Virus database annotations assist in tracing information on patients infected with emerging pathogens

Abstract

The global pandemic of SARS-CoV-2 has disrupted human social activities. In restarting economic activities, successive outbreaks by new variants are concerning. Here, we evaluated the applicability of public database annotations to estimate the virulence, transmission trends and origins of emerging SARS-CoV-2 variants. Among the detectable multiple mutations, we retraced the mutation in the spike protein. With the aid of the protein database, structural modelling yielded a testable scientific hypothesis on viral entry to host cells. Simultaneously, annotations for locations and collection dates suggested that the variant virus emerged somewhere in the world in approximately February 2020, entered the USA and propagated nationwide with periodic sampling fluctuation likely due to an approximately 5-day incubation delay. Thus, public database annotations are useful for automated elucidation of the early spreading patterns in relation to human behaviours, which should provide objective reference for local governments for social decision making to contain emerging substrains. We propose that additional annotations for past paths and symptoms of the patients should further assist in characterizing the exact virulence and origins of emerging pathogens.

Olfactory marker protein contains a leucine-rich domain in the Ω-loop important for nuclear export

“…2 a). The conventional information entropy [ 28 ] and the recently released taxon-related LIST-S2 [ 27 ] elucidated the cyclic nucleotide-binding domain (CNBD) at approximately sites 120–130 (Fig. 2 a–c) [ 2 ], but the entropy profile results were rather spiky (Fig.…”

“…To identify the vital residues with unknown functions in OMP, we utilized a secondary moment-based metric defined as PKV. With the aid of bioinformatics, putative functional residues might be highlighted [ 27 , 28 ]; the completely or mostly conserved residues are especially detectable. However, for many proteins, vital residues and their actions remain unknown mostly because the effects of mutations may be deleterious [ 27 ] and eliminated from genetic pools or subtle and compensated for by other molecules.…”

“…Although the evolutionarily conserved residues were clustered by PKV, the molecular actions of these regions should be predicted according to the characteristics of the residues to some extent and experimentally verified through reverse-genetics manipulations and biophysical experiments [ 2 , 42 ]. As an option to start with, PKV could be helpful in combination with other metrics [ 27 , 28 ] and de novo approaches to study important residues, such as directed evolution [ 43 , 44 ] and large-scale mutagenesis [ 45 ].…”

“…The LIST-S2 scores for OMP were obtained online [ 27 ]. The information entropy at the i th partition with amino acid diversity (Di) and its emergence probability (P Di ) was calculated as follows [ 28 ]: …”

Genetic diversity of SARS-CoV-2 in South America: demographic history and structuration signals

“…Spike haplotypes containing both variants were found in SA, with the G mutation being the most frequent. The 614G polymorphism appears to affect viral infectivity and transmissibility [69][70][71]. Considering that a) under drift, polymorphism is expected to be fixed or get lost randomly, b) this variant had positive selection signals, and c) 614G has almost completely replaced the 614D variant worldwide, it is feasible to think that this mutation has been fixed by directional selection.…”