Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease (COVID-19) pandemic, is frequently shed in faeces during infection, and viral RNA has recently been detected in sewage in some countries. We have investigated the presence of SARS-CoV-2 RNA in wastewater samples from South-East England between 14th January and 12th May 2020. A novel nested RT-PCR approach targeting five different regions of the viral genome improved the sensitivity of RT-qPCR assays and generated nucleotide sequences at sites with known sequence polymorphisms among SARS-CoV-2 isolates. We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. Low levels of viral RNA were detected in a sample from 11th February, 3 days before the first case was reported in the sewage plant catchment area. SARS-CoV-2 RNA concentration increased in March and April, and a sharp reduction was observed in May, showing the effects of lockdown measures. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations.

Wastewater-based epidemiology—surveillance and early detection of waterborne pathogens with a focus on SARS-CoV-2, Cryptosporidium and Giardia

“…Had this testing been in place at the time, it would have provided public health officials with more time to coordinate and implement actions to slow the spread of disease. A study in the UK reported that clinical testing underestimated the prevalence of COVID-19 and that large reductions in SARS-CoV-2 RNA in wastewater coincided with lockdowns (Martin et al 2020 ).…”

“…A comprehensive study using WGS assessed the geographic and temporal distribution of SARS-CoV-2 lineages across Europe (Alm 2020) and this approach was used in the Netherlands to identify separate introductions to mink farms (Oreshkova et al 2020 ). A study in England used WBE to detect virus variants that were particularly prevalent in the UK and also identified the increasing dominance of the Spike protein G614 variant using Whole Genome sequencing (WGS) (Martin et al 2020 ). Similarly, phylogenetic analyses of a SARS-CoV-2 genome from a WWTP in Bozeman, Montana (USA), showed that it was more closely related to isolates from California and Australia than the Wuhan WA1 linage (Nemudryi et al 2020 ).…”

Uncertainties in estimating SARS-CoV-2 prevalence by wastewater-based epidemiology

“…human excretion), and catchment population, the catchment-level prevalence can be estimated. To date, the existence of SARS-CoV-2 virus RNA in wastewater have been confirmed in many countries, including, Australia [8] , [9] , Brazil [10] , China [11] , [12] , Czech Republic [13] , Ecuador [14] , France [15] , [16] , India [17] , [18] , Italy [19] , [20] , [21] , [22] , Japan [23] , Spain [24] , [25] , the Netherlands [7] , United Kingdom (UK) [26] , Slovenia [27] , Sweden [28] , United Arab Emirates (UAE) [29] , [30] and United States (USA) [31] , [32] , [33] , [34] , [35] . The successful detection of SARS-CoV-2 virus RNA through reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and sequencing approaches in wastewater demonstrated the high potential of applying WBE as a tool to estimate the COVID-19 prevalence in their communities.…”

Water science under the global epidemic of COVID-19: Bibliometric tracking on COVID-19 publication and further research needs

“…For example, Lodder and de Roda Husman [22] provided perspective on “SARS-CoV-2 in wastewater: potential health risk, but also data source”, saying that the wastewater could be a sensitive surveillance system and early warning tool in pandemic. Wastewater-based epidemiology (WBE) has been quickly and widely tested in many countries and regions around the world, such as Spain [11] , [23] , Italy [8] , [24] , [25] , UK [26] , Netherlands [13] , USA [27] , [28] , India [14] , [29] , Japan [15] , Germany [7] , Australia [17] , [30] , and United Arab Emirates [16] . Many countries, such as Ireland and China, were conducting such kind of research to closely monitor wastewater related SARS-CoV-2.…”