SARS-CoV-2 virus variant that showed rapid transmission in Assam, can help predicting local spread of the disease
The Covid-19 pandemic had caused over 3 million deaths worldwide. The virus mutated into several Variants of Concern (VOCs) that showed a pattern of invasion in specific populations or countries and several variants have been reported from different parts of the world.
According to the World Health Organization (WHO), there are five variants of concern (VOC) globally: alpha (α), beta (β), gamma (γ), delta (δ), and omicron . Reportedly, α, δ and the recently evolved omicron variant have shown increased transmissibility.
Although the global transmission of the virus has been tracked based on the designated VOCs mentioned above, it does not provide a deep insight into possible acquisition of selective advantage associated with temporal and geographical spread of the virus . A few previous large-scale genomic studies have found upsurges of haplotypes of SARS-CoV-2 associated with a particular geographic region. Nonetheless, some studies found that SARS-CoV-2 produces a highly mutant replication intermediate which expresses variant SARS-CoV-2 proteins in different populations . The same replication intermediate also produces a high number of mutations and deletions across the genome, favoring quasispecies dynamics and also conferring immune evasion.
It is apparent that the geographical and temporal spread of the virus has been driven by many unique changes in the genome that may provide selective advantages. A deep understanding of those genomic features will provide valuable information for effective pandemic responses in different regions rather than a less-effective universal response.
It is matter of great pride that it has been found out by Indian scientists that a dominant haplotype of the delta variant of A SARS-CoV-2 virus that had been rapidly transmitting in Assam by evading the immune system of humans has revealed the dynamics of viral haplotype transmission in a regional population and novel secrets of viral evolution. The study which shows that this particular variant, though detected in other areas, spread rapidly particularly among the Assamese population, can help develop models for future prediction of the disease at the local level.
A study conducted by a team of scientists comprising of Prof. Ashis Mukherjee, Director, Dr. Mojibur Rohman Khan, Associate Professor, Dr. Maloyjo Joyraj Bhattacharjee, Project Scientist and Mr. Anupam Bhattacharya, Senior Research Associate from the Institute of Advanced Study in Science and Technology (IASST), Guwahati in collaboration with Prof. Wen-Hsiung Li of Academia Sinica Taipei, Taiwan and University of Chicago, USA novel found that haplotype of the delta variant of SARS-CoV-2 underwent selective sweep in Assam in 2021.
The research published in Virology Journal was based on a comprehensive genomic analysis of SARS-CoV-2 samples from nasopharyngeal swabs of COVID-19 positive individuals in Assam. The team sequenced 91 SARS-CoV-2 samples by next-generation sequencing (NGS). Comparative analysis of the genomes from Assam with those from outside revealed that a specific haplotype of the delta variant carrying 13 mutations underwent selective sweep and transmitted very fast in the Assam population. This process was facilitated by a mutation in ORF8, which is involved in immune evasion.
The team further analyzed the expression pattern of the viral genes among the patients and observed a negative correlation of the Ct value of qRT-PCR of the patients with abundant ORF6 transcripts, suggesting that ORF6 can be used as a marker for estimating viral titer. The team concluded that this study revealed an understudied mechanism and dynamics of viral haplotype transmission in a regional population may aid in tracking the viral evolution for better disease management strategy.