Genetic Polymorphisms in Ace2 Transcripts of Sars-Cov-2 Positive Individuals from Four Selected West African Countries

Abstract

Coronavirus disease 2019 (COVID-19) claimed the lives of millions of people worldwide but with great disparity in the number of cases and deaths across different populations. Multiple hypotheses have been proposed to explain the relatively low COVID-19 in the West African population compared to other parts of the world. The role of host-genetics has been explored in a quest to explain the disparity. Multiple population-specific polymorphisms within receptors which allow SARS-CoV-2 cellular invasion have been identified with varying effects on COVID-19 severity. Using targeted sequencing, this study sought to explore SNPs (Single Nucleotide Variations) within ACE2 (Angiotensin-converting enzyme 2); the primary receptor for SARS-CoV-2 cellular entry, and their impact on its function in COVID-19 severity for four West African countries; Ghana, Nigeria, Benin and Guinea. RNA (n = 330) was extracted from archived respiratory samples of SARS-CoV-2 positive individuals across the four countries. The RNA was converted to cDNA and PCR optimization for twelve overlapping primers targeting ACE2 was carried out. Six out of these primers targeting eleven ACE2 exons were optimized successfully and sequenced on the Oxford Nanopore Technology platform. Following bioinformatic analyses, twelve SNPS in total were identified. Five previously reported ACE2 missense variants (G353V, T434K, V573A, L585P and S607G) were identified at low frequencies within the sites used in this study. The substitution G352V has been previously described to confer protection against SARS-CoV-2. PolyPhen-2 analysis of the other four previously reported SNPs indicated possible structural changes to ACE2 which may affect its interaction with SARS-CoV-2. Seven novel ACE2 SNPs; W349*, D350E, D350V, G352W, G352R, G352E, and K353Q were also identified within the four sites. D350G had a high frequency across all the four West African countries (countries (Benin – 100%, Ghana – 56.2%, Guinea – 84.2% and Nigeria – 77.4%). The modelled structure of ACE2 with each of the three of the novel SNPs, their interactions with Spike receptor binding domain (RBD) and estimated binding affinity was simulated using I-TASSER, ClusPro and PRODIGY respectively. All modelled variants had a relatively lower binding interaction with the Spike protein compared to wild-type ACE2. The lower binding interactions observed potentially suggest a lower rate of SARS-CoV-2 cellular invasion which may be one of the reasons for the low severity of SARS CoV-2 observed in West Africa.