Abstract
As the COVID-19 pandemic swept through an immunologically naïve human population, academics and public health professionals scrambled to establish methods and platforms for genomic surveillance and data sharing. This offered a rare opportunity to study the ecology and evolution of SARS-CoV-2 over the course of the ongoing pandemic. Here, we use population genetic and phylogenetic methodology to characterize the population dynamics of SARS-CoV-2 and reconstruct patterns of virus introductions and local transmission in Norway against this backdrop. The analyses demonstrated that the epidemic in Norway was largely import driven and characterized by the repeated introduction, establishment, and suppression of new transmission lineages. This pattern changed with the arrival of the B.1.1.7 lineage, which was able to establish a stable presence concomitant with the imposition of severe border restrictions.
Highlights
The COVID-19 pandemic has brought about the rapid development and uptake of genomic epidemiology globally
The analyses demonstrated that the epidemic in Norway was largely import driven and characterized by the repeated introduction, establishment, and suppression of new transmission lineages
The wealth of sequence data shared and analysed via GISAID (Elbe and Buckland-Merrett 2017) and NextStrain (Hadfield et al, 2018) puts us in a unique position to understand the dynamics of the pandemic in response to both intrinsic viral characteristics, such as the evolution of increased transmissibility, as well as infection control measures, such as travel restrictions and other nonpharmaceutical interventions (NPIs)
Summary
The COVID-19 pandemic has brought about the rapid development and uptake of genomic epidemiology globally. More than 2 million SARS-CoV-2 sequences have been shared through the GISAID initiative (Elbe and Buckland-Merrett 2017) as of June 2021. Genome sequences sampled across time and space are optimally suited for tracking and making sense of the evolution and spread of pathogens. In the case of SARS-CoV-2, both GISAID and NextStrain (Hadfield et al, 2018) have become essential platforms for tracking the dispersal of viral variants and mutations globally. A hallmark of the COVID-19 pandemic has been the wavelike regional and global sweeps of new variants. The second half of 2020 was characterized by parallel regional sweeps of P.1 in South America (Gamma variant) (Faria et al, 2021) and B.1.351 (Beta variant) in Africa (Tegally et al, 2020; O’Toole et al, 2021), both of which being less efficiently inhibited by neutralizing antibodies (Hoffmann et al, 2021). B.1.1.7, B.1.351, and P.1 were all recognized as variants of concern (VOCs) by the European Centre for Disease Prevention and Control (https://www.ecdc.europa.eu/en/covid-19/variantsconcern, last accessed on 1 May 2021)
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