</a>, <a href="/search?value1=Olga+Mirochnichenko&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Mirochnichenko Olga</a>, <a href="/search?value1=Tatiana+Zagorodnyaya&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Zagorodnyaya Tatiana</a>, <a href="/search?value1=Majid+Laassri&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Laassri Majid</a>, <a href="/search?value1=Sohail+Z+Zaidi&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Zaidi Sohail Z</a>, <a href="/search?value1=Lubna+Rehman&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Rehman Lubna</a>, <a href="/search?value1=Muhammad+M+Alam&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Alam Muhammad M</a>, <a href="/search?value1=Vladimir+Chizhikov&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Chizhikov Vladimir</a>, <a href="/search?value1=Konstantin+Chumakov&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Chumakov Konstantin</a></span>. Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction. <a href="/content/ecdc">Euro Surveill.</a> 2016;21(15):pii=30193. <a href="https://doi.org/10.2807/1560-7917.ES.2016.21.15.30193" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2016.21.15.30193</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 14 Jul 2015;&nbsp;&nbsp; <span class="generated">Accepted</span>: 14 Apr 2016 </span> </p>
/content/10.2807/1560-7917.ES.2016.21.15.30193
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