Detection of SARs-CoV-2 in wastewater using the existing environmental surveillance network: A potential supplementary system for monitoring COVID-19 transmission

Abstract

The ongoing COVID-19 pandemic is caused by SARs-CoV-2. The virus is transmitted from person to person through droplet infections i.e. when infected person is in close contact with another person. In January 2020, first report of detection of SARS-CoV-2 in faeces, has made it clear that human wastewater might contain this virus. This may illustrate the probability of environmentally facilitated transmission, mainly the sewage, however, environmental conditions that could facilitate faecal oral transmission is not yet clear. We used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value. A total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID 19 patients and quarantine center strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater. This study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as supplementary system to monitor viral tracking and circulation in cities with lower COVID-19 testing capacity or heavily populated areas where door-to-door tracing may not be possible. However, attention is needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.

Second Wave of COVID-19 in Bangladesh: An Integrated and Coordinated Set of Actions Is Crucial to Tackle Current Upsurge of Cases and Deaths

“…Furthermore, wastewater based epidemiological (WBE) surveillance using sewage samples can be implemented to detect genetic materials of the SARS-CoV-2 in densely populated urban areas (16,17). This will essentially help identify communities with positive cases where mass-testing is not possible, and aid in adopting timely public health interventions to mitigate further spread of the disease.…”

Insights into Gastrointestinal Virome: Etiology and Public Exposure

“…It is important to note that the RNA of the pandemic SARS-CoV-2 was detected in treated wastewater, representing a critical issue for usage in irrigation [272]. Therefore, SARS-CoV-2 RNA was investigated in various water resources for their incidence frequency (Figure 4) and prevalence using different genes (e.g., RdRP, S, N1, N2, N3, ORF1ab, and E) as genetic tracers [273][274][275][276][277][278][279][280][281][282][283][284][285]. However, the highest SARS-CoV-2 detection specificity was obtained when RdRP was applied in RT-qPCR and compared to other SARS-CoV-2 genes [286].…”

“…Thus, traceability procedures provide a mandate to determine fecal contamination sources so that the risk can be assessed to initiate a proper water management to counteract it at its source. [274,[276][277][278][281][282][283][284][285][286]291]. SW: sewage water, TWW: Treated wastewater, RW: River water, SS: Wastewater sludge samples, Av.…”

“…Figure 4. Frequency of SARS-CoV-2 RNA in various water environments[274,[276][277][278][281][282][283][284][285][286]291]. SW: sewage water, TWW: Treated wastewater, RW: River water, SS: Wastewater sludge samples, Av.…”

Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing

“…Sequencing of wastewater samples is, however, currently mainly used to reconstruct the consensus genome sequence of the most prevalent SARS-CoV-2 strain in the sample and LFV are often not investigated ( Nemudryi et al, 2020 ; Bar-Or et al, 2021 ; Crits-Christoph et al, 2021 ; Sharif et al, 2021 ). This consensus sequence can be useful to demonstrate that the detected strain in wastewater corresponds to the dominant strain that circulates in individuals within the same community ( Crits-Christoph et al, 2021 ).…”