Imperial College London
Alternate

DrIsobelBlake

Faculty of Medicine, School of Public Health

Lecturer
 
 
 
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Contact

 

isobel.blake

 
 
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Location

 

Desk 1103Sir Michael Uren HubWhite City Campus

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Summary

 

Publications

Citation

BibTex format

@article{Shaw:2022:infdis/jiab518,
author = {Shaw, A and Cooper, L and Gumede, N and Bandyopadhyay, AS and Grassly, N and Blake, I},
doi = {infdis/jiab518},
journal = {Journal of Infectious Diseases},
pages = {453--462},
title = {Time taken to detect and respond to polio outbreaks in Africa and the potential impact of direct molecular detection and nanopore sequencing},
url = {http://dx.doi.org/10.1093/infdis/jiab518},
volume = {226},
year = {2022}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - BackgroundDetection 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.MethodsWe 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.ResultsVDPV2 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%).ConclusionsDDNS could accelerate poliovirus outbreak response, reducing their size and the cost of eradication.
AU  - Shaw,A
AU  - Cooper,L
AU  - Gumede,N
AU  - Bandyopadhyay,AS
AU  - Grassly,N
AU  - Blake,I
DO  - infdis/jiab518
EP  - 462
PY  - 2022///
SN  - 0022-1899
SP  - 453
TI  - Time taken to detect and respond to polio outbreaks in Africa and the potential impact of direct molecular detection and nanopore sequencing
T2  - Journal of Infectious Diseases
UR  - http://dx.doi.org/10.1093/infdis/jiab518
UR  - https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiab518/6384638
UR  - http://hdl.handle.net/10044/1/92596
VL  - 226
ER  -
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