Mutational spectra of SARS-CoV-2 isolated from animals

Elaswad, Ahmed; Fawzy, Mohamed; Basiouni, Shereen; Shehata, Awad A.

doi:10.7717/peerj.10609

Cited by 43 publications

(63 citation statements)

References 59 publications

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“…This number is higher than that obtained by [ 19 ] who reported mismatches in seven out of 27 assays. This result may be due to the ongoing adaptation of SARS-CoV-2 in animal hosts resulting in higher variations in animal isolates compared with human isolates [ 26 ]. These variations highlighted the need for frequent evaluation of currently available diagnostic PCR assays to successfully control the SARS-CoV-2 pandemic.…”

Section: Discussionmentioning

confidence: 99%

“…The N and E genes encode essential coronavirus capsid structural proteins, while other proteins regulate a range of molecular processes during viral replication [ 62 ]. The E gene is highly conserved with no mutations [ 26 ]. The single-nucleotide mismatch observed here in Won-E reverse primer is likely due to the primer design, not the evolution of animal SARS-CoV-2 at this site, because this mismatch is present in all the studied genomes including the reference sequence (Wuhan-Hu-1).…”

Section: Discussionmentioning

confidence: 99%

“…The single-nucleotide mismatch observed here in Won-E reverse primer is likely due to the primer design, not the evolution of animal SARS-CoV-2 at this site, because this mismatch is present in all the studied genomes including the reference sequence (Wuhan-Hu-1). The N gene may be under positive selective pressure where it is accumulating a significant number of mutations in human and animal isolates [ 26 , 63 ].…”

Section: Discussionmentioning

confidence: 99%

“…Despite the presence of an RNA proofreading exoribonuclease (nsp14-ExoN) [ 25 ], the circulating SARS-CoV-2 genome exhibited several mutations either in humans or animals [ 26 , 27 ]. These mutations may lead to mismatches if occurred at primer or probe binding regions, resulting in false-negative results [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

“…After cross-species transmission, the virus begins to acquire mutations to adapt to the new hosts, which may result in new viral strains [ 49 ]. We previously reported several unique mutations in SARS-CoV-2 isolated from cats, dogs, minks, and mice when compared with SARS-CoV-2 isolates from humans at the same time and geographic region [ 26 ]. These acquired nucleotide variations may occur all over the genome including the targets of diagnostic PCR assays.…”

Section: Introductionmentioning

confidence: 99%

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

Elaswad

Fawzy

2021

Pathogens

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Elaswad

Fawzy

2021

Pathogens

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Massive‐scale genomic analysis reveals SARS‐CoV‐2 mutation characteristics and evolutionary trends

Sun

Wang

Lin

et al. 2022

mLife

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The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic resulted in significant societal costs. Hence, an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 pandemic. In this study, we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 genomes. All possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed, including zinc finger antiviral proteins, sequence context, amino acid change, and translation efficiency. As a result, we proposed that when adenine (A) and tyrosine (T) bases are in the context of AM (M stands for adenine or cytosine) or TA motif, A or T base has lower mutation frequency. Furthermore, we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection, which explains why SARS‐CoV‐2 prefers AT3 codons usage. In addition, we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome, which provides a new basis for determining the origin of the SARS‐CoV‐2. Finally, we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.

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SARS‐CoV‐2 infection of companion animals in Egypt and its risk of spillover

Hamdy

El‐Deeb

Hagag

et al. 2022

Veterinary Medicine & Sci

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Background Reverse zoonoses occur because of interactions between humans and animals. Homology of ACE‐2 cell receptors in different hosts and high mutation rate of SARS‐CoV‐2 enhance viral transmission among species. Objectives This study aimed to investigate spillover of SARS‐CoV‐2 between humans and companion animals. Methods A cross‐sectional study was constructed using nasopharyngeal/oropharyngeal swabs, serum and blood samples collected from 66 companion animals (33 cats and 33 dogs) that were in contact with SARS‐CoV‐2‐positive owners from December 2020 to March 2021. Swabs were screened by rRT‐PCR and some positive cases were confirmed by partial spike gene sequencing. Clinical pathology and pathological studies were also performed. Results Our findings revealed that 30% of cats (10/33) and 24% of dogs (8/33) were SARS‐CoV‐2 positive. While 33% of these animals were asymptomatic (6/18), 28% showed mild respiratory signs (5/18) and 39% displayed severe respiratory signs (7/18) including 4 dead cats 40% (4/10). Partial spike gene sequencing of 6 positive samples collected in December 2020 were identical to SARS‐CoV‐2 that was detected in humans in Egypt in that time frame. Clinical pathology findings revealed thrombocytopenia, lymphocytopenia, as well as elevated levels of D‐dimer, LDH, CRP, and ferritin. Post‐mortem and histopathological examinations illustrated multisystemic effects. Conclusions There is a potential occurrence of SARS‐CoV‐2 spillover between humans and pet animals. Impacts The present study highlighted the potential occurrence of SARS‐CoV‐2 spillover between humans and their companion animals. Biosecurity measures should be applied to decrease spread of SARS‐CoV‐2 among humans and pet animals.

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Mutational spectra of SARS-CoV-2 isolated from animals

Cited by 43 publications

References 59 publications

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

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

Massive‐scale genomic analysis reveals SARS‐CoV‐2 mutation characteristics and evolutionary trends

SARS‐CoV‐2 infection of companion animals in Egypt and its risk of spillover

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