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Genomics study by Nimhans throws light on mysterious Covid spread at Karnataka pharma firm

As many as 67 people were infected at the Jubilant Generics pharma firm in Nanjangud which saw infections spreading to the Mandya and Vijayapura region in the March to May period. There were no deaths reported in the cluster.

Written by Johnson T A | Bengaluru | Updated: January 6, 2021 8:14:38 am
Karnataka covid cases, Karnataka covid spread, Covid spread at Karnataka pharma firm, Genomics study, NIMHANS, karnataka news, Indian expressNow, a scientific study which looked at the genomics of the Sars-CoV-2 virus as well as the spread of the Covid 19 infection in Karnataka has provided some answers to the mysterious spread of the virus. (File)

During the early stages of the Covid-19 infection in the country, the rapid spread of the virus among workers at a pharmaceutical factory in Mysore despite none of them travelling abroad at the time had become a mystery.

As many as 67 people were infected at the Jubilant Generics pharma firm in Nanjangud which saw infections spreading to the Mandya and Vijayapura region in the March to May period. There were no deaths reported in the cluster.

Now, a scientific study which looked at the genomics of the Sars-CoV-2 virus as well as the spread of the Covid 19 infection in Karnataka has provided some answers to the mysterious spread of the virus.

The study, conducted by Prof V Ravi and others at the department of neurovirology at the National Institute of Mental Health and Neurosciences (NIMHANS) and reported in an open access science journal in December, has found that the workers at the pharma firm cluster were infected with strains of the virus that were predominantly found in Europe at the time.

Published in PLOS One, a peer-reviewed open access scientific journal by the Public Library of Science, the study has found that four samples for positive persons in the Mysore cluster that was sequenced for genomic data had the B.1 strain of the virus and three had the B.1.1 lineage. “The B.1 and B.1.1 are European clades. Both lineages harbour the D614G mutation on the Spike protein. It has been suggested that viruses with this mutation are more infectious and the mutation was present at higher frequency in samples across the world. Of these two lineages, B.1 was a major contributor to the Italian outbreak,” says the study.

The study has reported that the index case in the Mysuru pharma firm cluster ‘had no history of international travel but was an employee of a company which had a number of international visitors until mid-February 2020, including visitors from Europe’. “The presence of two lineages is indicative of multiple introductions of the virus in this cluster,” the Nimhans study has reported.

“The infections in the Mysore pharma firm cluster involved a virus strain with European lineage. This provides an idea of the origin of the virus in the cluster,” Prof V Ravi said.

Genomic sequencing

The Nimhans lab is currently one of the 10 labs in the country carrying out genomic sequencing to identify the new mutant B.1.1.7 mutant strain of the coronavirus first reported by UK health officials late last year.

As many as 11 persons who have returned from the UK to Karnataka have been found to have been infected by the new, more contagious variant of Covid 19 so far at the lab.

“Mortality, clinical manifestation of B.1.1.7 is the same as the other strains but the only difference is the propensity to spread. Otherwise clinical manifestation, clinical phenotype is no different. There have been 11 cases so far of the new variant in Karnataka,” Prof Ravi said.

‘Seven known strains of the virus’

The study of the molecular profiles of the Sars-CoV-2 virus among infected persons in Karnataka – carried out during the early phase of the spread of the disease from March 8 to May 21 – has revealed the presence of seven known strains of the virus. It has reported that a B6 strain of the virus was detected in the majority of samples sequenced.

The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel,” says the study.

The study titled ‘Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka’ is unique in its use of genomic data and epidemiological information to assess the nature of the Sars-Cov-2 virus responsible for the early spread in the state.

The seven different strains of the virus in Karnataka were found in 17 infection clusters (the largest being the 67 member cluster from the factory in the Mysore region), and 24 cases with no contacts, with 14 of the 17 contact clusters having a single strain of the virus, the study reported – suggesting that this showed that the virus was introduced into the state from multiple locations.

Of the 91 genomic sequences studied by the researchers, 47 belonged to the B.6 lineage, including eleven of 24 cases with no known contacts, indicating continuous transmission of this strain.

The study has reported that 13 of the 17 clusters and 13 of the 24 cases with no known contact had the B/B.6 strain.

A second large cluster in Karnataka with 50 patients and largely restricted to a quarantine centre in Bengaluru had infections of the B.4 and B.6 strains. “The B.4 is a clade which was first associated with travellers from Iran and has been sampled from the UK, Australia, and India,” says the study. Another large Bengaluru cluster with 35 persons who tested positive had a variation of the B.1 strain – the B.1.80 strain which has been sampled from India, Australia, and Luxembourg.

Four of the 91 sequences in the study belonged to lineage A and were from individuals with travel history to other states within India. “Lineage A and B of the virus were sequenced in China in January 2020. These form the reference sequences and are probably ancestral sequences to other circulating lineages. Viruses from both lineages are now circulating in different countries of the world,” the Nimhans study said.

Over 1500 SARS-CoV-2 genomes have been sequenced in different parts of India. In an earlier study the analysis of 361 complete genome sequences from India showed that five global strains of the virus were circulating in India – B, B4, A2a, A3, and a distinct clade A3i. The A2a clade was found to be the most prevalent, followed by A3i.

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