Amid fears over new variants of the novel coronavirus and as COVID-19 cases rise rapidly, the Centre for Cellular and Molecular Biology (CCMB) has said that roughly 5% of the samples from COVID-19 patients that have been sequenced, from the regions that fall under its purview, had the double mutant variant (classified as B.1.617). Based in Hyderabad, the CCMB has been doing genome sequencing for samples sent from Andhra Pradesh, Telangana, and north Karnataka. However, the director of CCMB Rakesh Mishra said that not enough samples have been sequenced yet, in terms of quantity and variety, to conclude whether any of the emerging variants are present in alarming numbers and are driving the surge in the Telugu states.
The CCMB is one of ten labs that are part of the consortium INSACOG (Indian SARS-CoV-2 Consortium on Genomics) that has been set up for genomic surveillance of the SARS-CoV-2 virus. Along with genome sequencing, CCMB has been culturing the double mutant virus to establish vaccine efficacy according to Mishra. “We will know in a week or so, whether the vaccine is effective on the variant,” he said.
"As reinfections have not been reported in alarming numbers yet, this is likely to be an indication that immunity acquired upon the first infection has been protecting people and therefore the vaccine may also be effective," added Mishra. However, he cautioned that it’s also likely that reinfections are going unnoticed as people who were asymptomatic during the first wave may not have been tested, and are therefore possibly unaware of the first infection.
It was reported earlier in March that sequencing was progressing at a slow pace due to various reasons including shortage of samples sent from states to the labs. Mishra said that while the number of samples sent by states has continued to be less, the variation of samples being sent has also been inadequate. "Most of the samples received from Telangana have been from the airport, belonging to travellers who tested positive," he said.
“Even now, we are not getting a lot of samples locally. We mostly get positive samples from the airport. Other than that, we get samples from hospitals in special cases, like when a vaccinated doctor is infected. Some community samples we are getting from Andhra Pradesh. But it has to be expedited. We need to get samples regularly from all the districts and towns, because only then will we be able to monitor properly if there is a new variant emerging, or which variant is spreading which way. Accordingly, proper controls and logistics and strategies can be put in place,” he said.
According to INSACOG guidelines, the sequencing efforts planned to cover 5% of all positive samples, selected through a random sampling technique, while including brief socio-demographic, clinical and travel information of the patient for each sample. Samples from all international travellers who tested positive for the coronavirus during screening were also to be sequenced, as well as positive samples of people who have been infected after vaccination, and those who have been re-infected.
While CCMB has the capacity to sequence several thousand samples in a week since the countrywide genomic surveillance efforts began in December, it has sequenced around 1,500 samples from Telangana and Andhra Pradesh, including a few from north Karnataka and Nagpur. Mishra said, “Many of them may not be whole genome sequences, as some samples are sent for targeted sequencing to quickly determine whether it is a particular variant or not. From the coming week, we will do large scale sequencing of the whole genome to figure out if new variants are emerging."
So far, samples from the Hyderabad airport have largely had the UK variant, and in some cases, the South Africa variant according to Mishra. However, he said that in the community, these variants are likely to be small in number so far. “Only the double mutant (B.1.617) seems to be increasing in number, but our guess is at the moment, it’s present in around 5% of the samples or less. So the rise in the cases here (in Andhra Pradesh and Telangana) is more likely because of change in people’s behaviour and lack of precautions than these variants,” he said. The double mutant variant was first found in Maharashtra, and it was recently reported that around 61% (220 out of 361) genome sequenced samples from the state had the double mutant variant.
Stressing on the responsibility of state health departments to send varied samples, Mishra said samples must be sent from varied geographical locations, from places where a sudden surge is observed, and from hospitals observing severity in mortalities or clinical symptoms. He said that this is needed to understand if a new variant is responsible for certain clinical symptoms or surges. “If we sequence only Hyderabad samples, for instance, it doesn’t serve much purpose,” he added.
Noting that variants are constantly emerging, Mishra said that variants like the N440K, which has been around for several weeks now and has been found in the southern states in large numbers, is also not necessarily the cause for the sudden surge. With precautions being ignored over the past few months, Mishra said, “To some extent, the variants might have improved the efficiency with which the virus is spreading, but human behaviour is the more significant reason for the present surge.”
However, he added that a large number of people continuing to be infected is fertile ground for a new variant. “If we wear masks and take precautions, even without lockdowns, we don’t need to care about variants because they will die down as they will not have a host to infect. Otherwise, we may create bigger problems when viruses may start reinfecting and vaccines may be ineffective," he added.
Although the double mutant is present in Andhra Pradesh, Mishra said it’s too early to put emphasis on numbers, as the sequencing done so far doesn’t necessarily reflect reality. “If we sequence around 5,000 samples, then things are likely to become clearer, maybe in a few days,” he said.
Once reliable data starts to emerge from sequencing, the government will be equipped to make decisions like containing localities or cities where a new variant that is more transmissible or virulent has emerged, without affecting lives and livelihoods in large numbers. “Constant, repeated sequencing from all geographical locations is to enable the government to decide where to put restrictions, where to isolate more people and where to not worry much,” said Mishra.