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Time taken to detect and respond to polio outbreaks in Africa and the potential impact of direct molecular detection and nanopore sequencing

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Title: Time taken to detect and respond to polio outbreaks in Africa and the potential impact of direct molecular detection and nanopore sequencing
Authors: Shaw, A
Cooper, L
Gumede, N
Bandyopadhyay, AS
Grassly, N
Blake, I
Item Type: Journal Article
Abstract: Background Detection of poliovirus outbreaks relies on a complex laboratory algorithm of cell-culture, PCR and sequencing to distinguish wild-type and vaccine-derived polioviruses (VDPV) from Sabin-like strains. We investigated the potential for direct molecular detection and nanopore sequencing (DDNS) to accelerate poliovirus detection. Methods We analysed laboratory data for time required to analyse and sequence serotype-2 VDPV (VDPV2) in stool collected from children with acute flaccid paralysis in Africa (May 2016-February 2020). Impact of delayed detection on VDPV2 outbreak size was assessed through negative binomial regression. Results VDPV2 confirmation in 525 stools required a median of 49 days from paralysis onset (10th-90th percentile: 29-74), comprising collection and transport (median: 16 days), cell-culture (7 days), intratypic differentiation RT-qPCR (3 days) and sequencing (including shipping if required) (15 days). New VDPV2 outbreaks were confirmed a median of 35 days (27-60) after paralysis onset, which we estimate could be reduced to 16 days by DDNS (9-37). Because longer delays in confirmation and response were positively associated with more cases (p<0.001), we estimate that DDNS could reduce the number of VDPV2 cases before a response by 28% (95% CrI 12-42%). Conclusions DDNS could accelerate poliovirus outbreak response, reducing their size and the cost of eradication.
Issue Date: 8-Oct-2021
Date of Acceptance: 5-Oct-2021
URI: http://hdl.handle.net/10044/1/92596
DOI: 10.1093/infdis/jiab518
ISSN: 0022-1899
Publisher: Oxford University Press
Journal / Book Title: Journal of Infectious Diseases
Copyright Statement: © The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor/Funder: Bill & Melinda Gates Foundation
Bill & Melinda Gates Foundation
World Health Organization
Bill & Melinda Gates Foundation
Medical Research Council (MRC)
Funder's Grant Number: OPP1207299
OPP1171890
2020/1014353-0
INV-024477
MR/R015600/1
Keywords: AFP
Poliovirus
VDPV
direct-detection
nanopore
outbreak
stool
surveillance
06 Biological Sciences
11 Medical and Health Sciences
Microbiology
Publication Status: Published online
Online Publication Date: 2021-10-08
Appears in Collections:Faculty of Medicine
School of Public Health



This item is licensed under a Creative Commons License Creative Commons