Recent findings: Patients infected with two sarS-COV-2 mutations can also undergo gene recombination


Since the discovery of SARS-COV-2, more than 1,000 lineages have been identified during the 2019 global coronavirus disease (COVID-19) pandemic.Co-infection of two or more SARS-COV-2 mutants is possible due to simultaneous transmission of multiple variants in the same site, which may lead to the generation of new variants through homologous recombination of the virus.To date, no recombination events have been observed at the individual level.On January 27, 2022, Lili Ren, Kun Li, And Other researchers from Shenzhen Center for Infectious Disease Control and Prevention, Shenzhen Center for Disease Control and Prevention, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, and Beijing Institute of Genomics, Chinese Academy of Sciences (National Center for Biological Information) received the new Microbes in the Emerging & AMP;Infections online article “Possible Recombination between Two variants of Concern ina COVID-19 patient”This paper reports on gene recombination events between different mutant strains in COVID-19 patients infected with two SARS-COV-2 mutants.Photo credit: Emerging Microbes & AMP;An outbreak of COVID-19 occurred on a flight from Johannesburg, South Africa to Shenzhen, China (arrival date: 10 June 2021) with 39 passengers infected.Four viral lineages were identified, including two Delta strains (delta-I and delta-II), one Beta strain and one C.1.2 strain.Our analysis found the highest number of in-host mutations (iSNV) in case 49H, where all 65 mutations of the delta-I and Beta strains were detected, suggesting co-infection in this setting.Notably, case 49H also had some low-level mutations not observed in delta-I or Beta strains.These mutations have not been observed simultaneously in the genomes of delta-II, C.1.2 strains, or any of the viruses in public databases, and are therefore unlikely to represent the presence of a third strain, suggesting that they may represent intra host mutations following infection.Photo credit: Emerging Microbes & AMP;To further validate the co-existence of two SARS-COV-2 mutants, seven genomic regions shorter than 90 base pairs were selected.And included at least two different mutation sites between Beta and delta-I strains for haplotype analysis.Two major haplotypes were identified in readings from samples at three time points across the seven regions, corresponding to the delta-I and Beta genomes respectively, suggesting that case 49H was indeed co-infected with delta-I and Beta mutants.The researchers then calculated the ratio of delta-I and Beta variants in the sample by examining the frequency of mutated alleles at 60 different sites between the delta-I and Beta mutants.The results showed that the relative abundance ratio between the two variants remained at 1:9 (Beta: Delta) for 14 days.Notably, in the Orf1ab and Spike genes, the ratio of the other 13 mutation sites was about 1 to 1 or 1 to 3, which clustered into three regions 174-2692, 5839, and 21801-22281.The researchers say the distribution of these different locations is unlikely to be random.This suggests that there are other haplotypes besides delta-I and Beta haplotypes in the body.Photo credit: Emerging Microbes & AMP;The authors conclude by suggesting that co-infection and recombination events may not be uncommon and that other studies have recently reported co-infection and recombination events between different SARS-COV-2 variants.Especially considering that hundreds of variants have circulated in the population in the past 28 days (as of 11 January 2022) and there have been more than 30 million new infections.The researchers suggest that non-medical interventions, such as the use of masks and social distancing, should be continued, and that patients infected with different virus variants should be isolated to prevent the emergence of new recombinant viruses.

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