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Petrini S, Curini V, Righi C, Cammà C, Di Lollo V, Tinelli E, Mincarelli LF, Rossi E, Costantino G, Secondini B, Pirani S, Giammarioli M, Feliziani F. Genomic Characterization of a Wild-Type Bovine alphaherpesvirus 1 (BoAHV-1) Strain Isolated in an Outbreak in Central Italy. Viruses 2024; 16:150. [PMID: 38275960 PMCID: PMC10818397 DOI: 10.3390/v16010150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Bovine alphaherpesvirus-1 (BoAHV-1) infection is common in cattle worldwide. However, information on the spread of BoAHV-1-circulating strains in Italy remains limited. In this study, we investigated an outbreak characterized by severe respiratory symptoms in a cattle herd (n = 30) located in Central Italy. BoAHV-1 was isolated from three cattle in a cell culture, which confirmed viral infection. Next, we characterized one (16453/07 TN) of the three isolates of BoAHV-1 using whole-genome sequencing. BLASTn and phylogenetic analysis revealed a nucleotide identity >99% with all BoAHV-1 strains belonging to subtype 1.1, highlighting the genetic stability of the virus. This study reports the first full genomic characterization of a BoAHV-1 isolate in Italy, enriching our understanding of the genetic characteristics of the circulating BoAHV-1 strain in Italy.
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Affiliation(s)
- Stefano Petrini
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
| | - Valentina Curini
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Istituto Zooprofilattico Sperimentale Abruzzo-Molise “G. Caporale”, 64100 Teramo, Italy; (V.C.); (C.C.); (V.D.L.); (L.F.M.); (B.S.)
| | - Cecilia Righi
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Istituto Zooprofilattico Sperimentale Abruzzo-Molise “G. Caporale”, 64100 Teramo, Italy; (V.C.); (C.C.); (V.D.L.); (L.F.M.); (B.S.)
| | - Valeria Di Lollo
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Istituto Zooprofilattico Sperimentale Abruzzo-Molise “G. Caporale”, 64100 Teramo, Italy; (V.C.); (C.C.); (V.D.L.); (L.F.M.); (B.S.)
| | - Elena Tinelli
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
| | - Luana Fiorella Mincarelli
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Istituto Zooprofilattico Sperimentale Abruzzo-Molise “G. Caporale”, 64100 Teramo, Italy; (V.C.); (C.C.); (V.D.L.); (L.F.M.); (B.S.)
| | - Elisabetta Rossi
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
| | - Giulia Costantino
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
| | - Barbara Secondini
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Istituto Zooprofilattico Sperimentale Abruzzo-Molise “G. Caporale”, 64100 Teramo, Italy; (V.C.); (C.C.); (V.D.L.); (L.F.M.); (B.S.)
| | - Silvia Pirani
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
| | - Monica Giammarioli
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
| | - Francesco Feliziani
- National Reference Centre for Infectious Bovine Rhinotracheitis (IBR), Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, 06126 Perugia, Italy; (S.P.); (E.T.); (E.R.); (G.C.); (S.P.); (M.G.); (F.F.)
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Ortiz-González AD, Buitrago HAL, Bulla-Castañeda DM, Lancheros-Buitrago DJ, Garcia-Corredor DJ, Díaz-Anaya AM, Tobón-Torreglosa JC, Ortiz-Ortega D, Pulido-Medellín MO. Seroprevalence and risk factors associated with bovine herpesvirus 1 in dairy herds of Colombia. Vet World 2022; 15:1550-1556. [PMID: 35993084 PMCID: PMC9375214 DOI: 10.14202/vetworld.2022.1550-1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Infectious bovine rhinotracheitis (IBR) is an infectious disease widely distributed globally and is considered the main cause of various reproductive and respiratory tract diseases in cattle and buffaloes. This study aimed to estimate seroprevalence and determine risk factors associated with the presentation of IBR in the municipality of Sotaquirá, Boyacá (Colombia).
Materials and Methods: A descriptive cross-sectional study with simple random sampling was performed, and the sample size was 1,000 cattle. Blood samples were obtained by coccygeal venipuncture and processed through indirect enzyme-linked immunosorbent assay using the Synbiotics® kit (Zoetis, New Jersey, USA) with a sensitivity and specificity of 96% and 98%, respectively. Data were processed using the statistical program EpiInfo® (Centers for Disease Control and Prevention; Atlanta, Georgia).
Results: A high seroprevalence of 57.5% was established. Seroprevalence was the highest in cattle >4 years of age (65.0% apparent seroprevalence [AS]; 67% true seroprevalence [TS]) and in the Holstein breed (65.5% AS; 67.8% TS). The breed and age of the animals were significantly associated with each other. The Holstein breed, age group >4 years, uncertified semen, and fetal death were established as risk factors for IBR. In comparison, the age groups of <1 and 1–2 years and the Normande breed were established as protective factors against the bovine herpesvirus-1 virus.
Conclusion: Management factors, such as livestock from other owners and animal purchases, which affect disease presentation, are evident. The implementation and development of novel prevention and control measures for IBR at the national level are necessary.
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Affiliation(s)
- Aura Daniela Ortiz-González
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - H. Alexander Lopez Buitrago
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Diana María Bulla-Castañeda
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - D. Johana Lancheros-Buitrago
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Diego Jose Garcia-Corredor
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Adriana Maria Díaz-Anaya
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia; Doctoral Program in Biomedical and Pharmaceutical Sciences, University of Namur, Namur, Belgium
| | | | - Diego Ortiz-Ortega
- Corporación Colombiana de Investigación Agropecuaria, Mosquera, Colombia
| | - Martín Orlando Pulido-Medellín
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
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Saha I, Ghosh N, Pradhan A, Sharma N, Maity D, Mitra K. Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. Brief Bioinform 2021; 22:1106-1121. [PMID: 33725111 PMCID: PMC7989641 DOI: 10.1093/bib/bbab025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/24/2020] [Accepted: 01/19/2021] [Indexed: 01/21/2023] Open
Abstract
Whole genome analysis of SARS-CoV-2 is important to identify its genetic diversity. Moreover, accurate detection of SARS-CoV-2 is required for its correct diagnosis. To address these, first we have analysed publicly available 10 664 complete or near-complete SARS-CoV-2 genomes of 73 countries globally to find mutation points in the coding regions as substitution, deletion, insertion and single nucleotide polymorphism (SNP) globally and country wise. In this regard, multiple sequence alignment is performed in the presence of reference sequence from NCBI. Once the alignment is done, a consensus sequence is build to analyse each genomic sequence to identify the unique mutation points as substitutions, deletions, insertions and SNPs globally, thereby resulting in 7209, 11700, 119 and 53 such mutation points respectively. Second, in such categories, unique mutations for individual countries are determined with respect to other 72 countries. In case of India, unique 385, 867, 1 and 11 substitutions, deletions, insertions and SNPs are present in 566 SARS-CoV-2 genomes while 458, 1343, 8 and 52 mutation points in such categories are common with other countries. In majority (above 10%) of virus population, the most frequent and common mutation points between global excluding India and India are L37F, P323L, F506L, S507G, D614G and Q57H in NSP6, RdRp, Exon, Spike and ORF3a respectively. While for India, the other most frequent mutation points are T1198K, A97V, T315N and P13L in NSP3, RdRp, Spike and ORF8 respectively. These mutations are further visualised in protein structures and phylogenetic analysis has been done to show the diversity in virus genomes. Third, a web application is provided for searching mutation points globally and country wise. Finally, we have identified the potential conserved region as target that belongs to the coding region of ORF1ab, specifically to the NSP6 gene. Subsequently, we have provided the primers and probes using that conserved region so that it can be used for detecting SARS-CoV-2. Contact: indrajit@nitttrkol.ac.in Supplementary information: Supplementary data are available at http://www.nitttrkol.ac.in/indrajit/projects/COVID-Mutation-10K
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Affiliation(s)
- Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India
| | - Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Ayan Pradhan
- Department of Computer Science and Engineering, Techno India University, West Bengal, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Debasree Maity
- Department of Electronics and Communication Engineering, MCKV Institute of Engineering, Howrah, West Bengal, India
| | - Kaushik Mitra
- Department of Community Medicine, Burdwan Medical College, Barddhaman, West Bengal, India
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Saha I, Ghosh N, Maity D, Sharma N, Sarkar JP, Mitra K. Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104457. [PMID: 32659347 PMCID: PMC7351671 DOI: 10.1016/j.meegid.2020.104457] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 01/15/2023]
Abstract
The wave of COVID-19 is a big threat to the human population. Presently, the world is going through different phases of lock down in order to stop this wave of pandemic; India being no exception. We have also started the lock down on 23rd March 2020. In this current situation, apart from social distancing only a vaccine can be the proper solution to serve the population of human being. Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. This fast motivated us to analyze publicly available 566 Indian complete or near complete SARS-CoV-2 genomes to find the mutation points as substitution, deletion and insertion. In this regard, we have performed the multiple sequence alignment in presence of reference sequence from NCBI. After the alignment, a consensus sequence is built to analyze each genome in order to identify the mutation points. As a consequence, we have found 933 substitutions, 2449 deletions and 2 insertions, in total 3384 unique mutation points, in 566 genomes across 29.9 K bp. Further, it has been classified into three groups as 100 clusters of mutations (mostly deletions), 1609 point mutations as substitution, deletion and insertion and 64 SNPs. These outcomes are visualized using BioCircos and bar plots as well as plotting entropy value of each genomic location. Moreover, phylogenetic analysis has also been performed to see the evolution of SARS-CoV-2 virus in India. It also shows the wide variation in tree which indeed vivid in genomic analysis. Finally, these SNPs can be the useful target for virus classification, designing and defining the effective dose of vaccine for the heterogeneous population.
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Affiliation(s)
- Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
| | - Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Orissa, India
| | - Debasree Maity
- Department of Electronics and Communication Engineering, MCKV Institute of Engineering, Howrah, West Bengal, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Jnanendra Prasad Sarkar
- Larsen & Toubro Infotech, Pune, India,Department of Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Kaushik Mitra
- Department of Community Medicine, Burdwan Medical College, Barddhaman, West Bengal, India
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Ackermann M, Hatt J. To treat or not to treat? VETERINARY RECORD CASE REPORTS 2019. [DOI: 10.1136/vetreccr-2019-000847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Mathias Ackermann
- Institute of Veterinary VirologyVetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Jean‐Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and WildlifeUniversity of ZurichZurichSwitzerland
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Kanokudom S, Mahony TJ, Smith DR, Assavalapsakul W. Modulation of bovine herpesvirus 1 infection by virally encoded microRNAs. Virus Res 2018; 257:1-6. [PMID: 30193942 DOI: 10.1016/j.virusres.2018.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 12/27/2022]
Abstract
Bovine herpesvirus 1 (BoHV-1), is a member of the subfamily Alphaherpesvirinae in the order Herpesviridae and is a ubiquitous pathogen of cattle responsible for significant economic loss worldwide. The BoHV-1 genome encodes at least 10 BoHV-1 microRNA (miRNA) genes, whose functions remain poorly understood. This study sought to understand the role of three BoHV-1 miRNA genes, Bhv1-miR-B6, Bhv1-miR-B8 and Bhv1-miR-B9, which are located proximal to the BoHV-1 origins of replication (OriS). Therefore, plasmids expressing the precursor miRNA hairpins for the Bhv1-miR-B6, Bhv1-miR-B8, and Bhv1-miR-B9 genes were constructed and transfected into Madin-Darby bovine kidney cells prior to BoHV-1 infection. Interestingly, transient expression of either Bhv1-miR-B8 or Bhv1-miR-B9 in Madin-Darby bovine kidney cells prior to infection resulted in partial suppression of BoHV-1 replication, quantified through estimating levels of glycoprotein C mRNA and protein levels. Putative interactions between the mature miRNA bhv1-miR-B8-3p and bhv1-miR-B9 and BoHV-1 transcripts were identified providing plausible pathways for these molecules to affect virus replication. Therefore, these two miRNAs are implicated in the post-transcriptional regulation of BoHV-1 transcripts important for virus replication and could be used to limit BoHV-1 replication.
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Affiliation(s)
- Sitthichai Kanokudom
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Timothy J Mahony
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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