Homology‐based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content

Forni, Diego; Cagliani, Rachele; Molteni, Cristian; Arrigoni, Federica; Mozzi, Alessandra; Clerici, Mario; Gioia, Luca De; Sironi, Manuela

doi:10.1111/mec.16531

Cited by 17 publications

(16 citation statements)

References 117 publications

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“…Conversely, some inter-species genetic distances of Coronaviridae are shorter than the intra-species genetic distances, such as those for OC43 and 229E, which may be the intermediate states of different species or subspecies in the whole evolutionary history of Coronaviridae. It suggested that these probably represent another independent acquisition though either speci c horizontal gene transfer or recombination events [29][30][31]. The relationship between variants and frequency in different geographical regions has been characterized, and the value of using age information in interpreting variants of functional and selective importance, such as using allele age estimates to power a rapid approach for inferring the ancestry shared between individual genomes in order to quantify genealogical relationships, has been demonstrated [3].…”

Section: Resultsmentioning

confidence: 99%

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

Ji¹,

Shao²

2023

Preprint

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The lack of virus fossilization precludes any references or ancestors for inferring evolutionary processes, and viruses have no cell structure, metabolism, or space to reproduce outside host cells. Most mutations yielding high pathogenicity become removed from the population, but adaptive mutations could be epidemically transmitted and fixed in the population. Therefore, determining how viruses originated, how they diverged and how an infectious disease was transmitted are serious challenges. To predict potential epidemic outbreaks, we tested our strategy, Epi-Clock, which applies the ZHU algorithm on different SARS-CoV-2 datasets before outbreaks to search for real significant mutational accumulation patterns correlated with the outbreak events. We imagine that specific amino acid substitutions are triggers for outbreaks. Surprisingly, some inter-species genetic distances of Coronaviridae were shorter than the intra-species distances, which may represent the intermediate states of different species or subspecies in the evolutionary history of Coronaviridae. The insertions and deletions of whole genome sequences between different hosts were separately associated with new functions or turning points, clearly indicating their important roles in the host transmission and shifts of Coronaviridae. Furthermore, we believe that non-nucleosomal DNA may play dominant roles in the divergence of different lineages of SARS-CoV-2 in different regions of the world because of the lack of nucleosome protection. We suggest that strong selective variation among different lineages of SARS-CoV-2 is required to produce strong codon usage bias, significantly appear in B.1.640.2 and B.1.617.2 (Delta). Interestingly, we found that an increasing number of other types of substitutions, such as those resulting from the hitchhiking effect, have accumulated, especially in the pre-breakout phase, even though some previous substitutions were replaced by other dominant genotypes. From most validations, we could accurately predict the potential pre-phase of outbreaks with a median interval of 5 days before. Using our pipeline, users may review updated information on the website https://bioinfo.liferiver.com.cn with easy registration.

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Section: Resultsmentioning

confidence: 99%

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

Ji¹,

Shao²

2023

Preprint

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“…Some variation in the presence of the accessory genes 7b, 9b and 10 was found amongst the isolates studied. These genes are not essential for viral replication, but are modulators of the host's innate immune system response and as such can affect strain pathogenicity [73][74][75]. All three of these genes interfere with MAVS (Mitochondrial Antiviral Signalling Protein) and IFN-β signalling and probably act synergistically in IFN inhibition in human SARS-CoV-2 infection [73,[75][76][77].…”

Section: Discussionmentioning

confidence: 99%

Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology

Apaa

Withers

Staley

et al. 2023

Journal of General Virology

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Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV and SARS-CoV- 2. Despite the devastating impact of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecoviruses in their natural hosts, leaving large gaps in our pandemic preparedness. Here we describe the results of PCR testing for sarbecoviruses in the two horseshoe bat species (Rhinolophus hipposideros and R. ferrumequinum) present in Great Britain, collected in 2021–22 during the peak of COVID-19 pandemic. One hundred and ninety seven R. hipposideros samples from 33 roost sites and 277 R. ferrumequinum samples from 20 roost sites were tested. No coronaviruses were detected in any samples from R. ferrumequinum whereas 44 and 56 % of individual and pooled (respectively) faecal samples from R. hipposideros across multiple roost sites tested positive in a sarbecovirus-specific qPCR. Full genome sequences were generated from three of the positive samples (and partial genomes from two more) using Illumina RNAseq on unenriched samples. Phylogenetic analyses showed that the obtained sequences belong to the same monophyletic clade, with >95 % similarity to previously-reported European isolates from R. hipposideros. The sequences differed in the presence or absence of accessory genes ORF 7b, 9b and 10. All lacked the furin cleavage site of SARS-CoV-2 spike gene and are therefore unlikely to be infective for humans. These results demonstrate a lack, or at least low incidence, of SARS-CoV-2 spill over from humans to susceptible GB bats, and confirm that sarbecovirus infection is widespread in R. hipposideros. Despite frequently sharing roost sites with R. ferrumequinum, no evidence of cross-species transmission was found.

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“…Some variation in the presence of the accessory genes 7b, 9b and 10 was found amongst the isolates studied. These genes are not essential for viral replication, but are modulators of the host’s innate immune system response and as such can affect strain pathogenicity (Fang, Fang et al 2021, Forni, Cagliani et al 2022, McGrath, Xue et al 2022). Plasticity in accessory gene complement has also been evident in different SARs-CoV-2 isolates and appears to be a feature of Sarbecovirus isolate variability (Forni, Cagliani et al 2022, McGrath, Xue et al 2022).…”

Section: Discussionmentioning

confidence: 99%

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology

Apaa

Withers

Staley

et al. 2023

Preprint

View full text Add to dashboard Cite

Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV-1 and 2. Despite the devastating impacts of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecoviruses in their original hosts, leaving large gaps in our pandemic preparedness. Here we describe the results of PCR testing for sarbecoviruses in the two horseshoe bat species (Rhinolophus hipposideros and R. ferrumequinum) present in Great Britain, collected in 2021-22 during the COVID-19 pandemic. One hundred and ninety seven R. hipposideros samples from 33 roost sites and 277 R. ferremequinum samples from 20 roost sites were tested. No coronaviruses were detected in any samples from R. ferrumequinum whereas 44% and 56% of individual and pooled (respectively) faecal samples from R. hipposideros across multiple roost sites tested positive in a sarbecovirus-specific qPCR. Full genome sequences were generated from three of the positive samples (and partial genomes from two more) using Illumina RNAseq on unenriched samples. Phylogenetic analyses showed that the obtained sequences belong to the same monophyletic clade, with >95% similarity, as previously reported European isolates from R. hipposideros. The sequences differed in the presence or absence of accessory genes ORF 7b, 9b and 10. All lacked the furin cleavage site of SARS-CoV-2 spike gene and are therefore unlikely to be infective for humans. These results demonstrate a lack, or at least low incidence, of SARS-CoV-2 spill over from humans to high-risk GB bats, and confirm that sarbecovirus infection is widespread in R. hipposideros. Despite frequently sharing roost sites with R. ferrumequinum, no evidence of cross-species transmission was found.

show abstract

Homology‐based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content

Cited by 17 publications

References 117 publications

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology

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