Complete Genome Sequence of Classical Swine Fever Virus Subgenogroup 2.1 from Assam, India

Ahuja, Anuj; Bhattacharjee, Uttaran; Chakraborty, A. K.; Karam, Amarjit; Ghatak, Sandeep; Puro, K.; Das, Samir; Shakuntala, I.; Ngachan, S. V.

doi:10.1128/genomea.01437-14

Cited by 15 publications

(10 citation statements)

References 8 publications

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“…The lineage formed by sequences of CSFV strains that circulated in India during 2012–2013 formed a statistically supported cluster (Figure and Table S1). These sequences showed a genetic divergence of 11.9% with the Subgenotype 2.1, where the strains were previously located (Ahuja et al., ), and a genetic divergence compared to the remaining subgenotypes into CSFV Genotype 2 that ranged between 9.1% and 13.8% (Table ). Hence, we propose this lineage to be defined as Subgenotype 2.4 (Figure ).…”

Section: Resultsmentioning

confidence: 75%

Revisiting the genetic diversity of classical swine fever virus: A proposal for new genotyping and subgenotyping schemes of classification

Rios

Núñez

Arce

et al. 2018

Transbound Emerg Dis

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Classical swine fever (CSF) is a highly contagious febrile viral disease caused by CSF virus (CSFV), and it is considered one of the most important infectious diseases that affect domestic pigs and wild boar. Previous molecular epidemiology studies have revealed that the diversity of CSFV comprises three main genotypes and different subgenotypes defined using a reliable cut-off to accurately classify CSFV at genotype and subgenotype levels. However, a growing number of CSFV both complete genome and full E2 gene sequences have been submitted to GenBank (more than 500 sequences are currently available, revised on December 1, 2017). Therefore, the aim of this study was to revisit the taxonomy of CSFV at genotype and subgenotype levels, to unify nomenclature and to provide an update to the classification of CSFV. We propose here a new genotyping scheme with five well-defined CSFV genotypes (CSFV Genotypes 1-5) and 14 subgenotypes (seven for each of the CSFV Genotype 1 and CSFV Genotype 2). The findings showed in this study are relevant for molecular epidemiology approaches and will help to better understand the genetic diversity and spreading of CSFV at a global scale. The update in the classification of CSFV will allow the scientific community to establish more accurately the links among different outbreaks of the disease.

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Section: Resultsmentioning

confidence: 75%

Revisiting the genetic diversity of classical swine fever virus: A proposal for new genotyping and subgenotyping schemes of classification

Rios

Núñez

Arce

et al. 2018

Transbound Emerg Dis

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“…Inner Mongolia) from pigs showing clinical symptoms and pathological lesions resembling mild classical swine fever[48], and characterized as genotype M[49] (PNS BVDV-1.15). Zhu et al[10] reported a noncytopathic strain, genetically closely related to the pig strain ZM-95, associated with a disease cha-AS/GHY/G4 [KM362426][53]. According to E2 region primary sequence analysis, these strains were clustered in the CSFV sub-genogroup 2.1[45] [53].…”

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confidence: 99%

“…Zhu et al[10] reported a noncytopathic strain, genetically closely related to the pig strain ZM-95, associated with a disease cha-AS/GHY/G4 [KM362426][53]. According to E2 region primary sequence analysis, these strains were clustered in the CSFV sub-genogroup 2.1[45] [53]. The E2 regions of the bovine strains CS/ML/911/IDP/13 [KY860532] and CS/ML/AF/Umiam/14 [KY860531] showed 99% nucleotide identity with…”

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confidence: 99%

Heterogeneity of <i>Pestivirus</i> Species in Asia

Giangaspero¹,

Zhang²,

Apicella³

2019

AiM

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Pestivirus are responsible for cosmopolitan diseases affecting cattle, pigs and other ruminants, presenting a wide range of clinical manifestations, with relevant impact on zootechnic production. Understanding genomic characteristic and virus taxonomy is fundamental in order to sustain control and prophylactic programs. Given the recent various studies reporting a relatively high number of new strains, in particular from Asian countries, in the present study, six hundred-fifty-one genomic sequences have been considered applying the palindromic nucleotide substitutions method for genotyping. Based on the secondary structure analysis of the 5' untranslated region of RNA, sequence characteristics among Asian genomic clusters within the different Pestivirus species suggested geographic segregation and occurrence of micro-evolutive steps in the genus evolutionary history. This aspect was particularly evident in atypical sequences originated from China or Turkey, indicating risk of diffusion by animals and products trade or contamination of biological products as bovine calf serum, with potential diagnostic and control difficulties.

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“…-6]. It has been reported that subgenotype 2.1 isolates are distributed in many Asian and European countries and play a dominant role in CSF outbreaks occurring in China, Korea and other countries [3,5,7,8]. With more sequences of 2.1 isolates deposited in the GenBank database, CSFV subgenotype 2.1 has been further divided into 10 sub-subgenotypes (2.1a-2.1j) based on a nucleotide sequence of 190-nt and the 1,119-nt E2 gene [8].…”

mentioning

confidence: 99%

“…The ORF encodes a 3898-amino-acid polyprotein that can be further processed to four structural proteins (Core, E rns , E1, and E2) and eight nonstructural proteins (N pro , P7, NS2, NS3, isolate for GD19/2011 is the sub-subgenotype 2.1a strain Paderborn from Germany [5], and the most distant isolate is the sub-subgenotype 2.1d strain IND/AS/GHY/G4 collected from India [7]. Sequence identity values from the comparison of GD19/2011 and other subgenotype 2.1 isolates at the genome and individual gene levels are shown in Table 1.…”

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confidence: 99%

Complete genome sequence of a novel sub-subgenotype 2.1g isolate of classical swine fever virus from China

Gong

Zhang

et al. 2016

Arch Virol

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Current subgenotype 2.1 isolates of classical swine fever virus (CSFV) play a dominant role in CSF outbreaks in China, and a novel sub-subgenotype 2.1g of CSFV was recently identified, but the complete genome sequence of this new sub-subgenotype has not been reported. In this study, complete genome of 2.1g isolate GD19/2011 collected from Guangdong province of China in 2011 was sequenced. It was found to be 12,298 nucleotides (nt) in length, including a 375-nt 5'UTR, a 11,697-nt opening reading frame (ORF), and a 227-nt 3'UTR. GD19/2011 shared 91.0-93.7 % and 95.6-97.5 % nt and amino acid sequence identity, respectively, with other subgenotype 2.1 isolates. The topology of a phylogenetic tree constructed based on complete genome sequences of GD19/2011 and other CSFV isolates was identical to that obtained with full-length E2 gene sequences, but it was significantly different from those obtained with the 5'UTR and core sequences. Serial passages of GD9/2011 in PK-15 cells generated a highly cell-adapted virus stock with an infectious titer of 10(7.8) TCID50/ml at the 12(th) passage in which two amino acid substitutions, S476R and N2494S, were observed in comparison with the complete polyprotein sequence of the original isolate from kidney tissue, GD19/2011. This is the first report of the complete genome sequence of a 2.1g isolate, and the GD19/2011 isolate will be useful for further analysis of the evolution and virulence of CSFV isolates.

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Complete Genome Sequence of Classical Swine Fever Virus Subgenogroup 2.1 from Assam, India

Cited by 15 publications

References 8 publications

Revisiting the genetic diversity of classical swine fever virus: A proposal for new genotyping and subgenotyping schemes of classification

Revisiting the genetic diversity of classical swine fever virus: A proposal for new genotyping and subgenotyping schemes of classification

Heterogeneity of <i>Pestivirus</i> Species in Asia

Complete genome sequence of a novel sub-subgenotype 2.1g isolate of classical swine fever virus from China

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Complete Genome Sequence of Classical Swine Fever Virus Subgenogroup 2.1 from Assam, India

Cited by 15 publications

References 8 publications

Revisiting the genetic diversity of classical swine fever virus: A proposal for new genotyping and subgenotyping schemes of classification

Revisiting the genetic diversity of classical swine fever virus: A proposal for new genotyping and subgenotyping schemes of classification

Heterogeneity of &lt;i&gt;Pestivirus&lt;/i&gt; Species in Asia

Complete genome sequence of a novel sub-subgenotype 2.1g isolate of classical swine fever virus from China

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Heterogeneity of <i>Pestivirus</i> Species in Asia