Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations

Author:

Majumdar Manasi1,Sharif Salmaan2,Klapsa Dimitra1,Wilton Thomas1,Alam Muhammad Masroor2,Fernandez-Garcia Maria Dolores3,Rehman Lubna2,Mujtaba Ghulam2,McAllister Gina4,Harvala Heli4,Templeton Kate4,Mee Edward T1,Asghar Humayun5,Ndiaye Kader3,Minor Philip D1,Martin Javier1

Affiliation:

1. Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom

2. NIH, Islamabad, Pakistan

3. Institut Pasteur, Dakar, Senegal

4. Edinburgh Royal Infirmary, United Kingdom

5. World Health Organization Eastern Mediterranean Regional Office, Amman, Jordan

Abstract

Abstract Background Enteroviruses are common human pathogens occasionally associated with severe disease, notoriously paralytic poliomyelitis caused by poliovirus. Other enterovirus serotypes such as enterovirus A71 and D68 have been linked to severe neurological syndromes. New enterovirus serotypes continue to emerge, some believed to be derived from nonhuman primates. However, little is known about the circulation patterns of many enterovirus serotypes and, in particular, the detailed enterovirus composition of sewage samples. Methods We used a next-generation sequencing approach analyzing reverse transcriptase polymerase chain reaction products synthesized directly from sewage concentrates. Results We determined whole-capsid genome sequences of multiple enterovirus strains from all 4 A to D species present in environmental samples from the United Kingdom, Senegal, and Pakistan. Conclusions Our results indicate complex enterovirus circulation patterns in human populations with differences in serotype composition between samples and evidence of sustained and widespread circulation of many enterovirus serotypes. Our analyses revealed known and divergent enterovirus strains, some of public health relevance and genetically linked to clinical isolates. Enteroviruses identified in sewage included vaccine-derived poliovirus and enterovirus D-68 stains, new enterovirus A71 and coxsackievirus A16 genogroups indigenous to Pakistan, and many strains from rarely reported serotypes. We show how this approach can be used for the early detection of emerging pathogens and to improve our understanding of enterovirus circulation in humans.

Funder

NIBSC Regulatory Science Research Unit

Bill and Melinda Gates Foundation

Publisher

Oxford University Press (OUP)

Subject

Infectious Diseases,Oncology

Reference40 articles.

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4. Enterovirus D68 and acute flaccid myelitis-evaluating the evidence for causality;Messacar;Lancet Infect Dis,2018

5. Phylogeography of coxsackievirus A16 reveals global transmission pathways and recent emergence and spread of a recombinant genogroup;Hassel;J Virol,2017

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