Indian Journal of Experimental Biology Vol. 56, May 2018, pp. 322-326 Complete genome sequence analyses of an Indian cattle strain of bovine viral diarrhoea virus 2 (BVDV-2) Niranjan Mishra*, Sthita Pragnya Behera, Semmannan Kalaiyarasu, Ram Kumar Nema, Pooja Dubey & Katherukamem Rajukumar ICAR-National Institute of High Security Animal Diseases, Anand Nagar, Bhopal, Madhya Pradesh-462 022, India Received 28 August 2015; revised 16 February 2017 Bovine viral diarrhea virus (BVDV) is a pestivirus which infects cattle worldwide causing substantial economic losses in cattle farming. BVDV is divided into two recognized species, BVDV-1 and BVDV-2 and one tentative species, BVDV-3. Since, complete genome sequence analysis can provide better insights into molecular epidemiology of BVD, we report here the first complete genome sequence analyses of an Indian BVDV-2 strain isolated from cattle. The full-genome of strain Ind 141353 contains 12285 nucleotides (nt) with a single large open reading frame which codes for 3898 amino acids. Phylogenetic analysis indicated that this strain belongs to the BVDV-2a subtype and has highest (93%) level of genetic identity with the Chinese cattle strain JZ05-1. It was inferred that although introduction from China is possible, introduction of BVDV-2 into Indian and Chinese cattle from a common trade source cannot be ruled out completely. The results in this study extend the spectrum of pestivirus molecular data and provide important insights into BVDV molecular epidemiology. Keywords: Cattle, Pestivirus, Phylogenetic analysis Bovine viral diarrhoea (BVD) causes significant economic losses in cattle farming and is prevalent worldwide. The causative agents of BVD, bovine viral diarrhoea virus 1 (BVDV-1) and bovine viral diarrhoea virus 2 (BVDV-2) together with border disease virus (BDV) and classical swine fever virus (CSFV) belong to the genus Pestivirus in the family Flaviviridae 1 . However, BVD can also be caused by the HoBi-like viruses, which have been proposed to represent the BVDV-3 species. BVDV-2, first detected in cattle of USA and Canada as a cause of haemorrhagic disease with high mortalities was found later in several other countries of South America, Europe and Asia 2-4 . However, BVDV-2 viruses vary in virulence and most of them can cause asymptomatic infection. Depending on their pathogenicity in cultured cells, BVDV strains are classified into two biotypes, noncytopathic (ncp) and cytopathic (cp). The ncp strain has the unique ability to produce persistent infection (PI) and the PI animals constantly shed large amounts of virus thereby spread the disease. The BVDV genome is approximately 12.3 kb long single stranded positive sense RNA containing a single ORF encoding about 4000 amino acids flanked by untranslated regions (UTR) at 5 and 3 ends 5 . Analysis of complete genomic sequences provides better insight into pestivirus phylogeny, evolution and molecular epidemiology. However, only partial sequences are commonly deposited in GenBank databases and analyzed. Complete genomic sequences are available for BVDV-1 and BVDV-2 isolated from cattle in other countries of the world with most of the complete genomic sequences available in literature are of BVDV-1. The exception is that no complete genomic sequence and its characterization have been reported so far for any Indian BVDV-1 or BVDV-2 strain. In India, BVDV-2 has been identified in goats 6 , sheep 7 , and cattle 8 , but genomic characterization has been limited to partial sequence analyses. Here, we report analyses of the full length genomic sequence of a previously reported Indian cattle BVDV-2 strain, Ind 141353 and its phylogenetic relationship with other BVDV-2 viruses. Materials and Methods RT-PCR amplification The Indian BVDV-2 isolate Ind 141353 originating from cattle and available in our laboratory was used to infect pestivirus free Madin Darby bovine kidney (MDBK) cells using standard procedure 7 . After 5 days incubation at 37°C, the cultures were frozen and thawed thrice and the clarified supernatant was used for RNA isolation using QIAamp viral RNA mini kit (Qiagen, Germany) following the manufacturer’s —————— *Correspondence: Phone: +91 755 2759204; Fax: +91 755 2758842 E-mail: mishranir@rediffmail.com