PT  - JOURNAL ARTICLE
AU  - B Korber
AU  - WM Fischer
AU  - S Gnanakaran
AU  - H Yoon
AU  - J Theiler
AU  - W Abfalterer
AU  - B Foley
AU  - EE Giorgi
AU  - T Bhattacharya
AU  - MD Parker
AU  - DG Partridge
AU  - CM Evans
AU  - TM Freeman
AU  - TI de Silva
AU  - on behalf of the Sheffield COVID-19 Genomics Group
AU  - CC LaBranche
AU  - DC Montefiori
TI  - Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2
AID  - 10.1101/2020.04.29.069054
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.04.29.069054
4099  - http://biorxiv.org/content/early/2020/05/05/2020.04.29.069054.short
4100  - http://biorxiv.org/content/early/2020/05/05/2020.04.29.069054.full
AB  - We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified thirteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.Competing Interest StatementThe authors have declared no competing interest.