Phylogenetic analysis of NS5B gene of classical swine fever virus isolates indicates plausible Chinese origin of Indian subgroup 2.2 viruses

Abstract

Twenty-three CSFV isolates recovered from field outbreaks in various parts of India during 2006-2009 were used for genetic analysis in the NS5B region (409 nts). Seventeen of these were studied earlier [16] in the 5'UTR region. Phylogenetic analysis indicated the continued dominance of subgroup 1.1 strains in the country. Detailed analysis of a subgroup 2.2 virus indicated the plausible Chinese origin of this subgroup in India and provided indirect evidence of routes of CSFV movement within South East Asia region.

Genetic clustering of recent classical swine fever virus isolates from Karnataka, India revealed the emergence of subtype 2.2 replacing subtype 1.1

“…Present and previous studies of genetic typing [15] in Karnataka had indicated that there has been a switch in virus populations from subgroup 1.1 to 2.2 after 2008 and 2.2 viruses has dominated the field infections. Even though subgroup 1.1 viruses were predominant in India, the subgroup 2.2 viruses are gradually spreading as confirmed by frequent detection/ isolation of subgroup 2.2 viruses in the recent years, particularly from the northern India [14,15] and neighbouring country like Nepal [18]. During 2012-13, the prevalence of subgroup 2.2 isolates was also reported from Andhra Pradesh, Punjab, Orissa, Meghalaya and Arunachal Pradesh states (Unpublished data from NIVEDI, Bangalore).…”

“…In China, 94 % of the virus strains isolated from field outbreaks during 1986-1999 were belonging to 2.1 and 2.2 subgroups [27].As the present isolates and some of the Indian isolates belonged to subgroup 2.2, it can be inferred that the viruses may have had Chinese origin at some point of time. Recently, Patil et al [15] have also shown the plausible Chinese origin of the Karnataka isolate IND-294/08 which belongs to subgroup 2.2.…”

“…A compilation of data from OIE indicates that there were 1308 outbreaks of CSF in India during 1996-2008 [16]. It is one of the top five viral diseases of livestock in the country according to data available in NIVEDI [15]. Many outbreaks in the country were undiagnosed because of the sporadic nature of the disease, lack of awareness and scarcity of good diagnostic laboratories.…”

“…Few reports have been documented the occurrence of 1.1 and 2.2 genotype CSF viruses in India [14,15,24] using molecular epidemiological techniques. Phylogenetic analysis by Patil et al [14, Electronic supplementary material The online version of this article (doi:10.1007/s13337-015-0273-9) contains supplementary material, which is available to authorized users.…”

“…Phylogenetic analysis by Patil et al [14, Electronic supplementary material The online version of this article (doi:10.1007/s13337-015-0273-9) contains supplementary material, which is available to authorized users. & S. S. Patil sharanspin123@rediffmail.com 15] indicated the dominance of subgroup 1.1 strains in the country and detailed analysis of subgroup 2.2 viruses indicated the plausible Chinese origin of this subgroup in India using the lone isolate from Karnataka. Their analysis was constrained by the lack of large number of subgroup 2.2 sequences from India and they also suggested the studies involving other regions of the genome for better resolution of the epidemiology of subgroup 2.2.…”