Full-Genome Sequences of Alphacoronaviruses and Astroviruses from Myotis and Pipistrelle Bats in Denmark

Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.

Section: Discussionsupporting

confidence: 62%

Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020

Nguyen

Chung

et al. 2021

“…About 1-2 million reads that mapped to the ASFV genome were analyzed here from each of the inoculated pigs at 6 dpi. Another advantage obtained from selecting the poly(A)+ mRNA is that reads derived from residual ASFV DNA should be further diminished beyond that achieved by DNAseI treatment alone, which may not be completely effective [32]. However, some reads may be derived from residual ASFV DNA (there are only short regions of the genome that are not included in any reads), along with other incompletely digested host DNA, e.g., pig mitochondrial DNA.…”

Section: Discussionmentioning

confidence: 99%

Identification of African Swine Fever Virus Transcription within Peripheral Blood Mononuclear Cells of Acutely Infected Pigs

Olesen

Kodama

Lohse

et al. 2021

Self Cite

African swine fever virus (ASFV) has become widespread in Europe, Asia and elsewhere, thereby causing extensive economic losses. The viral genome includes nearly 200 genes, but their expression within infected pigs has not been well characterized previously. In this study, four pigs were infected with a genotype II strain (ASFV POL/2015/Podlaskie); blood samples were collected before inoculation and at both 3 and 6 days later. During this period, a range of clinical signs of infection became apparent in the pigs. From the blood, peripheral blood mononuclear cells (PBMCs) were isolated. The transcription of the ASFV genes was determined using RNAseq on poly(A)+ mRNAs isolated from these cells. Only very low levels of virus transcription were detected in the PBMCs at 3 days post-inoculation (dpi) but, at 6 dpi, extensive transcription was apparent. This was co-incident with a large increase in the level of ASFV DNA within these cells. The pattern of the virus gene expression was very reproducible between the individual pigs. Many highly expressed genes have undefined roles. Surprisingly, some genes with key roles in virus replication were expressed at only low levels. As the functions of individual genes are identified, information about their expression becomes important for understanding their contribution to virus biology.

“…The novel Swedish alpha-CoV sequence formed a cluster, mainly with other alpha-CoVs isolated from M. daubentonii. The sequence was highly similar to full-length viral genome sequences from M. daubentonii from Denmark [12] and Finland [13]. Within the cluster, there were relatively closely related alpha-CoV sequences from other bat species, one from a Danish alpha-CoV detected in Pipstrellus pygmaeus in Denmark, 2014, and another from a Miniopterus shreibersii in China, 2021 [33] (Figure 3).…”

Section: Discussionmentioning

confidence: 89%

“…This was the first report of coronavirus presence in bats in Sweden, while it has previously been found in Denmark, Finland and other European countries [11][12][13]. For detection and sequencing of the coronavirus, we used a method comprising next-generation sequencing with virus-specific targets.…”

Section: Discussionmentioning

confidence: 99%

“…In Fennoscandia (Denmark, Norway, Sweden and Finland), there is limited surveillance on bat CoVs. Nevertheless, in Denmark, alphacoronaviruses (alpha-CoVs) were found in the feces of five bat species ( Myotis (M) daubentonii , M. dasycneme , M. nattereri , Pipistrellus pygmaeus and Eptesicus serotinus ) sampled at the entrances of their hibernacula [ 11 , 12 ]. The CoV sequences found in M. daubentonii resembled those found in conspecifics in Germany and United Kingdom [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

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Alphacoronavirus in a Daubenton’s Myotis Bat (Myotis daubentonii) in Sweden

Lwande

Thalin

Jong

et al. 2022

The ongoing COVID-19 pandemic has stimulated a search for reservoirs and species potentially involved in back and forth transmission. Studies have postulated bats as one of the key reservoirs of coronaviruses (CoVs), and different CoVs have been detected in bats. So far, CoVs have not been found in bats in Sweden and we therefore tested whether they carry CoVs. In summer 2020, we sampled a total of 77 adult bats comprising 74 Myotis daubentonii, 2 Pipistrellus pygmaeus, and 1 M. mystacinus bats in southern Sweden. Blood, saliva and feces were sampled, processed and subjected to a virus next-generation sequencing target enrichment protocol. An Alphacoronavirus was detected and sequenced from feces of a M. daubentonii adult female bat. Phylogenetic analysis of the almost complete virus genome revealed a close relationship with Finnish and Danish strains. This was the first finding of a CoV in bats in Sweden, and bats may play a role in the transmission cycle of CoVs in Sweden. Focused and targeted surveillance of CoVs in bats is warranted, with consideration of potential conflicts between public health and nature conservation required as many bat species in Europe are threatened and protected.