Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection.
By
Chao Zhang,
Anurag Verma,
Yuanqing Feng,
Marcelo C. R. Melo,
Michael McQuillan,
Matthew Hansen,
Anastasia Lucas,
Joseph Park,
Alessia Ranciaro,
Simon Thompson,
Meghan A. Rubel,
Michael C. Campbell,
William Beggs,
JIBRIL HIRBO,
Sununguko Wata Mpoloka,
Gaonyadiwe George Mokone,
Regeneron Genetic Center,
Thomas Nyambo,
Dawit Wolde Meskel,
Gurja Belay,
Charles Fokunang,
Alfred K. Njamnshi,
Sabah A. Omar,
Scott Williams,
Daniel J Rader,
Marylyn D. Ritchie,
Cesar de la Fuente Nunez,
Giorgio Sirugo,
Sarah Tishkoff
Posted 01 Jul 2021
medRxiv DOI: 10.1101/2021.06.28.21259529
We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.
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