PT  - JOURNAL ARTICLE
AU  - Tom W. Ouellette
AU  - Jim Shaw
AU  - Philip Awadalla
TI  - Using image-based haplotype alignments to map global adaptation of SARS-CoV-2
AID  - 10.1101/2021.01.13.426571
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.13.426571
4099  - http://biorxiv.org/content/early/2021/01/13/2021.01.13.426571.short
4100  - http://biorxiv.org/content/early/2021/01/13/2021.01.13.426571.full
AB  - Quantifying evolutionary change among viral genomes is an important clinical device to track critical adaptations geographically and temporally. We built image-based haplotype-guided evolutionary inference (ImHapE) to quantify adaptations in expanding populations of non-recombining SARS-CoV-2 genomes. By combining classic population genetic summaries with image-based deep learning methods, we show that different rates of positive selection are driving evolutionary fitness and dispersal of SARS-CoV-2 globally. A 1.35-fold increase in evolutionary fitness is observed within the UK, associated with expansion of both the B.1.177 and B.1.1.7 SARS-CoV-2 lineages.Competing Interest StatementThe authors have declared no competing interest.