Numerical taxonomy of the genus Pestivirus: New software for genotyping based on the palindromic nucleotide substitutions method

Giangaspero, Massimo; Apicella, Claudio; Harasawa, Ryô

doi:10.1016/j.jviromet.2013.04.023

Cited by 11 publications

(10 citation statements)

References 13 publications

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“…All 24 isolates from the BVDV-positive samples were classified as Pestivirus A, and on the basis of phylogenetic analysis of 5 ′ -UTR and Npro genes (Figure 2) further classified into five genotypes: Pestivirus A 1b (six isolates), Pestivirus A 1m (six isolates), Pestivirus A 1q (two isolates), Pestivirus A 1u (one isolate), and the other nine Pestivirus A isolates cluster in the same genotype with Chinese strain XH-2 which was assigned as Pestivirus A 1o, but phylogenetic analysis showed this cluster of isolates were under different cluster from other Pestivirus A 1o strains, further analyzed by the PNS software which available at www.pns-software.com (45), these cluster should be members of a new sub-genotype (1.7.2) within the genotype 1o (1.7). In addition, five isolates from Pestivirus H-positive samples were classified as Pestivirus H, and all further were classified into genotype "Pestivirus H a" based on the results of phylogenetic analysis of the 5 ′ -UTR and Npro genes (46) (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Genetic Diversity of Bovine Pestiviruses Detected in Backyard Cattle Farms Between 2014 and 2019 in Henan Province, China

Shi

Zhang

et al. 2020

Front. Vet. Sci.

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Bovine pestiviruses include Pestivirus A (BVDV-1), Pestivirus B (BVDV-2), and Pestivirus H, which was originally called HoBi-like pestivirus. We conducted an epidemiological investigation for pestiviruses circulating in backyard cattle farms in central China. RT-PCR assays and sequences analysis were conducted on 54 nasal swabs, 26 serum samples, and three lung samples from cattle with respiratory infections and identified 29 pestivirus strains, including 24 Pestivirus A and five Pestivirus H strains. Phylogenetic analysis based on partial 5 ′-UTR and Npro sequences showed that the genotypes of 24 Pestivirus A strains included Pestivirus A 1b (six isolates), Pestivirus A 1m (six isolates), Pestivirus A 1q (two isolates), Pestivirus A 1u (one isolates), and Pestivirus A 1o (nine isolates, a putative new sub-genotype). In addition, a single Pestivirus H agenotype included all five Pestivirus H strains. This study revealed extensive genetic variations within bovine pestivirus isolates derived from cattle in backyard farms in Central China, and this epidemiological information improves our understanding of the epidemics of bovine Pestiviruses, as well as will be useful in designing and evaluating diagnostic methods and developing more effective vaccines.

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Section: Resultsmentioning

confidence: 99%

Genetic Diversity of Bovine Pestiviruses Detected in Backyard Cattle Farms Between 2014 and 2019 in Henan Province, China

Shi

Zhang

et al. 2020

Front. Vet. Sci.

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“…BVDV can be divided into two types (BVDV1 and BVDV2) based on sequence similarity of the 5' untranslated region (UTR) in the viral genome. In addition to these two types, BVDV3 was recently proposed as tentative species together with other Pestivirus species (e.g., border disease virus type 2, Pronghorn, and Bungowannah) [46]. Each type can be further divided into two biotypes (cytopathic and noncytopathic) based on their ability to cause lytic cytopathic effects in cell culture.…”

Section: Virusesmentioning

confidence: 99%

An overview of calf diarrhea - infectious etiology, diagnosis, and intervention

2014

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Calf diarrhea is a commonly reported disease in young animals, and still a major cause of productivity and economic loss to cattle producers worldwide. In the report of the 2007 National Animal Health Monitoring System for U.S. dairy, half of the deaths among unweaned calves was attributed to diarrhea. Multiple pathogens are known or postulated to cause or contribute to calf diarrhea development. Other factors including both the environment and management practices influence disease severity or outcomes. The multifactorial nature of calf diarrhea makes this disease hard to control effectively in modern cow-calf operations. The purpose of this review is to provide a better understanding of a) the ecology and pathogenesis of well-known and potential bovine enteric pathogens implicated in calf diarrhea, b) describe diagnostic tests used to detect various enteric pathogens along with their pros and cons, and c) propose improved intervention strategies for treating calf diarrhea.

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“…BVDV-2 in cattle was found in the USA [15], Canada [16], Brazil [17], Argentina [18], Uruguay [19], Germany [20], Slovakia [21], Italy [22], South Korea [23], Japan [24] and Mongolia [25]. This type, which is considered more virulent, is divided into six subtypes (2a-2f) [26] and prevails in the USA and Canada (up to 50 % of all isolated strains) [1]. For virus species differentiation, the nucleotide sequencing of genomic RNA is used with the study of a 5´-nontranslated region (5´-UTR) suitable for amplification [28,29].…”

Section: Introductionmentioning

confidence: 99%

Genetic Polymorphism of the Bovine Viral Diarrhea Viruses in Big Dairy Farms in Siberia

Koteneva¹,

Nefedchenko²,

Glotova³

et al. 2018

s-h. biol.

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A b s t r a c tBovine viral diarrhea is a widespread disease in the Russian Federation and causes significant economic damage to dairy cattle, especially under intensive commercial farming. The seropositivity of livestock in various Russian regions reaches 65-100 %. The disease is caused by two different virus species, BVDV-1 and BVDV-2, of which the latter is considered more virulent. The persistently infected (PI) animals which are a constant endogenous source of the virus in the herd play a major role in maintaining the stationary trouble of the farms. Short-term sources of the pathogen are transitively infected (TI) animals in which disease proceeds in acute form. Genetic structure of viruses circulating in local livestock populations gives necessary information about the evolution, geography and pathways of the pathogen. However, studies on the genetic polymorphism of viruses in Russia are not enough. This paper is the first to report on a phylogenetic analysis of two types of viral diarrhea virus, isolated from animals of foreign and domestic origin with different clinical manifestations of the disease. These data show the prevalence of BVDV-1b in PI and TI animals, as well as BVDV-2b and BVDV-2c circulation among Siberian dairy complexes (note, BVDV-2b and BVDV-2c in animals of foreign and domestic origin are detected in Russia for the first time). Phylogenetic analysis of viruses circulating among PI and TI of highly productive dairy cattle was based on a comparison of conserved region of viral genome (5´-UTR) using reverse transcriptase PCR (RT-PCR) method. Studies were conducted in five regions of Western and Eastern Siberia: Tyumen, Novosibirsk, Irkutsk regions, the Krasnoyarsk Territory and Northern Kazakhstan on big dairy farms with a population of 800 or more milking cows with an average annual productivity of 7,000-10,000 liters, where at the time of the research vaccination was not carried out or inactivated vaccines were used. The imported livestock was kept mainly in the Tyumen region and the Republic of Kazakhstan. Biomaterial (blood, serum, nasal discharge, lymphoid organs, lungs, vaginal discharges) was collected from clinically healthy persistently infected animals, transitively infected animals with reproductive disorders and respiratory syndrome, as well as aborted fetuses. A total of 479 samples were examined. According to our findings, two BVDV species circulate among the PI and TI animals on the big dairy farms. The phylogenetic analysis reveals seven subtypes of BVDV-1, i.e. 1a (5 %), 1b (35 %), 1c (5 %), 1d (10 %), 1f (20 %), 1i (5 %), 1p (5 %) and two subtypes of BVDV-2, i.e. 2b (10 %) and 2c (5 %). Taking into account the fact that the strategy of livestock breeding is changing in Russia, the number of dairy mega farms" is increasing, which receive animals with different infectious status from many sources. Thence, the study of the genetic polymorphism of the virus is topical. Comparison of data on the origin of animals with the results of phylogenetic analyses can help in determina...

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Numerical taxonomy of the genus Pestivirus: New software for genotyping based on the palindromic nucleotide substitutions method

Cited by 11 publications

References 13 publications

Genetic Diversity of Bovine Pestiviruses Detected in Backyard Cattle Farms Between 2014 and 2019 in Henan Province, China

Genetic Diversity of Bovine Pestiviruses Detected in Backyard Cattle Farms Between 2014 and 2019 in Henan Province, China

An overview of calf diarrhea - infectious etiology, diagnosis, and intervention

Genetic Polymorphism of the Bovine Viral Diarrhea Viruses in Big Dairy Farms in Siberia

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