Analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

Transmission electron micrograph of SARS-CoV-2 (Wikipedia)

COVID-19 is caused by the strain of corona virus named Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), belonging to the category of betacoronaviruses. The virus mainly causes respiratory illness, varying in severity for different individuals. The COVID-19 pandemic is affecting the whole world. India is one among the worst hit nation by the COVID-19 pandemic. The western part of India is badly affected by the COVID-19 pandemic, the Maharashtra state is a major hotspot for this disease, having around 1/5th of total reported infections in India.

A collaborative research conducted by researchers from NCCS Pune, B. J. Government Medical College, Pune and Armed Forces Medical College Pune present the first comprehensive study on genome and mutation pattern analysis of SARS-CoV-2 from the western part of India. In this study, researchers have investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in three different regions of Maharashtra, the western state in India. Total 90 genomes were sequenced. The analysis revealed three unique linked mutations which are common in most of the sequences studied. These may act as molecular markers to track the spread of the SARS-CoV-2 virus to different areas.

Nasopharyngeal/throat swabs of suspected COVID-19 patients were collected, samples confirmed with SARS-CoV-2 infection were used for the study. The age of the patients selected in the present study ranged from 2-78, with 80% patients were in the age range of 30-60 years. COVID-19 patient samples with a particular range Ct value for E gene were selected for the genome sequencing. Fast qc tool and BWA (Burrows-Wheeler Aligner) were used for data analysis. Neighbor joining method was used for phylogenomic analysis. Structural and bioinformatics analysis of SARS-CoV-2 variants was performed and comparative study among the Indian samples was also done. The observed mutation pattern was further analyzed to check any relationship with gender, age, and symptoms.

Phylognetic analysis of the genomes revealed that mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples, indicating a newly emerging pattern of linked mutations. The Satara district viral strains showed mutations primarily at the 3´ end of the genome, while Nashik district viral strains displayed mutations at the 5´ end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic patients was performed. The analysis showed mutations were prevalent in symptomatic cases, and were more prominent in females. These three mutations were present in more than 30% studied samples of age group 10-25. Interestingly, these mutations were not detected in the higher age group of 61-80.

Study of region-wise mutation pattern among the viral sequences indicated that, a specific pattern of mutation was prevalent in all districts. The relationship of mutation pattern with age, gender and symptoms was studied. A distinct pattern was observed in age-wise distribution, some of the mutations were prevalent in the age group of 10-25. The proportion of three mutations C313T, C5700A, G28881A were found relatively higher (~80%) in symptomatic patient samples as compared to asymptomatic (40-50%). Also, the mutation C241T was found in 90% of all the sequences and is located in the 5′ UTR region and found predominantly in severely affected patients. However, the role of this mutation has not been studied yet.

The comparative study indicated that, distinct sub-clones of virus were prevalent in different parts of India at the same time period. The type 19A clade virus was predominant in Delhi (Northern part) whereas in Maharashtra (western part) 20A, 20B clade virus was dominant in April-May 2020. While in Telangana (southern part), 19A clade was dominant in April, and it shifted completely to 20A and 20B in May 2020. Because of lockdown, factors contributing to transmission of SARS-CoV-2 virus was restricted. The researchers are assertive about prevalence of a specific viral variant in a region could be attributed to human host susceptibility for specific viral variants. This susceptibility seems to be based on mutations prevalent in the viral variants in that region.


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