An interesting preprint by Smyth and others in medRxiv suggested that waste-water based epidemiology may provide an alternative and complimentary approach for monitoring communities for the novel variants.  

Given that SARS-CoV-2 can infect the cells of the human gut and is found in high concentrations in faeces, waste-water may be a valuable source of SARS-CoV-2 RNA, which can be deep sequenced to provide information on the circulating variants in a community.  

Currently most SARS-CoV-2 genetic surveillance is conducted via the genome sequencing of viral RNA obtained from clinical specimens.  This sequencing is limited by cost, coverage, quality and throughput concerns. 

In developed countries these issues are not readily apparent, but sequencing efforts in underdeveloped countries have been restricted.

Another disadvantage of focusing on clinical strains stems from the large number of asymptomatic or mildly symptomatic infections. 

SARS-CoV-2 sequencing efforts will suffer biases if genomic information is more frequently obtained from seriously ill patients, rather than from the asymptomatic patient. 

Those who follow government health advice and stay at home will also not be sequenced.  

Waste-water based epidemiology may provide an alternative and complementary approach to give a more representative SARS-CoV-2 genetic data analysis.  

The team authors in conjunction with the New York City Department of Environmental Protection, monitored the genetic signal of SARS-CoV-2 in the wastewater of 14 wastewater treatment plants in New York City. This is an area that encompasses a population of 8.419 million persons since June 2020.  

They identified 75 unique mutations resulting in amino acid substitutions, 20 unique synonymous mutations, and 18 deletions resulting in a frame shift.  

The five mutations found at highest frequency were all associated with known variants of concern. 

The authors concluded that their approach offered a viable alternative to whole genome sequencing for detection of known variants and could be rapidly deployed to detect additional emerging variants of concern. 

The London General Practice commends any technique which is able to identify SARS-CoV-2 and any of its new variants.

Dr Paul Ettlinger

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