Mutations in Animal SARS-CoV-2 Induce Mismatches with the Diagnostic PCR Assays.

Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detected in several animal species. After transmission to animals, the virus accumulates mutations in its genome as adaptation to the new animal host progresses. Therefore, we investigated whether these mutations result in mismatches with the diagnostic PCR assays and suggested proper modifications to the oligo sequences accordingly. A comprehensive bioinformatic analysis was conducted using 28 diagnostic PCR assays and 793 publicly available SARS-CoV-2 genomes isolated from animals. Sixteen out of the investigated 28 PCR assays displayed at least one mismatch with their targets at the 0.5% threshold. Mismatches were detected in seven, two, two, and six assays targeting the ORF1ab, spike, envelope, and nucleocapsid genes, respectively. Several of these mismatches, such as the deletions and mismatches at the 3' end of the primer or probe, are expected to negatively affect the diagnostic PCR assays resulting in false-negative results. The modifications to the oligo sequences should result in stronger template binding by the oligos, better sensitivity of the assays, and higher confidence in the result. It is necessary to monitor the targets of diagnostic PCR assays for any future mutations that may occur as the virus continues to evolve in animals.

Mutational spectra of SARS-CoV-2 isolated from animals.

Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94-99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2.

The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control.

A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global increases in the number of cases daily. Therefore, the WHO has declared COVID-19 a pandemic. The disease is characterized by fever, dry cough, and chest pain with pneumonia in severe cases. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. To date, there are no available vaccines or specific therapeutic drugs to treat the virus. There are many knowledge gaps about the newly emerged SARS-CoV-2, leading to misinformation. Therefore, in this review, we provide recent information about the COVID-19 pandemic. This review also provides insights for the control of pathogenic infections in humans such as SARS-CoV-2 infection and future spillovers.

Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review.

COVID-19 caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan (Hubei province, China) during late 2019. It has spread across the globe affecting nearly 21 million people with a toll of 0.75 million deaths and restricting the movement of most of the world population during the past 6 months. COVID-19 became the leading health, economic, and humanitarian challenge of the twenty-first century. In addition to the considerable COVID-19 cases, hospitalizations, and deaths in humans, several cases of SARS-CoV-2 infections in animal hosts (dog, cat, tiger, lion, and mink) have been reported. Thus, the concern of pet owners is increasing. Moreover, the dynamics of the disease requires further explanation, mainly concerning the transmission of the virus from humans to animals and vice versa. Therefore, this study aimed to gather information about the reported cases of COVID-19 transmission in animals through a literary review of works published in scientific journals and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. Although many instances of transmission of the SARS-CoV-2 have been reported, caution and further studies are necessary to avoid the occurrence of maltreatment in animals, and to achieve a better understanding of the dynamics of the disease in the environment, humans, and animals. Future research in the animal-human interface can help formulate and implement preventive measures to combat the further transmission of COVID-19.