Molecular surveillance and detection of SARS-CoV-2, polio, and non-polio enteroviruses in wastewater samples from Enugu and Ebonyi States

Abstract

Wastewater-based epidemiology (WBE) has emerged as a critical tool for monitoring the community-level spread of viral pathogens, particularly in resource-limited settings. This study employed molecular surveillance to detect SARS-CoV-2, poliovirus, and non-polio enteroviruses (NPEVs) in wastewater samples from Nsukka, Enugu, and Abakaliki metropolises. A total of 148 wastewater samples were collected between November 2023 and April 2024 from open drainages and a sewage treatment plant across nine sites in both states.

Samples were concentrated using polyethylene glycol precipitation. For poliovirus and NPEVs, concentrated samples were inoculated into L20B and RD cell lines for viral culture and observed for cytopathic effects (CPE) following the World Health Organization (WHO) environmental surveillance algorithm. Reverse transcription real-time PCR (rRT-PCR) was employed for the detection of SARS-CoV-2 RNA. Pan-enterovirus rRT-PCR for enteroviruses, and poliovirus-specific rRT-PCR for differentiation of polioviruses.

SARS-CoV-2 RNA was detected in 11 (7.4%) of the total samples, all of which originated from the University of Nigeria Nsukka (UNN) sewage plant in Enugu State, indicating an 18.3% positivity rate in that location. NPEVs was detected in 9 (6.1%) samples, also exclusively from the UNN site. No poliovirus (VDPV2 or nOPV2) was detected in any sample, and all samples from Ebonyi State and open drainage systems were negative for all targeted viruses.

These findings underscore the value of WBE as a complementary surveillance tool to strengthen Nigeria’s public health response to emerging and re-emerging viral infections.