SARS-CoV-2’s high rate of genetic mutation under immune selective pressure: from oropharyngeal B.1.1.7 to intrapulmonary B.1.533 in a vaccinated patient

• Published in: International journal of infectious diseases 2022-05, Vol.118, p.169-172
• Main Authors: Musso, Nicolò, Maugeri, Jessica Giuseppina, Bongiorno, Dafne, Stracquadanio, Stefano, Bartoloni, Giovanni, Stefani, Stefania, Di Stefano, Emanuela Daniela
• Format: Article
• Language: English
• Subjects: Aged, 80 and over; Case Report; COVID-19; COVID-19 - diagnosis; Humans; Intra-Host Mutations; Lineages; Male; Mutation; NGS; Post-vaccine; RNA, Viral - genetics; SARS-CoV-2 - genetics
• ISSN: 1201-9712; 1878-3511
• DOI: 10.1016/j.ijid.2022.02.044

•It could be useful to know the infection status before SARS-CoV-2 vaccination.•SARS-CoV-2 virus can mutate inside the human host.•SARS-CoV-2 virus tends to change under selective pressure. 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.