Time Taken to Detect and Respond to Polio Outbreaks in Africa and the Potential Impact of Direct Molecular Detection and Nanopore Sequencing

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.

Early detection of vaccine-derived poliovirus outbreaks using nested PCR and nanopore sequencing in the Democratic Republic of Congo, 2021-2022

“…DDNS VP1 sequences for VDPV2 positive samples were on average being generated a median 14 days after stool collection. This is similar to, but slightly slower than the 12 days we predicted when estimating the performance of DDNS based on stool sample collections from 2016-2020 10 . These earlier estimates did not account for sample batching to maximise e ciency and minimise costs.…”

“…For samples required to con rm three of the four cVDPV2 lineages, DDNS generated the VP1 sequence required to initiate a response a mean of 23 days (range 6-30 days) quicker than culture. Earlier detection and response to outbreaks leads to few cases and a higher probability of truncating ongoing transmission 2,10 . During this research study, sequences were not used to inform outbreak response because the method has not yet been accepted or recommended by the Global Polio Laboratory Network (GPLN) 17 .…”

“…Gaps in immunisation coverage, particularly due to low routine immunisation by IPV with an estimated 65% of infants were fully vaccinated in 2021 8,9 , have put the DRC at high risk of additional cVDPV outbreaks. Logistical challenges in sample shipment to the laboratory, in laboratory testing of the samples and in international shipment (to South Africa) for sequencing cause delayed detection of new poliovirus outbreaks, with case numbers stemming from an outbreak increasing by approximately 12% per additional week 10 . The World Health Organisation (WHO) identify delays in detection as one of the major challenges facing the eradication programme 11 .…”

“…These aims could be achieved through the implementation of the direct detection by nanopore sequencing (DDNS) method 13 . This method combines faster, direct detection from stool samples with on-site sequencing, avoiding time-consuming, international transport of samples and facilitating rapid detection of the chain of transmission and quick response to outbreaks 10 . It can be implemented in most laboratories familiar with PCR, including INRB where both Illumina and Nanopore sequencing have been used for Ebolavirus, measles, monkeypox and SARS-CoV-2 14,15 .…”

Automated detection and classification of polioviruses from nanopore sequencing reads using piranha

“…Standard lab algorithms for this characterisation involves culturing stool or environmental samples in poliovirus-susceptible cell lines, intratypic differentiation (ITD) by qPCR and then Sanger sequencing the programmatically important isolates [1,2]. This approach is regarded as the gold standard, however on average it can take 2-3 weeks for cell culturing results.…”