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COVID-19 cases spike again in India: Is this a new variant of COVID strain?

The increase in COVID-19 cases in India in the last one week, especially in states such as Maharashtra, Punjab, Kerala, Chhattisgarh and Tamil Nadu, is raising concerns whether the spurt in new cases is linked to new variants of SARS-CoV-2 or is it attributable to any super spreading event locally? 
India saw 16,738 fresh COVID-19 cases on February 24, nearly half of them from Maharashtra. It is well established that the variants of the UK, South Africa and Brazil are highly transmissible. The South Africa strain is known to reduce the efficacy of vaccines as well.
 
Here is an explainer on how dangerous are new variants, when have they been discovered and is there any link between them and new cases? Will these strains reduce vaccine efficacy or have a bearing on RT-PCR testing and how are we preparing for it?
 
Why is SARS-CoV-2 virus mutating, and what is the consequence of the mutations?
 
Viruses mutate all the time, more so for viruses that contain RNA as their genetic material like Coronavirus. Most mutations are so small that they don’t significantly affect how the virus works, or sometimes make the virus weaker. 
 
In certain cases, a mutation helps the virus to acquire the ability to dodge the immune system, infect people and reproduce. These strains tend to become dominant. For instance, the SARS-CoV-2 virus makes around one or two mutations a month. This is normal and much lower than for other viruses, such as HIV and influenza. 
 
The more the virus circulates the more the chance of its mutating. Measures such as face masking, hand hygiene and social distancing, coupled with mass vaccination will help in cutting the scope for viruses to mutate.
 
Two new mutant variants of the SAR-CoV-2 virus, N440K and E484Q, have been detected in Maharashtra and some other states. The government had earlier clarified that the current upsurge of COVID-19 cases in Maharashtra cannot be attributed to these two strains.
 
ICMR has further explained that these two virus strains have been detected in other countries too and are not India-specific. Moreover, they have been found earlier in some states in India. 
 
The E484Q strain was detected in four sequences in Maharashtra as early as March and July 2020. The N440K mutation has been reported on 13 different occasions between May and September 2020 in Telangana, Andhra Pradesh and Assam. ICMR said it has been closely monitoring the situation.
 
Then what is the reason behind the spike of cases in
Maharashtra?

 
Experts such as Dr V Ravi, Retired Professor of Neurobiology at NIMHAN and Nodal Officer for Genomic Confirmation of SARS-CoV-2, Government of Karnataka, says there is absolutely no evidence to suggest that there is a new variant in Maharashtra, that is causing a spike in cases. He says that the latest upsurge is triggered by super spreading events that have led to community spillover and the subsequent lack of testing, tracking and tracing.
 
“There have been two amino acid changes noted in the spike protein, but that does not constitute a new variant,” Dr Ravi said.
He added: “It is not true that we have our own Indian variant that has emerged with the amino acid mutations that have been seen in Maharashtra. These changes have been witnessed in other places as well. We have been doing genomic sequencing at NIMHANS. We have found both the 440 and the 484 mutations isolated in variants that have been circulating ever since the post lockdown period. There is no variant that has a propensity to spread higher what has been identified in India.”
 
Will these strains reduce the efficacy of the vaccine or have any bearing on RT-PCR testing?
 
Experts say there still isn't any evidence that these new variants affect the efficacy of the COVID-19 vaccine. So far verification from large clinical trials suggests that the vaccine will help in preventing severe COVID-19 that results in hospitalisation and death.
 
Will RT-PCR test kits detect new variants?
 
The current RT-PCR tests do pick up the new variants, says Dr Saranya Narayan, Chief Microbiologist at Neuberg Diagnostics.
“So if every kit targets a minimum of two strands of viral protein genome, they will be able to pick up the variants,” he explained.
 
How are we tracking the new variants?

 
To be sure India is keeping a close watch on possible new variants, both from incoming travellers from overseas and also domestically. To sequence the viral genome, the government has set up Indian SARS-CoV-2 Genomics Consortium (INSACOG) Labs. 
 
Ten laboratories such as NIBMG Kolkata, ILS Bhubaneswar, NIV Pune, CCS Pune, CCMB Hyderabad, CDFD Hyderabad, InSTEM Bengaluru, NIMHANS Bengaluru, IGIB Delhi and NCDC Delhi are part of this consortium.
 
Samples of all inbound international passengers, who test positive to COVID-19 on screening at arrival, are now sent for genomic sequencing. 
 
All positive samples from people who are either participating in vaccine trials or have been vaccinated, all positive samples from people with a prior history of infection and confirmed re-infection, are also included. 
 
For general surveillance - the government randomly collects samples of 5 percent of positive COVID-19 cases across India. Samples from metro cities, COVID clusters and new clinical symptoms are given priority for sequencing.
 

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