Surveillance of sewage water with genome sequencing tools can help identify genetic changes in Covid-19

Regular surveillance of sewage water with genome sequencing tools can help identify troublesome genetic changes in SARS-CoV-2 weeks in advance, Indian scientists said after discovering the Delta variant in Ahmedabad wastewater one month before the first clinical case was reported in the Gujarat capital.

From the whole genome sequencing of the virus found in wastewater, the researchers spotted the signature mutations of the Delta variant in February 2021 – one month before it was found in a patient.

"Scanning the sewage water has many advantages as a routine surveillance technique. It saves a lot of time and energy,” Chaitanya G Joshi, a scientist at the Gujarat Biotechnology Research Centre and a member of the team that found the Delta in Ahmedabad in February told DH.

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Earlier CSIR laboratories conducted two such surveillance studies to show the method’s efficacy. While one of the studies was carried out in eight cities by three CSIR laboratories, a second study was undertaken in Pune by the National Chemical Laboratory.

"The results correlated with the national sero prevalence survey carried out by the Indian Council of Medical Research. The wastewater surveillance is an effective way to monitor the spread of the disease,” commented Shekhar Mande, CSIR director-general, who is not associated with the Gujarat study.

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A similar survey by the National Centre for Disease Control is going on in Delhi whereas, in Nagpur, the Central India Institute of Medical Sciences has initiated one such study.

The genomic surveillance of SARS-CoV-2 variants in wastewater samples, according to Joshi, offers early information about circulating novel variants and their transmission pattern. It is useful to detect and identify variants of concerns, variants of interest and new mutations within a population.

A continuous and large-scale time-series monitoring of wastewater can identify disease outbreaks and clustering of VOCs & VUIs, and explain their genesis, virulence, transmission, and intensity of spread within a population.

The GBRC team along with their collaborators with the Indian Institute of Technology, Gandhinagar was monitoring Ahmedabad wastewater since September 2020. Initially, they carried out RTPCR tests looking for positive cases to identify the disease clusters. Subsequently, they started whole genome sequencing to identify new mutations in the virus.

Since diarrhoea is one of the symptoms of Covid-19 and happened before the respiratory symptoms, the wastewater contains the virus. A Covid-19 patient would shed more virus compared to those who are asymptomatic.

In their research, the scientists found that 57% of the samples they analysed carry the Delta variant, which gives a clear indication about the arrival of a new strain in a city of 55 lakh individuals.

“Our study revealed the genetic signs of the B.1.617.2 (Delta variant) in wastewater in February 2021, more than a month in advance the first case of such a variant was reported in clinical samples in March in Ahmedabad,” the team said in a study, which is yet to be peer-reviewed and released on a preprint server.