COVID-19: Kerala to begin genome sequencing to better understand virus and its origin

The study, which will begin in a couple of weeks, will be done in partnership with the CSIR-Institute of Genomics and Integrative Biology, New Delhi.
Covid-19 vaccine
Covid-19 vaccine
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Kerala will conduct genome sequencing to get a better understanding of the mutation of the novel coronavirus and validate the policies implemented to contain its transmission. The objective of the study is to identify outbreaks, ways to contain transmission, and confirm the efficiency of the steps taken to mitigate the spread. Genome sequencing maps minute changes in the virus to identify particular types. It is widely used to understand the unique characteristics of the virus and also understand its origin.

The state government has tied up with the CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi for the study, which will begin in a couple of weeks. The state’s National Health Mission will head the study. The study will be done as a partnership between the Union and the state governments. The state will pay for the consumables and the rest of the cost will be borne by the institute.

The first case of COVID-19 in the country was reported in Kerala in January this year. In August, Kozhikode Medical College conducted a study in which it was found that the virus transmitted in the state has high infectivity. The study was done jointly with the CSIR-IGIB and the Academy of Scientific and Innovative Research, Ghaziabad. The study also found that the virus transmitted in the state is genetically mutated and that this mutated virus is not from international travellers.

The approach of the previous study was a high-throughput sequencing based on the genetic epidemiology of the virus. A total of 200 isolates of the virus from the district were processed for genome sequencing in the study.

The new study is an elaborate extension of the previous one. The previous one was based on samples collected from Kozhikode district, while the new study will include samples collected from all the 14 districts in the state on a regular basis, probably once a month.

“This new study is to learn about the transmission, the type of virus, where it originated, etc. It will analyse whether the findings of the previous study, where samples were collected from Kozhikode, will be the same or different,” Dr Chandni Radhakrishnan, who led the Kozhikode Medical College study, told TNM.

According to Vinod Scaria, a scientist at CSIR-IGIB, this is the first time that regular surveillance of this kind is being done in India, with only very few countries doing this even globally.

Molecular contact tracing

The study will be based on molecular contact tracing, which helps in tracing the origin of the infection.

Speaking to TNM, Vinod explains, “The novel coronavirus mutates once every 10 days. So, if you do a screening of individuals in a particular area, using the mutation we can trace the origin of infection for every case. In genome sequencing, this is done through molecular contact tracing. We can also find clusters of outbreaks and understand how these outbreaks are related to each other, which is not possible except through contact tracing. Now diagnosis is based on RT-PCR (considered to be the most accurate) or rapid antigen test (based on whether an antibody is formed in the body against the virus) and the result is only a yes or no. The source of infection is untraced and contact tracing is also not possible as there is a surge in the number of cases and everything is open.”

Advantages and Outcome 

Strategies to contain the epidemic, such as the lockdown, were done without knowledge about the outcome. The new study aims to validate such strategies that have already been implemented.

“Now we know that the quarantine measures the state put in place were more effective. But there is no evidence at the moment. The study will aim to build evidence about which policies worked and which didn’t,” Vinod adds.

Another expected outcome of the study is to learn if genetic variations can affect the diagnostic efficacy while using RT-PCR or rapid antigen tests. “If the virus has mutated, it can escape detection. The study aims to learn about the efficiency and accuracy of the testing kits. Also, in the future, we need to understand what percent of the population will benefit from vaccines. Vaccines essentially depend on our bodies to recognise a specific epitope of the virus. If there are mutations in those epitopes, the virus can evade an immune response,” Vinod says.

The study also aims at identifying the effectiveness of vaccines in the population in question (in Kerala). Countries like the UK have been using genome sequencing and have completed 10,000 genome sequences. It has been used very rarely until now and no one has used it on this scale.

Also Read: Explained: Can you be reinfected by the novel coronavirus?

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