The new genetic variant (#B117) of the novel #coronavirus SARS-CoV-2 (the UK variant) was identified as causing a reinfection in a severely ill patient who had previously been diagnosed with COVID-19 eight months earlier and who had developed antibodies. This is the first reported case of #reinfection with the UK #Variant of Concern. This video presents the case report confirming reinfection with the new variant in a 78-year-old man with multiple comorbidities who was receiving regular PCR testing due to his dialysis.
Whole #genome sequencing identified the initial infection as B.2 pangolin lineage, which is 19A using Nextstrain clade nomenclature or V clade in the GISAID clade system, while the sample collected on December 8 was classified as the B.1.1.7 variant with its 9 amino acid changes to the spike protein, including on the receptor binding domain or RBD.
We cover a lot of ground, explaining important concepts along the way, including how RNA viruses mutate, how to correctly use the terms #mutation, variant, and strain, as well as the differences in the many genomic nomenclature systems used.
Bookmarks:
0:00 Summary of Reinfection Study
2:05 Mutations in RNA viruses
3:27 Correct terminology for mutation, variant, and strain
5:39 Pangolin lineage, Nextstrain clade, GISAID clade
7:49 The B.1.1.7 Variant
8:47 Case History of Reinfection
11:27 Considerations for Immunity
*** Sources and References ***
Confirmed Reinfection with SARS-CoV-2 Variant VOC-202012/01 |
Genetic Variants of SARS-CoV-2—What Do They Mean? |
Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations |
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology |
Mutant coronavirus in the United Kingdom sets off alarms, but its importance remains unclear |
Comment on recent spike protein changes |
Travel bans aren’t an effective response to the new Covid variant |
Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study |
Could new COVID variants undermine vaccines? Labs scramble to find out |
