Early detection of poliovirus outbreaks in the DRC from 2021–2022

Abstract

Detecting poliovirus outbreaks promptly is crucial for eradication. We prospectively evaluated the efficacy of direct molecular detection and nanopore sequencing (DDNS) on stool samples from suspected polio cases in the Democratic Republic of Congo (DRC) from August 10th, 2021, to February 4th, 2022. DDNS identified polioviruses in 62 out of 2,339 samples (2.7%), comparable to 2.2% detection rate by the standard algorithm of cell culture, qPCR, and Sanger sequencing. DDNS provided the VP1 sequence for confirmation on average seven days after sample receipt, significantly faster than the standard algorithm (30 days). This allowed the detection of three new circulating vaccine-derived poliovirus type 2 (cVDPV2) outbreaks in a mean of 23 days (range 6–30 days). The sensitivity and specificity of DDNS were not significantly different from cell culture. Importantly, the mean sequence similarity between sequences obtained by DDNS and the standard algorithm was 99.98%. The continued implementation of DDNS in DRC, along with its potential expansion to other countries, will facilitate a more comprehensive evaluation of this method. The positive outcomes observed suggest that DDNS could be a valuable tool and inform its potential recommendation by the Global Polio Laboratory Network.

Biography

Alex, a Research Fellow at Imperial College London, specializes in characterizing bacteria and viruses in stool and sewage. His work includes developing direct sequencing methods for poliovirus, allowing more rapid outbreak confirmation, and supporting global eradication efforts. Currently expanding his focus to a wider range of organisms, Alex aims to establish cost-effective pipelines for wastewater surveillance, generating data tailored for public health actions.