The XBB.1.16 Omicron recombinant first detected in India on December 25, 2022 has become the dominant variant in the country. Based on 2,856 genome sequences from India posted on GISAID between December 1, 2022 and April 8, 2023, a team led by Dr. Rajesh P. Karyakarte, Head of the Microbiology Department at the BJ Medical College, Pune found that the XBB.1.16 lineage had grown from 9.3% in the first week of February to 79.17% in the first week of April. The results of the study, which is yet to be peer-reviewed, was posted on medRxiv preprint server.
The number of cases in India detected through RT-PCR testing began to slowly rise in the first week of March and reached a peak on April 19 with 12,591 infections and a daily test positivity rate of 4.39%. With daily testing remaining very low, the number of cases detected does not reflect the actual spread of the XBB.1.16 variant.
In contrast, environmental surveillance carried out by testing sewage water samples from 28 sewage treatment plants spread across Bengaluru by the Tata Institute for Genetics and Society (TIGS) has revealed the true extent of spread of the virus in the city. One sample collected once a week from each of the 28 treatment plants shows that RNA fragments found in the sewage water began increasing from early-March and peaked on April 1.
At its peak, over 80,000 virus copies per ml were present in the city. That would mean that thousands of people were infected in Bengaluru alone.
“We find only RNA fragments of the virus and not the virus particle itself in wastewater samples. Since one infected individual can shed 10 million copies, it is possible to calculate the number of infected people by taking into consideration the total volume of wastewater treated in each plant,” says Dr. Rakesh Mishra, director, TIGS, which has been undertaking environmental surveillance of SARS-CoV-2 in Bengaluru since August 2021.
“It appears that Bengaluru witnessed an invisible wave of COVID-19 that was far bigger than the third wave driven by BA.1 and BA.2 Omicron variants in January 2022,” he says. And this must be the case across India as XBB.1.16 had spread across the country in March-April. There was another silent wave in Bengaluru in June 2022 driven by one of the Omicron variants.
“Since the treatment plants are spread across Bengaluru, we can tell which area of the city has a greater number of infected people by measuring the pathogen load. Wastewater surveillance can provide a granular picture of infections in the city. And this will help in advising and cautioning the civic authorities about any new variant or increase in infections even when it is not apparent,” he says.
Not only has daily testing numbers dropped sharply, people have become reluctant to get tested even when symptoms are obvious. In many instances, the infected remain asymptomatic.
Wastewater testing is an active form of environmental surveillance, and has been in place for decades in the case of polio. It provides a fairly accurate measure of pathogen load in the wastewater and by extension, the extent of virus spread in the community. The biggest advantage is that wastewater surveillance does not require infected people getting tested nor testing facilities to be in place. Testing of wastewater for RNA fragments is also fairly easy.
“We share the results of wastewater surveillance with the civic authorities (BBMP) every week. We have been able to undertake this surveillance due to the willingness of the civic authorities,” says Dr. Mishra. “With the SARS-CoV-2 virus here to stay, and the virus continuing to evolve, it is essential to undertake environmental surveillance in every city in the next one-two years.”