Detection of potentially pathogenic enteric viruses in environmental samples from Kenya using the bag-mediated filtration system

Abstract

Enteric virus environmental surveillance via a highly sensitive method is critical, as many enteric viruses have low infectious doses and can persist in the environment for extended periods. This study determined the potential of the novel bag-mediated filtration system (BMFS) to recover human enteric viruses and pepper mild mottle virus (PMMoV) from wastewater and wastewater-impacted surface waters, examined PMMoV use as a fecal contamination indicator in Kenya, and identified potential BMFS process controls. From April 2015 to April 2016, BMFS samples were collected from seven sites in Kenya (n = 59). Enteroviruses and PMMoV were detected in 100% of samples, and human adenovirus, human astrovirus, hepatitis A virus, norovirus GI, norovirus GII, sapovirus, and human rotavirus were detected in the majority of samples. The consistent detection of enteroviruses and PMMoV suggests that these viruses could be used as indicators in similarly fecally contaminated sites and BMFS process controls. As contamination of surface water sources remains a global issue, enteric virus environmental surveillance is necessary. This study demonstrates an effective way to sample large volumes of wastewater and wastewater-impacted surface waters for the detection of multiple enteric viruses simultaneously.

Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa

“…For example, 4%, 25%, 16.6%, 8.3% and 12.5% of water samples collected from the Rosetta branch of the Nile in 2017 and 2018 were contaminated with AiV, AstV, NoV, RV and HBoV, respectively (Shaheen et al 2018 , 2019a ; Shaheen and Elmahdy 2019 ), while more recently, Rizk and Allayeh, ( 2020 ) detected RVA RNA in 18.75% of Nile water samples collected in Giza. Similarly, enteric viruses have been found in major surface waters in Kenya, Chad, Nigeria and Uganda (Kiulia et al 2010 , 2014 ; Guerrero-Latorre et al 2011 ; Katukiza et al 2013a , 2013b ; Baker et al 2018 ; Bauza et al 2019 ; van Zyl et al 2019 ; Muhammad et al 2020 ). For example, two separate studies detected EV and HAdV in water samples from Homa Bay, Lake Victoria (Sadik 2016 ; Opere 2019 ).…”

“… (Ibrahim et al 2016 ) N.D. Nested RT-PCR, RT-qPCR & ICC PCR VP7 SW (river) South Africa Mar 2011–Jan 2012 (Singh 2012 ) N.D. RT-qPCR VP7 WW (effluent) South Africa Sep 2012–Aug 2013 (Osuolale and Okoh 2017 ) N.D. RT-qPCR N.R. SW (river) & WW (effluent) Kenya Apr 2015–Apr 2016 (van Zyl et al 2019 ) G1, G3 & G9;P[4], P[6] & P[8] Nested RT-PCR † VP4 † , VP6 † & VP7 † Egypt Oct 2015–Mar 2017 (El-Senousy et al 2020 ) Group A Illumina Miseq N.A. DNW Kenya Jun–Aug 2016 (Hendriksen et al 2019 ) N.D. RT-qPCR N.R.…”

“… (Dongdem et al 2011 ) N.D. RT-PCR (following amplification by cell culture) Partial 3′UTR SW (river & dam) South Africa Jun 1997–May 1998 (Taylor et al 2001 ) Genogroups A & B Competitive multiplex RT-PCR † Partial ORF1a † SWG, WW (effluent) & DW Egypt Nov 1998–Oct 1999 (El-Senousy et al 2007 ) Genotypes 1, 2, 3, 4, 5, 7, & 8 RT-PCR † (following cell culture amplification) † 3' end of ORF2 † , partial capsid & ORF1a † SWG & WW (effluent) South Africa Apr 1999–Oct 2000 (Nadan et al 2003 ) N.D. RT-qPCR Partial 3′UTR SW (river) & SWG Kenya May 2007–Feb 2008 (Kiulia et al 2010 ) Genotypes 1 & 6 RT-PCR † Partial capsid † WW Tunisia Jan–Dec 2011 (Ibrahim et al 2017b ) N.D. RT-qPCR N.R. SW (river) & WW (effluent) Kenya Apr 2015–Apr 2016 (van Zyl et al 2019 ) 1, MLB3 Illumina Mis...…”

“… (Hamza Ewess 2016 ) N.D. RT-qPCR N.R. SW (river) & WW (effluent) Kenya Apr 2015–Apr 2016 (van Zyl et al 2019 ) N.D. RT-qPCR N.R. SW (river) South Africa Jun–Nov 2016 (Potgieter et al 2020 ) N.D. RT-qPCR 5'UTR SW (river) Egypt Sep–Dec 2017 (Shaheen et al 2019b ) Aichivirus A RT-PCR † 3CD junction † SWG & WW Tunisia Jan 2003–Apr 2007 (Sdiri-Loulizi et al 2010b ) B RT-PCR † 3CD junction † WW Tunisia 2011 (Months N.R.)…”

Identification of enteroviruses along Lake Victoria shoreline - a potential indicator of sewage pollution

“…In Kenya, there is limited data on the correlation between the prevalence of enteric viruses including enteroviruses and the proximity of source waters to probable sources of faecal contamination [9]. Environmental contamination with enteric pathogens has been reported in Kenya [27, 28] [9, 29, 30]. However, these studies have been carried out in other parts of the country but not in western Kenya where Homa Bay County is located.…”