Decoding asymptomatic COVID-19 infection and transmission

Wang, Rui; Hozumi, Yuta; Yin, Changchuan; Wei, Guo-Wei

Coronavirus disease 2019 (COVID-19) is a continuously devastating public health and the world economy. One of the major challenges in controlling the COVID-19 outbreak is its asymptomatic infection and transmission, which are elusive and defenseless in most situations. The pathogenicity and virulence of asymptomatic COVID-19 remain mysterious. Based on the genotyping of 20656 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome isolates, we reveal that asymptomatic infection is linked to SARS-CoV-2 11083G>T mutation, i.e., leucine (L) to phenylalanine (F) substitution at the residue 37 (L37F) of nonstructure protein 6 (NSP6). By analyzing the distribution of 11083G>T in various countries, we unveil that 11083G>T may correlate with the hypotoxicity of SARS-CoV-2. Moreover, we show a global decaying tendency of the 11083G>T mutation ratio indicating that 11083G>T hinders SARS-CoV-2 transmission capacity. Sequence alignment found both NSP6 and residue 37 neighborhoods are relatively conservative over a few coronaviral species, indicating their importance in regulating host cell autophagy to undermine innate cellular defense against viral infection. Using machine learning and topological data analysis, we demonstrate that mutation L37F has made NSP6 energetically less stable. The rigidity and flexibility index and several network models suggest that mutation L37F may have compromised the NSP6 function, leading to a relatively weak SARS-CoV subtype. This assessment is a good agreement with our genotyping of SARS-CoV-2 evolution and transmission across various countries and regions over the past few months.