Genetic Characterisation and Comparison of Three Human Coronaviruses (HKU1, OC43, 229E) from Patients and Bovine Coronavirus (BCoV) from Cattle with Respiratory Disease in Slovenia

Coronaviruses (CoV) are widely distributed pathogens of human and animals and can cause mild or severe respiratory and gastrointestinal disease. Antigenic and genetic similarity of some CoVs within the Betacoronavirus genus is evident. Therefore, for the first time in Slovenia, we investigated the genetic diversity of partial 390-nucleotides of RNA-dependent-RNA polymerase gene (RdRp) for 66 human (HCoV) and 24 bovine CoV (BCoV) positive samples, collected between 2010 and 2016 from human patients and cattle with respiratory disease. The characterized CoV strains belong to four different clusters, in three separate human clusters HCoV-HKU1 (n = 34), HCoV-OC43 (n = 31) and HCoV 229E (n = 1) and bovine grouping only as BCoVs (n = 24). BCoVs from cattle and HCoV-OC43 were genetically the most closely related and share 96.4–97.1% nucleotide and 96.9–98.5% amino acid identity.

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Detection and molecular epidemiology of ferlaviruses in farmed snakes with respiratory disease in Guangxi Province, China

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638720911023 ◽

2020 ◽

Vol 32 (3) ◽

pp. 429-434

Author(s):

Jie-Yu Su ◽

Jun Li ◽

Teng-Cheng Que ◽

Hai-Lan Chen ◽

Yun Zeng

Keyword(s):

Molecular Epidemiology ◽

Respiratory Disease ◽

Genetic Relationships ◽

Bacterial Isolates ◽

Polymerase Gene ◽

Guangxi Province ◽

Rna Dependent Rna Polymerase ◽

Reverse Transcription Pcr ◽

Rna Polymerase Gene ◽

Isolated Species

We screened 104 snakes with respiratory disease, collected from 52 snake farms in Guangxi Province, China, for pathogens. Ferlaviruses were detected in 70 of 104 lung samples by reverse-transcription PCR; 34 of 52 of the snake farms were positive for ferlaviruses. No reovirus, adenovirus, sunshine virus, or nidovirus was detected in any of the snakes. We obtained 96 bacterial isolates from snake organs, of which the most commonly isolated species were Salmonella (18) and Proteus (16). Sequence analysis, based on 27 partial RNA-dependent RNA polymerase gene ( L) sequences, revealed that ferlaviruses from Guangxi and the known GenBank strains clustered together and formed 3 genogroups. The nucleotide and deduced amino acid homologies of ferlaviruses were 84.3–100% and 95.0–100% within groups, respectively, and 77.0–81.6% and 90.4–95.2% between groups, respectively. Ferlaviruses from Guangxi had close genetic relationships with the known GenBank strains. Our results indicate that ferlaviruses are common in snakes with respiratory disease on the farms of Guangxi that we sampled, and that ferlavirus molecular epidemiology is both diverse and complex.

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Extensive genetic diversity and host range of rodent-borne coronaviruses

Virus Evolution ◽

10.1093/ve/veaa078 ◽

2020 ◽

Vol 6 (2) ◽

Author(s):

Wen Wang ◽

Xian-Dan Lin ◽

Hai-Lin Zhang ◽

Miao-Ruo Wang ◽

Xiao-Qing Guan ◽

...

Keyword(s):

Genetic Diversity ◽

Rodent Species ◽

Polymerase Gene ◽

Rna Dependent Rna Polymerase ◽

Reading Frame ◽

Genome Recombination ◽

Genomic Complexity ◽

Viral Subtype ◽

Rna Polymerase Gene ◽

Eothenomys Miletus

Abstract To better understand the genetic diversity, host associations and evolution of coronaviruses (CoVs) in China we analyzed a total of 696 rodents encompassing 16 different species sampled from Zhejiang and Yunnan provinces. Based on reverse transcriptase PCR-based CoV screening of fecal samples and subsequent sequence analysis of the RNA-dependent RNA polymerase gene, we identified CoVs in diverse rodent species, comprising Apodemus agrarius, Apodemus chevrieri, Apodemus latronum, Bandicota indica, Eothenomys cachinus, Eothenomys miletus, Rattus andamanensis, Rattus norvegicus, and Rattus tanezumi. CoVs were particularly commonplace in A. chevrieri, with a detection rate of 12.44 per cent (24/193). Genetic and phylogenetic analysis revealed the presence of three groups of CoVs carried by a range of rodents that were closely related to the Lucheng Rn rat CoV (LRNV), China Rattus CoV HKU24 (ChRCoV_HKU24), and Longquan Rl rat CoV (LRLV) identified previously. One newly identified A. chevrieri-associated virus closely related to LRNV lacked an NS2 gene. This virus had a similar genetic organization to AcCoV-JC34, recently discovered in the same rodent species in Yunnan, suggesting that it represents a new viral subtype. Notably, additional variants of LRNV were identified that contained putative non-structural (NS)2b genes located downstream of the NS2 gene that were likely derived from the host genome. Recombination events were also identified in the open reading frame (ORF) 1a gene of Lijiang-71. In sum, these data reveal the substantial genetic diversity and genomic complexity of rodent-borne CoVs, and extend our knowledge of these major wildlife virus reservoirs.

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Extreme Reduction of Disease in Oats Transformed with the 5′ Half of the Barley Yellow Dwarf Virus-PAV Genome

Phytopathology ◽

10.1094/phyto.1998.88.10.1013 ◽

1998 ◽

Vol 88 (10) ◽

pp. 1013-1019 ◽

Cited By ~ 27

Author(s):

Gennadiy Koev ◽

B. R. Mohan ◽

S. P. Dinesh-Kumar ◽

Kimberly A. Torbert ◽

David A. Somers ◽

...

Keyword(s):

Barley Yellow Dwarf Virus ◽

Yellow Dwarf ◽

Natural Resistance ◽

Polymerase Gene ◽

Transgenic Resistance ◽

Rna Dependent Rna Polymerase ◽

Disease Symptoms ◽

Barley Yellow Dwarf ◽

Yellow Dwarf Virus ◽

Rna Polymerase Gene

Barley yellow dwarf viruses (BYDVs) are the most serious and widespread viruses of oats, barley, and wheat worldwide. Natural resistance is inadequate. Toward overcoming this limitation, we engineered virus-derived transgenic resistance in oat. Oat plants were transformed with the 5′ half of the BYDV strain PAV genome, which includes the RNA-dependent RNA polymerase gene. In experiments on T2- and T3-generation plants descended from the same transformation event, all BYDV-inoculated plants containing the transgene showed disease symptoms initially, but recovered, flowered, and produced seed. In contrast, all but one of the BYDV-PAV-inoculated nontransgenic segregants died before reaching 25 cm in height. Although all of the recovered transgenic plants looked similar, the amount of virus and viral RNA ranged from substantial to undetectable levels. Thus, the transgene may act either by restricting virus accumulation or by a novel transgenic tolerance phenomenon. This work demonstrates a strategy for genetically stable transgenic resistance to BYDVs that should apply to all hosts of the virus.

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