V367F mutation in SARS-CoV-2 spike RBD emerging during the early transmission phase enhances viral infectivity through increased human ACE2 receptor binding affinity

Abstract

250 words 25 Importance: 150 words 26 Abstract 28 A novel coronavirus SARS-CoV-2 is associated with the current global pandemic of Coronavirus 29Disease 2019 . Spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the 30 critical determinant of viral tropism and infectivity. To investigate whether the mutations in the RBD 31 have altered the receptor binding affinity and caused these strains more infectious, we performed 32 molecular dynamics simulations of the binding affinity between the mutant SARS-CoV-2 RBDs to 33 date and the human ACE2 receptor. Among 1609 genomes of global SARS-CoV-2 strains, 32 34 non-synonymous RBD mutants were identified and clustered into 9 mutant types under high positive 35 selection pressure. Three mutant types (V367F, W436R, and D364Y) emerging in Wuhan, Shenzhen, 36 Hong Kong, and France, displayed higher human ACE2 affinity, and probably higher infectivity. This 37 is due to the enhanced structural stabilization of the RBD beta-sheet scaffold. High frequencies of 38 RBD mutations were identified: V367F from five France and one Hong Kong mutants, 13 V483A and 39 7 G476S mutants from the U.S.A. This suggested they originated as novel sub-lineages. The 40 enhancement of the binding affinity of the mutant type (V367F) was further validated by the 41 receptor-ligand binding ELISA assay. The molecular dynamics simulations also indicated that it 42 would be difficult for bat SARS-like CoV to infect humans. However, the pangolin CoV is potentially 43 infectious to humans. The analysis of critical RBD mutations provides further insights into the 44 evolutionary history of SARS-CoV-2 under high selection pressure. An enhancement of the 45 SARS-CoV-2 binding affinity to human ACE2 receptor reveals higher infectivity of the mutant 46 strains. 47 48 Importance 49 A novel coronavirus SARS-CoV-2 has caused the pandemic of COVID-19. The origin of 50 SARS-CoV-2 was associated with zoonotic infections. The spike protein receptor-binding domain 51 (RBD) is identified as the critical determinant of viral tropism and infectivity. Thus, whether the 52 mutations in the RBD of the circulating SARS-CoV-2 strains have altered the receptor binding 53affinity and caused these strains more infectious, should be paid more attentions to. Here, 32 54 non-synonymous RBD mutants were identified and clustered into 9 mutant types under high positive 55 . CC-BY-NC-ND 4.0 International license (which was not certified by peer review) is the author/funder. It is made available under a selection pressure, suggesting they originated as novel sub-lineages. Three mutant types displayed 56 higher human ACE2 affinity, and probably higher infectivity, one of which (V367F) was validated 57 by wet bench. The RBD mutation analysis provides insights into SARS-CoV-2 evolution. The 58 emergence of RBD mutations with increased human ACE2 affinity reveals higher risk of severe 59 morbidity and mortality during a sustained COVID-19 pandemic, particularly if no effective 60 precautions are implemented. 61 62

Stability of SARS-CoV-2 Phylogenies

“…For example, artefactual biases in mutational processes could confound signatures of mutational hotspots [28][29][30][31][32][33] . The issue of whether or not recombination has occurred during the outbreak is critical to the immunological battle against the virus and is under intense debate [6,[34][35][36][37][38][39][40] . Because many tests of recombination assume that all mutations can only occur once at each site, recurrent mutation and systematic errors can confound signatures of recombination [6,26,35] .…”

An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes

“…A number of literature contributions now discuss the potential role for bats, pangolins, and other possible progenitor/intermediate species in derivation of SARS-CoV-2 from different approaches and perspectives, with a diversity of approaches and interpretations in understanding the origin of the virus. In particular, there has been extensive discussion and debate about the possible pangolin origin of SARS-CoV-2 (19,(21)(22)(23)(24)(25)(26)(27)(28)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41). These studies provide useful insights into the evolution of SARS-CoV-2 but have limitations and uncertainty in drawing conclusions regarding the viral origin, as most studies were mainly performed through sequence-based comparison and simulation.…”

A short review on antibody therapy for COVID-19

“…They identified that the two groups of amino acid mutations in the SARS-CoV-2 RBD domain: the "similar affinity" group (F342L, R408I) and the "higher affinity" group (N354D D364Y, V367F, W436R). The "higher affinity" group RBD mutations under the positive selective pressure enhanced the infection efficiency of the SARS-CoV-2 [35]. Hence, epidemiology data and mutation surveillance are very important to reveal more exact spreading routes of the pandemic SARS-CoV-2.…”