Detection of Group 1 Coronaviruses in Bats in North America

Bats of 2 species harbor group 1 coronaviruses

VIGOR, an annotation program for small viral genomes

<p>Abstract</p> <p>Background</p> <p>The decrease in cost for sequencing and improvement in technologies has made it easier and more common for the re-sequencing of large genomes as well as parallel sequencing of small genomes. It is possible to completely sequence a small genome within days and this increases the number of publicly available genomes. Among the types of genomes being rapidly sequenced are those of microbial and viral genomes responsible for infectious diseases. However, accurate gene prediction is a challenge that persists for decoding a newly sequenced genome. Therefore, accurate and efficient gene prediction programs are highly desired for rapid and cost effective surveillance of RNA viruses through full genome sequencing.</p> <p>Results</p> <p>We have developed VIGOR (Viral Genome ORF Reader), a web application tool for gene prediction in influenza virus, rotavirus, rhinovirus and coronavirus subtypes. VIGOR detects protein coding regions based on sequence similarity searches and can accurately detect genome specific features such as frame shifts, overlapping genes, embedded genes, and can predict mature peptides within the context of a single polypeptide open reading frame. Genotyping capability for influenza and rotavirus is built into the program. We compared VIGOR to previously described gene prediction programs, ZCURVE_V, GeneMarkS and FLAN. The specificity and sensitivity of VIGOR are greater than 99% for the RNA viral genomes tested.</p> <p>Conclusions</p> <p>VIGOR is a user friendly web-based genome annotation program for five different viral agents, influenza, rotavirus, rhinovirus, coronavirus and SARS coronavirus. This is the first gene prediction program for rotavirus and rhinovirus for public access. VIGOR is able to accurately predict protein coding genes for the above five viral types and has the capability to assign function to the predicted open reading frames and genotype influenza virus. The prediction software was designed for performing high throughput annotation and closure validation in a post-sequencing production pipeline.</p

Phylogenetic investigation of enteric bovine coronavirus in Ireland reveals partitioning between European and global strains

Background: Bovine coronavirus is a primary cause of neonatal calf diarrhea worldwide, and is also associated with acute diarrhea in adult cattle during the winter season. There are no reports on molecular characterization of bovine coronavirus in Ireland, and little data exists apart from serological studies. Findings: In this study, 11 neonatal (mean age 9 days) calf BCoV strains from the south of Ireland were collected over a one year period and characterized using molecular methods. The spike gene which encodes a protein involved in viral entry, infectivity and immune response shows the most variability amongst the isolates and was subsequently selected for in depth analysis. Phylogenetic analysis of the spike gene revealed that the Irish strains clustered with novel BCoV strains from Europe in a unique clade, possibly indicating lineage partitioning. Direct analysis of alignments identified amino acid changes in the spike protein unique to the Irish clade. Conclusion: Thus, monitoring of bovine coronavirus in Ireland is important as the current isolates in circulation in the south of Ireland may be diverging from the available vaccine strain, which may have implications regarding future BCoV vaccine efficacy

Phylogenetic analysis of peste des petits ruminants virus from outbreaks in Turkey during 2008–2012

Peste des petits ruminants (PPR) is an important viral disease of sheep and goats and is endemic in all regions of Turkey. In this study, PPR virus infection was investigated by RT-PCR assay based on the fusion (F) gene in PPR-suspected sheep and goat samples. PPR virus RNA was detected in 65 small ruminants (51 sheep, 14 goats) from independent outbreaks during 2008-2012 in provinces in the central and Mediterranean regions and the central-west part of the Aegean region in Turkey. The virus was detected in an aborted sheep fetus sample by RT-PCR, and diagnosis was also confirmed by virus isolation. Vaccine strain Nigeria 75/1 was differentiated from field isolates by restriction fragment length polymorphism analysis of RT-PCR products using EcoRI. Phylogenetic analysis of 16 viruses indicated that all viruses, including the one from the aborted sheep fetus, belonged to lineage IV, as had the PPR viruses previously isolated in Turkey. Nucleotide sequence identity among 16 viruses was 99.1%-100%. Results showed that PPR virus lineage IV has been in circulation in Turkey since the first detection of the disease

Phylogenetic analysis of peste des petits ruminants virus from outbreaks in Turkey during 2008-2012

Peste des petits ruminants (PPR) is an important viral disease of sheep and goats and is endemic in all regions of Turkey. In this study, PPR virus infection was investigated by RT-PCR assay based on the fusion (F) gene in PPR-suspected sheep and goat samples. PPR virus RNA was detected in 65 small ruminants (51 sheep, 14 goats) from independent outbreaks during 2008-2012 in provinces in the central and Mediterranean regions and the central-west part of the Aegean region in Turkey. The virus was detected in an aborted sheep fetus sample by RT-PCR, and diagnosis was also confirmed by virus isolation. Vaccine strain Nigeria 75/1 was differentiated from field isolates by restriction fragment length polymorphism analysis of RT-PCR products using EcoRI. Phylogenetic analysis of 16 viruses indicated that all viruses, including the one from the aborted sheep fetus, belonged to lineage IV, as had the PPR viruses previously isolated in Turkey. Nucleotide sequence identity among 16 viruses was 99.1%-100%. Results showed that PPR virus lineage IV has been in circulation in Turkey since the first detection of the disease

Detection of respiratory and enteric shedding of bovine coronaviruses in cattle in northwestern Turkey

Bovine coronavirus (BCoV) is an important cause of diarrhoea in calves, winter dysentery in adult cattle and respiratory tract disease in feedlot cattle. Serum, faecal and nasal swab samples were collected from a total of 96 cattle with clinical signs in 29 barns of 23 villages in Northwestern Turkey. The cattle were subdivided into 3 distinct age groups (0-30 days old, 4-12 months old and 2-7 years old). An indirect antigen-capture ELISA and an antibody-detection ELISA as well as geometric mean BCoV antibody titres were used to detect BoCV shed in the faeces and in the nasal secretions, respectively. Relationships between BCoV shedding and age group, seroconversion and clinical signs in cattle were also analysed. The rate of faecal shedding of BoCV was 37.1% (13/35) in 0-30 days old calves, 25.6% (10/39) in 4-12 months old feedlot cattle and 18.2% (4/22) in 2-7 years old cows. The overall rate of BCoV faecal shedding was 28.1% (27/96) in the cattle examined. Only one animal in the 4-12 months old age group was found to shed BoCV nasally. The analysis showed that there was a significant difference (P < 0.0001) with respect to faecal shedding between the clinical signs and the age groups. BCoV antibody titre in 50% of all cattle was <= 100 as detected by ELISA while 27.1% of the cattle had high titres ranging between 1,600 and 25,600. The seroconversion rate was 7.3% (7/96) in animals shedding BoCV in the faeces and 42.7% (41/96) in cattle negative for faecal shedding as detected by ELISA, and 20.8% of cattle with no seroconversion shed BCoV in the faeces. There was no statistically significant association between seroconversion and nasal or faecal BCoV shedding. These findings confirm the presence of BCoV infections in Turkey. Further studies are needed to isolate BCoV strains in Turkey and to investigate their antigenic and genetic properties

Antigenic and genomic relatedness of turkey-origin coronaviruses, bovine coronaviruses, and infectious bronchitis virus of chickens

In earlier studies in our laboratory, we found that bovine coronavirus (BCV) was pathogenic for 1-day-old turkey poults. This finding prompted us to study the antigenic and genomic relatedness of turkey, origin coronaviruses (TOCVs) to BCV A one-step reverse transcription (RT -polymerase chain reaction (PCR) targeting a 730-base pair fragment of the nucleocapsid (N) gene of BCV and a nested PCR targeting a 407-base pair fragment of the N gene were used in an attempt to detect TOCV from North Carolina, Indiana, and a prototype turkey coronavirus (TCV) obtained from the American Type Culture Collection, Both the one-step RT-PCR and the nested PCR amplified cell culture-passaged isolates of calf diarrhea strains of BCV but none of the 15 tested TOCVs or transmissible gastroenteritis coronavirus of swine. TOCVs also did not cross-react in a BCV antigen-capture (AC) enzyme-linked immunosorbent assay (ELISA) system with monoclonal antibodies (MAbs) against N, spike glycoprotein, and hemagglutinin esterase glycoprotein proteins of BCV as coating antibodies. The same TOCVs could be detected with primers designed from the genome of infectious bronchitis virus (IBV of chickens. These primers amplified it 1082-base pair region spanning portions of thc membrane glycoprotein (M) and N protein genes of IBV and TCV. The TOCVs also cross-reacted in an AC-ELISA with MAbs against the M and subunit 2 of spike glycoprotein of IBV