SARS-CoV-2: Origin, Intermediate Host and Allergenicity Features and Hypotheses

Abstract

The goal of this study is to investigate the probable intermediate hosts and the allergenicity of the notorious virus SARS-CoV-2 to understand how this virus emerged. The phylogenetic analysis of the virus spike proteins indicates that SARS-CoV-2 falls into various small subclades that include a bat coronavirus RaTG13, suggesting bats as a likely natural origin. Refined alignment of the spike protein in NCBI found several fragments that are specific to SARS-CoV-2 and/or SARS-CoV are specific to Rattus norvegicus and/or Mus musculus, suggesting that rodents are the intermediate reservoir of SARS-CoV-2 and SARS-CoV. To evaluate the allergenicity values, the binding affinities of human leukocyte antigen (HLA) class I or II molecules with the spike proteins were calculated, and the results showed that both SARS-CoV-2 and SARS-CoV are predicted to bind to fourteen HLA class I and II molecules with super-high HLA allele-peptide affinities. The infection rate of individuals who have HLA alleles with very high binding affinities who might become infected and develop into refractory patients if there were no medical or non-medical interventions is about 7.36% and 4.78% of Chinese and Americans, respectively. Extremely high temperature and exceptionally low precipitation, the common climate factors between the outbreak sites of COVID-19 in Wuhan in 2019 and SARS in Guangdong in 2002, might have promoted coronavirus evolution into more virulent forms. Our hypothesis suggests that early immunization with an allergenically-engineered virus, in combination with continued surveillance of meteorological factors and viral mutations, may be one of the most powerful prophylactic modalities to fight this virus.

Identification of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir

“…SARS-CoV-1 (Betacoronavirus lineage B) and MERS-CoV (Betacoronavirus lineage C) are known to be enzoonotic in bats and other species such as civets or camels with occasional spillovers into human populations (63,68). Similarly, SARS-CoV-2 (Betacoronavirus lineage B) has most likely been transmitted zoonotically from bats (69)(70)(71)(72)(73)(74). Given that bats are a frequent source of dangerous viruses, we also tested the bat coronavirus HKU9-M pro (Betacoronavirus lineage D) (6,75).…”

The SARS-CoV-2 B.1.351 Variant Can Transmit in Rats But Not in Mice

“…We speculate that rats might be potential intermediate reservoirs of SARS-CoV-2. A recent study also proposed that rodents are the intermediate reservoirs of SARS-CoV-2 and SARS-CoV ( 23 ). To determine the potential prevalence of SARS-CoV-2 in rats, further serology and molecular surveillance of SARS-CoV-2 variants in domestic rats and wild rats should be performed in regions where B.1.351 and other variants circulate.…”

Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species

“…It may be due to the limitations of virus metagenomics technology that we cannot thoroughly know the diversity and richness of viruses that are carried by host animals. However, some studies have shown that rodents may serve as intermediate hosts of the coronavirus [75], which suggests that we need to further explore the complex viral ecosphere among virus hosts and discover the source and mode of transmission of zoonotic viruses.…”