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Emerg Infect Dis ; 28(9)2022 Aug 04.
Article in English | MEDLINE | ID: covidwho-1974606


We detected a highly divergent SARS-CoV-2 Alpha variant in an immunocompromised person several months after the latest detection of the Alpha variant in the Netherlands. The patient was infected for 42 weeks despite several treatment regimens and disappearance of most clinical symptoms. We identified several potential immune escape mutations in the spike protein.

Nat Med ; 27(9): 1518-1524, 2021 09.
Article in English | MEDLINE | ID: covidwho-1402106


The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.

COVID-19/epidemiology , Epidemiological Monitoring , Genome, Viral/genetics , Molecular Epidemiology/methods , SARS-CoV-2/genetics , Base Sequence/genetics , Clinical Decision-Making , Databases, Genetic , Humans , Public Health , Whole Genome Sequencing