Diversity of Dromedary Camel Coronavirus HKU23 in African Camels Revealed Multiple Recombination Events among Closely Related Betacoronaviruses of the Subgenus Embecovirus

So, R. T. Y.; Chu, Daniel K.W.; Miguel, Eve; Perera, Ranawaka A.P.M.; Oladipo, Jamiu O; Fassi-Fihri, Ouafaa; Aylet, Gelagay; Ko, Ronald C.; Zhou, Ziqi; Cheng, Mo-Sheung; Kuranga, S A; Roger, François; Chevalier, Véronique; Webby, Richard J.; Woo, Patrick C. Y.; Poon, Leo L M; Peiris, Malik

doi:10.1128/jvi.01236-19

Cited by 33 publications

(35 citation statements)

References 49 publications

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“…An ancestral BCoV is believed to be the progenitor of the other currently recognized BetaCoV1 viruses with divergence dates estimated at 100-150 years ago for OC43/PHEV [48] and 50 years ago for HKU23 [49]. Recombination with other betacoronaviruses has been previously described for HKU23, so we excluded it from our analysis [50]. The closest outgroup to BetaCoV1 , rabbit coronavirus HKU14 (RbCoV/HKU14) was reported to group closely with ECoV in some regions [51], but no detailed recombination analysis of the relationship between these viruses has been previously described.…”

Section: Resultsmentioning

confidence: 99%

Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

Brown

et al. 2021

Preprint

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The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Previously, four other known coronaviruses moved from animal reservoirs into humans and now cause primarily mild-to-moderate respiratory disease. The emergence of these viruses likely involved a period of intense transmission before becoming endemic, highlighting the recurrent threat to human health posed by animal coronaviruses. Enzootic and epizootic coronaviruses of diverse lineages pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with impacts on livestock or human health: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses, disrupting phylogenetic relationships and revealing contributions of unknown coronavirus lineages to the genetic diversity of established groups. Dynamic patterns of recombination impact inferences of relatedness between diverse coronaviruses and expand the genetic pool that may contribute to future zoonotic events. These results illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.

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Section: Resultsmentioning

confidence: 99%

Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

Brown

et al. 2021

Preprint

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“…In 2014, Woo et al reported on the identification of a new CoV from the genus Betacoronavirus, DcCoV UAE-HKU23, in dromedaries of Central Asia; in 2016, antibodies against this CoV were found in 98.3-100% of dromedaries in this region (Woo et al, 2014(Woo et al, , 2016). An article published in 2019 was devoted to the genetic diversity of various UAE-HKU23 strains, and its authors supposed that the evolutionary development of this CoV, which is based on acquisition of new genetic properties during replication, proceeds by the pathway of MERS-CoV, being evidence of its increasing emergence potential (So et al, 2019).…”

Section: Resultsmentioning

confidence: 99%

Coronavirus Infections of Animals: Future Risks to Humans

Донник

Popov

Середа

et al. 2021

Biol Bull Russ Acad Sci

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— Coronaviruses have tremendous evolutionary potential, and three major outbreaks of new human coronavirus infections have occurred in the recent history of humankind. In this paper, the patterns of occurrence of new zoonotic coronavirus infections and the role of bioveterinary control in preventing their potential outbreaks in the future are determined. The possibility of SARS-CoV-2 infection in companion animals is considered. Diverse human activities may trigger various interactions between animal species and their viruses, sometimes causing the emergence of new viral pathogens. In addition, the possibility of using probiotics for the control of viral infections in animals is discussed.

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“…Much needed information can be gained from sequencing of viral genomes in terms of viral adaptation [ 9 ], thus informing molecular epidemiological studies during outbreaks [ 18 ]. Current diagnostics may not remain fit for purpose due to recombination in coronaviruses (e.g., [ 5 , 19 ]). Interestingly, analysis of deletions that occurred in the SARS-CoV-2 genome in infected patients from this study identified several that mapped to genes encoding proteins involved in interferon and host antagonism.…”

Section: Discussionmentioning

confidence: 99%

Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism

Moore

Penrice-Randal

Alruwaili

et al. 2020

Viruses

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, particularly in the identification of emerging isolates with different pathogenic potential and to identify whether nucleotide changes in the genome will impair clinical diagnostic tools such as real-time PCR assays. Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. This can manifest itself in insertions and/or deletions in the viral genome. Therefore, sequencing strategies that underpin molecular epidemiology and inform virus biology in patients should take these factors into account. A long amplicon/read length-based RT-PCR sequencing approach focused on the Oxford Nanopore MinION/GridION platforms was developed to identify and sequence the SARS-CoV-2 genome in samples from patients with or suspected of COVID-19. The protocol, termed Rapid Sequencing Long Amplicons (RSLAs) used random primers to generate cDNA from RNA purified from a sample from a patient, followed by single or multiplex PCRs to generate longer amplicons of the viral genome. The base protocol was used to identify SARS-CoV-2 in a variety of clinical samples and proved sensitive in identifying viral RNA in samples from patients that had been declared negative using other nucleic acid-based assays (false negative). Sequencing the amplicons revealed that a number of patients had a proportion of viral genomes with deletions.

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Diversity of Dromedary Camel Coronavirus HKU23 in African Camels Revealed Multiple Recombination Events among Closely Related Betacoronaviruses of the Subgenus Embecovirus

Cited by 33 publications

References 49 publications

Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

Coronavirus Infections of Animals: Future Risks to Humans

Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism

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