The mutant SARS-CoV-2 variants believed to be behind the recent surge of covid-19 cases during the second wave of pandemic were introduced in India by foreign travellers and was transmitted within the country by migrant workers movements and religious gatherings, an Indian Council of Medical Research (ICMR) led study has said.
Published in the peer reviewed Multidisciplinary Digital Publishing Institute (MDPI) journal “Viruses” on Tuesday, the study looked upon the geographic distribution of the virus clades (group of similar viruses) and variants circulating in different parts of India between January and August 2020.
The study indicates that the SARS-CoV-2 variants (variant of concern (VOC), Variant Under investigation (VUI) or variant of interest, variant of high consequence and double mutant) were not observed during the early phase of virus transmission (January–August).
“This analysis demonstrates that the SARS-CoV-2 variant was not reported to be circulating in India until August, the samples of which were downloaded on 9th December 2020. The circulating clades in the country may be attributed to the early introductions into India through travellers as well as the mixing of clades,” said Dr Pragya Yadav scientist at NIV-ICMR, Pune.
“Besides, the early transmissions within the country could be chiefly traced to movements of migrant workers and the holding of religious gatherings. The independent identification of the amino acid mutations observed in the SARS-CoV-2 variants from the early phase samples indicates an evolutionary trend in the current circulating strain that is geared towards host adaptation,” she said.
Around 1603 Samples were collected from 25 states and Union Territories (UTs) in India –Andhra Pradesh, Assam, Chandigarh, Chhattisgarh, Delhi, Gujarat, Haryana, Himachal Pradesh, Jammu and Kashmir, Jharkhand, Karnataka, Kerala, Madhya Pradesh, Maharashtra, Manipur, Odisha, Punjab, Rajasthan, Sikkim, Tamil Nadu, Tripura, Telangana, Uttarakhand, Uttar Pradesh, and West Bengal.
In India, during the first covid-19 wave, a maximum number of cases was reached in the period between September and October 2020, and subsequently declined until February 2021. The recent exponential upsurge (second wave) of the covid-19 cases in India has been observed from April 2021, with more than 0.2 million new cases being reported as of 17 April 2021.
Three variants i.e. B.1.1.7 lineage, variant of Concern (VOC) and B.1.351 lineage have recently been reported from India. These variants are of concern due to antigenic drift, increased transmissibility, and immune escape (especially for B.1.351) mechanisms, the ICMR said. Recently, a new lineage (B.1.617) was identified in Indian SARS-CoV-2 sequences, with the E484Q and L452R mutation (commonly known as a double mutant) in the spike protein of SARS-CoV-2, which is considered to have higher transmission rates.
“The SARS-CoV2 sequence analyses during the period between January and August 2020 revealed the presence of the E484Q mutation in the spike protein. These sequences were found in Maharashtra in March and July 2020. Another immune escape mutation, the N440K amino acid in the spike protein, was also observed in Telangana, Andhra Pradesh, and Assam from May 2020,” said the study.
“This indicates that despite the absence of the double mutant variant during the early phase of infection, the presence of a single independent mutation could be seen. Furthermore, it was also observed that the multiple mutations found in the VOC, VUI, and variant of high consequence were not present during this period, although single independent mutations were seen, the study said.
“Most of the VUI and VOC has been brought from foreign travellers. In fact, all strains of coronavirus imported and established in India,” said Pragya Yadav scientist at ICMR-NIV Pune.
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