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

Abstract Delayed detection of poliovirus outbreaks is a major threat to polio eradication. Direct molecular Detection and Nanopore Sequencing (DDNS) of stool samples shows promise as a faster method to detect and confirm polio cases compared with cell culture but has not been assessed prospectively during routine surveillance. We report on the implementation of prospective testing of all stool samples received from suspected polio cases and their contacts in the Democratic Republic of Congo between 10 th August 2021 to 4 th February 2022. DDNS detected polioviruses in 62/2339 (2.7%) of samples whilst the standard algorithm of cell culture, qPCR and Sanger sequencing detected 51/2339 (2.2%). The sensitivity and specificity of DDNS was not significantly different from cell culture. DDNS provided the VP1 sequence required for case confirmation on average 7 days after sample receipt compared with 30 days for the standard algorithm, allowing detection of three new cVPDV2 outbreaks a mean of 23 days earlier (range 6-30 days) and was estimated to cost less per sample tested. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Continued implementation of DDNS in DRC and expansion to other countries will allow further evaluation of this method and inform its potential recommendation by the Global Polio Laboratory Network.