In a recent post on the bioRxiv* preprint server, researchers studied serial case data of coronavirus disease 2019 (COVID-19) from the Huanan seafood market in Beijing, China, to delineate populations of minor genome variants since the start of the pandemic. induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Huanan’s market in China has been the epicenter of the COVID-19-induced pandemic, where human-to-human transmission of the fatal SARS-CoV-2 began. Two market overflow events established the transmission of B and A lines in the human population and potentially stopped additional overflows. Therefore, the researchers believed that SARS-CoV-2 had limited genetic diversity at the beginning of the pandemic in humans. However, as the pandemic progressed and SARS-CoV-2 spread in China and around the world, its genomic sequences have become diverse.
The dominant genome series is maximally abundant in a pattern of a COVID-19 patient and a useful marker of viral population sequencing information. For example, in patients in the Huanan market, the dominant series of the SARS-CoV-2 genome were more than 99. 9% identical, indicating the recent emergence of SARS-CoV-2 in the human population. The current markers are minor genomic variants with lower abundance. They involve substitutions of synonymous and non-synonymous amino acids that confer merit under selective stress and therefore the phenotype of the disease.
In the study provided, the researchers knew the first samples from COVID-19 patients that would have been related to the Huanan market on the date of onset of symptoms or the deposition series. They know SARS-CoV-2 sequencing data from 16 patients (S1 to S16) and used other approaches to assign minor genomic variants from this knowledge.
The researchers separated the low-frequency variants from the errors of the Illumina DiversiTools series, whose algorithms use Illumina quality scores to calculate a p-value for each of the variants at each site of a nucleotide of a protein. Alternatively, they thought of a reading intensity arbitraria. de 10 or 100 nucleotides consistent with the site to identify minor variant genomes. The researchers thought of a threshold above and below the 20% threshold to examine minor genomic variants and their arrangement with amino acid substitutions and phenotypes.
The authors noted that the policy of minor variants varies across the genome, with some sites having higher and lower policies on sequencing information. In addition, they knew minor variant genomes in all genes in SARS-CoV-2 for the patient. The information indicated that amino acid substitutions at express sites of certain genes, adding the SARS-CoV-2 (E) envelope, membrane (M), open reading frame (ORF) 6, ORF7b and ORF10, were less frequent.
In particular, 3 patients, S9, S12 and S14, had little population diversity in the minor variant genomes of SARS-CoV-2. In contrast, patient S6 had a substitution frequency of about 40% (higher), C25R and V49I in the SARS-Gene ORF8 coV-2. For a threshold above 20%, patients S1, S6, S10 and S11 had a greater number of minor variant genomes in SARS-CoV-2. In addition, those genomes had untimely prevention codons (for example, patient S11 had a premature prevention codon in SARS-CoV-2 nonstructural protein 2 (NSP2).
More importantly, however, the authors were aware of several minor genomic variants at the peak (S) of SARS-CoV-2 and other proteins, later discovered in their fear variants (VOCs). The frequency and position of these genomic variants vary among patients. . However, knowledge indicated the presence of these characteristics of SARS-CoV-2 VOCs at the beginning of the pandemic. For example, the substitution of P323L in NSP12 in minor genomic variants of SARS-CoV-2 in patients S3, S9, S10 and S15.
In addition, those substitutions are less than 5% at the point of a minor variant of the genome, they have been shown to be subject to strong strain pressure. As a result, they had the possibility of becoming dominant a few days after SARS-CoV-2 infection. In particular, minor genomic variants of SARS-CoV-2 in patient 16 had multiple substitutions at a frequency diversity of 5% and 15%.
The existing study of known amino acid substitutions in minor variants of SARS-CoV-2 cases at the beginning of the COVID-19 pandemic was related to long-term VOCs. In addition, it showed the option of predicting the occurrence of VOCs based on the investigation of minor variant genomes and variable sites since the beginning of the COVID-19 outbreak. To conclude, this information on viral evolution can help to design timely treatment regimens and vaccination against SARS-CoV-2 VOCs in the long term.
bioRxiv publishes initial clinical reports that are not peer-reviewed and therefore should not be considered as conclusive clinical practices/health-related behaviors, nor treated as established information.
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Neha is a virtual marketing professional founded in Gurugram, India. He holds a master’s degree from the University of Rajasthan with a specialization in Biotechnology in 2008. He has enjoyed preclinical studies as part of his assignment of studies in Toxicology Decomposer from the prestigious Central Institute of Drug Research (CDRI), Lucknow, India. He also holds a certification in C programming.
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