Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study

Author:

Shaw Alexander G.ORCID,Mampuela Tresor Kabeya,Lofiko Emmanuel Lokilo,Pratt CatherineORCID,Troman Catherine,Bujaki Erika,O’Toole ÁineORCID,Akello Joyce OdekeORCID,Aziza Adrienne AmuriORCID,Lusamaki Eddy KingandaORCID,Makangara Jean ClaudeORCID,Akonga Marceline,Lay Yvonne,Nsunda Bibiche,White Bailey,Jorgensen David,Pukuta Elizabeth,Riziki Yogolelo,Rankin Kathleen E.,Rambaut AndrewORCID,Ahuka-Mundeke Steve,Muyembe Jean-Jacques,Martin Javier,Grassly Nicholas C.ORCID,Mbala-Kingebeni Placide

Abstract

AbstractTimely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6–30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.

Funder

Bill and Melinda Gates Foundation

Africa CDC Pathogen Genomics Initiative

Publisher

Springer Science and Business Media LLC

Subject

Cell Biology,Microbiology (medical),Genetics,Applied Microbiology and Biotechnology,Immunology,Microbiology

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