Abstract
This is the case report of an 84-year-old man affected by COVID-19 between the 2 doses of vaccination, with negative exitus. We analyzed nasopharyngeal samples of viral RNA collected during the disease and nasopharyngeal and lung samples collected postmortem by reverse transcription LAMP (RT-LAMP) PCR and Next Generation Sequencing (NGS). NGS results were analyzed with different bioinformatic tools to define virus lineages and the related single-nucleotide polymorphisms (SNPs). Both lung and nasopharyngeal samples tested positive for SARS-CoV-2 on RT-LAMP. Through bioinformatic analysis, 2 viral RNAs from the nasal swabs, which belonged to the B.1.1.7 lineage, and 1 viral RNA from the lung sample, which belonged to the B.1.533 lineage, were identified. This genetic observation suggested that SARS-CoV-2 tends to change under selective pressure. The high mutation rate of ORFa1b, containing a replicase gene, was a biological image of a complex viral survival system.
Keywords: COVID-19; Intra-Host Mutations; Lineages; NGS; Post-vaccine.
【저자키워드】 COVID-19, NGS, lineages, Intra-Host Mutations, Post-vaccine., 【초록키워드】 SARS-CoV-2, vaccination, Genetic, SNPs, polymorphism, lung, virus, Case report, B.1.1.7 lineage, RT-LAMP, survival, Viral, PCR, B.1.1.7, nasopharyngeal, LAMP, Lineage, Single-nucleotide polymorphisms, next generation sequencing, reverse transcription, Viral RNA, Postmortem, mutation rate, lineages, dose, observation, viral RNAs, complex, Nasopharyngeal samples, high mutation rate, selective, positive, nasal swabs, bioinformatic analysis, Post-vaccine, nasopharyngeal sample, tested, analyzed, affected, collected, the disease, suggested, to define, single-nucleotide, 【제목키워드】 SARS-CoV-2, Mutation, Genetic, immune, Patient, Oropharyngeal, selective, intrapulmonary,