New Delhi: Changes in the genome of the SARS-CoV-2 virus in an infected person reflect as variation at the population level, according to a study that researchers say is “very useful” in predicting spread and infectivity. Will happen. of viral covid strains.
Researchers said tracking changes in the virus inside a host in individuals and populations could provide important clues to viral sites that are favorable or disadvantageous for the survival of SARS-CoV-2, which causes COVID-19. are formed, the researchers said.
The team behind the recent study included researchers from national center for disease control and CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) in Delhi, as well as Institute of Life Sciences in Bhubaneswar, Academy of Scientific and Innovative Research at Ghaziabad, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB) at Hyderabad and Indian Institute of Technology, Jodhpur.
Reacting to the findings of the study, virologist Upasana Ray explained that the emergence of the viral variant is dependent on its successful reproduction in the host.
“Mutation is a very common event in the life cycle of any virus. While a virus undergoes replication and multiplies inside the host cell, small nucleotide changes occur,” Ray, a senior scientist at the CSIR-Indian Institute of Chemical Biology, Kolkata, told PTI.
“As a virus circulates more and more, it has a lot of opportunities to accumulate such changes within its host and thus lead to variations,” said Ray, who was not involved in the study.
In the yet-to-be-published study, to be posted on the preprint repository BioRxiv on July 27, researchers analyzed samples from Covid-19 diagnosed patients from two different time periods of the pandemic.
In Phase 1 of the study, the team used a genome-wide intra-host single nucleotide variation (iSNV) map in SARS collected from different subpopulations in China, Germany, Malaysia, UK, US and India as of June 2020. 1,347 samples were analyzed. -CoV-2 infected population.
A single nucleotide variation (SNV) is the replacement of a single nucleotide – a basic building block of the genetic material of a virus.
According to Ray, ISNVs are changes taking place inside the host. These mutations may or may not eventually reflect at the population level, he said.
“For an intra-host SNV to survive, such a variant must be able to multiply and spread and therefore establish itself,” the scientist said.
The researchers observed 18,146 ISNV sites spread across the viral genome, including sites defining the B.1 and B.6 lineages.
The alpha version was first detected in the UK, the beta version was first found in South Africa and delta The variant, which was first reported from India, belongs to the same lineage of SARS-CoV-2.
“Interestingly, 41 percent of all unique ISNVs identified in these samples were reported as SNVs in one or more samples submitted to GISAID as of 30 September 2020, increasing by 30 June 2021. 80 percent done.” study noted.
GISAID is a global science initiative and primary source of open access to genomic data on the influenza virus and the coronavirus responsible for the COVID-19 pandemic.
In Phase 2 of the study, the authors analyzed 1,798 samples sequenced in India between November 2020 and May 2021.
They found evidence that ISNVs can manifest into SNVs in a population over time.
“In these samples, ISNVs were recorded to be present in populations at most delta (b.1.617.2) and kappa (b.1.617.1) lineage-defined genomic positions prior to their determination as SNVs by February 2021.” can be done,” the researchers said.
“These results highlight the importance of recording ISNVs as an extension of genomic surveillance programs to enable more accurate models for viral epidemiology,” he said.
The authors also observed ISNVs in 87 percent of sites in the spike protein — which the virus uses to enter and infect human cells — that have recently been reported to confer antibody resistance.
Current vaccines are directed against the spike protein of the SARS-COV-2 virus.
“These mutations may have major implications in vaccine response because they can alter immunogenicity,” the authors said.
Immunogenicity is the ability of a vaccine to provoke an immune response in the body.
“The study reveals important insights about residues that are conducive to the survival of this virus and thus may help engineer the next generation of therapeutics that target these mutation prone proteins,” Ray said.
Researchers said tracking changes in the virus inside a host in individuals and populations could provide important clues to viral sites that are favorable or disadvantageous for the survival of SARS-CoV-2, which causes COVID-19. are formed, the researchers said.
The team behind the recent study included researchers from national center for disease control and CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) in Delhi, as well as Institute of Life Sciences in Bhubaneswar, Academy of Scientific and Innovative Research at Ghaziabad, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB) at Hyderabad and Indian Institute of Technology, Jodhpur.
Reacting to the findings of the study, virologist Upasana Ray explained that the emergence of the viral variant is dependent on its successful reproduction in the host.
“Mutation is a very common event in the life cycle of any virus. While a virus undergoes replication and multiplies inside the host cell, small nucleotide changes occur,” Ray, a senior scientist at the CSIR-Indian Institute of Chemical Biology, Kolkata, told PTI.
“As a virus circulates more and more, it has a lot of opportunities to accumulate such changes within its host and thus lead to variations,” said Ray, who was not involved in the study.
In the yet-to-be-published study, to be posted on the preprint repository BioRxiv on July 27, researchers analyzed samples from Covid-19 diagnosed patients from two different time periods of the pandemic.
In Phase 1 of the study, the team used a genome-wide intra-host single nucleotide variation (iSNV) map in SARS collected from different subpopulations in China, Germany, Malaysia, UK, US and India as of June 2020. 1,347 samples were analyzed. -CoV-2 infected population.
A single nucleotide variation (SNV) is the replacement of a single nucleotide – a basic building block of the genetic material of a virus.
According to Ray, ISNVs are changes taking place inside the host. These mutations may or may not eventually reflect at the population level, he said.
“For an intra-host SNV to survive, such a variant must be able to multiply and spread and therefore establish itself,” the scientist said.
The researchers observed 18,146 ISNV sites spread across the viral genome, including sites defining the B.1 and B.6 lineages.
The alpha version was first detected in the UK, the beta version was first found in South Africa and delta The variant, which was first reported from India, belongs to the same lineage of SARS-CoV-2.
“Interestingly, 41 percent of all unique ISNVs identified in these samples were reported as SNVs in one or more samples submitted to GISAID as of 30 September 2020, increasing by 30 June 2021. 80 percent done.” study noted.
GISAID is a global science initiative and primary source of open access to genomic data on the influenza virus and the coronavirus responsible for the COVID-19 pandemic.
In Phase 2 of the study, the authors analyzed 1,798 samples sequenced in India between November 2020 and May 2021.
They found evidence that ISNVs can manifest into SNVs in a population over time.
“In these samples, ISNVs were recorded to be present in populations at most delta (b.1.617.2) and kappa (b.1.617.1) lineage-defined genomic positions prior to their determination as SNVs by February 2021.” can be done,” the researchers said.
“These results highlight the importance of recording ISNVs as an extension of genomic surveillance programs to enable more accurate models for viral epidemiology,” he said.
The authors also observed ISNVs in 87 percent of sites in the spike protein — which the virus uses to enter and infect human cells — that have recently been reported to confer antibody resistance.
Current vaccines are directed against the spike protein of the SARS-COV-2 virus.
“These mutations may have major implications in vaccine response because they can alter immunogenicity,” the authors said.
Immunogenicity is the ability of a vaccine to provoke an immune response in the body.
“The study reveals important insights about residues that are conducive to the survival of this virus and thus may help engineer the next generation of therapeutics that target these mutation prone proteins,” Ray said.
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