Genetic recombination of bovine viral diarrhea virus subgenotype -1a and -1c in persistently infected dairy cattle

Sri Handayani Irianingsih(1*), Bagoes Poermadjaja(2), Hastari Wuryastuti(3), Raden Wasito(4)

(1) Disease Investigation Centre Wates, Jl. Raya Yogya-Wates Km. 27, Tromol Pos 18, Wates, Yogyakarta 55602
(2) Disease Investigation Centre Wates, Jl. Raya Yogya-Wates Km. 27, Tromol Pos 18, Wates, Yogyakarta 55602
(3) Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna No.2, Sleman, Yogyakarta 55281
(4) Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna No.2, Sleman, Yogyakarta 55281
(*) Corresponding Author


The bovine viral diarrhea virus (BVDV) is a major viral pathogen in cattle worldwide. In Indonesia,  diversity in subgenotypes of BVDV-1 has been observed, with the highest proportion of subgenotype -1a, followed by -1c, -1b, and -1d. So far, phylogenetic analysis of BVDV-1 is based on nucleotide sequences of the 5′ UTR and partial NS5B regions. Accuracy in identifying the subgenotype and antigenic type is critical for vaccine development and effective vaccination. The aim of this study was to determine genetic recombination of BVDV through phylogenetic analysis of five different regions (5′ UTR, NPro, E2, NS3, and NS5B) of BVDV in persistently infected dairy cattle. Five isolates were sequenced using next-generation sequencing, and data were analyzed with the CLC Genomic Workbench 9.0 and MEGA-X programs. Phylogenetic analysis based on the 5′ UTR (275 nt), NPro (504 nt), E2 (1,122 nt), NS3 (2,049 nt), and NS5B (2,157 nt) regions indicated  that one BVDV isolate from Banyumas, Central Java, could be classified into different subgenotypes based on the E2 region (-1c), but the same subgenotype based on the other four regions (-1a), suggesting  the presence of genetic recombination of the BVDV subgenotypes -1a and -1c in persistently infected dairy cattle.


BVD virus; persistent infection; phylogenetic; recombination; subgenotype

Full Text:



Bazzucchi M, Bertolotti L, Giammarioli M, Rossi E, Petrini S, Rosati S, De Mia GM. 2017. Complete genome sequence of a bovine viral diarrhea virus subgenotype 1G strain isolated in Italy. Genome Announc. 5(17):318–319. doi:10.1128/genomeA.00263­17.

Becher P, Tautz N. 2011. RNA recombination in pes­tiviruses: cellular RNA sequences in viral genomes highlight the role of host factors for viral persis­tence and lethal disease. RNA Biol. 8(2):216–224. doi:10.4161/rna.8.2.14514.

Booth RE, Thomas CJ, El­Attar LM, Gunn G, Brownlie J. 2013. A phylogenetic analysis of Bovine Viral Di­arrhoea Virus (BVDV) isolates from six different re­gions of the UK and links to animal movement data. Vet Res. 44(1):43. doi:10.1186/1297­9716­44­43.

Brodersen B. 2014. Bovine viral diarrhea virus infections: manifestations of infection and recent advances in un­derstanding pathogenesis and control. Vet Pathol. 51(2):453–464. doi:10.1177/0300985813520250.

Chernick A, van der Meer F. 2017. Evolution of Bovine viral diarrhea virus in Canada from 1997 to 2013. Vi­rol. 509:232–238. doi:10.1016/j.virol.2017.06.024.

Deregt D, Dubovi EJ, Jolley ME, Nguyen P, Burton KM, Gilbert SA. 2005. Mapping of two antigenic do­ mains on the NS3 protein of the pestivirus bovine viral diarrhea virus. Vet Microbiol. 108(1­2):13–22. doi:10.1016/j.vetmic.2005.02.010.

Dow N, Chernick A, Orsel K, van Marle G, van der Meer F. 2015. Genetic variability of bovine vi­ral diarrhea virus and evidence for a possible ge­netic bottleneck during vertical transmission in persistently infected cattle. PloS one 10(7):e0131972. doi:10.1371/journal.pone.0131972.

Firat I, Ak S, Bozkurt HH, Ak K, Turan N, Bagcigil F. 2002. Distribution of bovine viral diarrhoea virus (BVDV) in the genital system tissues of cattle. Vet Arhiv. 72(5):235–248.

Gao S, Du J, Shao J, Lang Y, Lin T, Cong G, Zhao F, Belák S, Liu L, Chang H, et al. 2014. Genome analy­ sis reveals a novel genetically divergent subgenotype of bovine viral diarrhea virus in China. Infect Genet Evol. 21:489. doi:10.1016/j.meegid.2013.06.010.

Giangaspero M, Harasawa R, Weber L, Belloli A. 2008. Taxonomic and epidemiological aspects of the bovine viral diarrhoea virus 2 species through the observation of the secondary structures in the 5’genomic untrans­lated region. Vet Ital. 44(2):319–345.

Goens SD. 2002. The evolution of bovine viral diarrhea: a review. Can Vet J. 43(12):946.

Houe H, Baker J, Maes R, Wuryastuti H, Wasito R, Ruegg P, Lloyd J. 1995. Prevalence of cattle persistently infected with bovine viral diarrhea virus in 20 dairy herds in two counties in central Michigan and comparison of prevalence of antibody­positive cattle among herds with different infection and vaccination status. J Vet Diagn Invest. 7(3):321–326. doi:10.1177/104063879500700304.

Irianingsih S, Wuryastuty H, Wasito R, Wibawa H, Rasa FT, Poermadjaja B. 2019. Genetic analysis of NS5B gene from bovine viral diarrhea virus­infected cat­ tle in Central and East Java, Indonesia. Vet World. 12(7):1108. doi:10.14202/vetworld.2019.1108­115.

Karimy MF. 2016. Ragam genetik bovine viral diarrhea virus genotipe 1 (Singer dan CP) dan genotipe 2 (890, Ngawi, dan Ngambal) pada NPro Region. Master’s thesis, Universitas Gadjah Mada, Yogyakarta.

Liebner­Tenorio, EM. 2005. Pathogenesis. In: SM In: Goyal, e Ridpath Julia F, editors, Bovine viral diarrhea virus: diagnosis, management, and control. Iowa USA, John Wiley & Sons, 1st edition. p. 121– 143.

Nagai M, Hayashi M, Sugita S, Sakoda Y, Mori M, Mu­rakami T, Ozawa T, Yamada N, Akashi H. 2004. Phylogenetic analysis of bovine viral diarrhea viruses using five different genetic regions. Virus Res. 99(2):103–113. doi:10.1016/j.virusres.2003.10.006.

Nagai M, Sakoda Y, Mori M, Hayashi M, Kida H, Akashi H. 2003. Insertion of cellular sequence and RNA re­ combination in the structural protein coding region of cytopathogenic bovine viral diarrhoea virus. J Gen Virol. 84(2):447–452. doi:10.1099/vir.0.18773­0.

Neill JD. 2013. Molecular biology of bovine viral diarrhea virus. Biol. 41(1):2–7. doi:10.1016/j.biologicals.2012.07.002.

Peterhans E, Schweizer M. 2010. Pestiviruses: how to outmaneuver your hosts. Vet Microbiol. 142(1­2):18– 25. doi:10.1016/j.vetmic.2009.09.038.

Reichel MP, Lanyon SR, Hill FI. 2018. Perspec­tives on Current Challenges and Opportunities for Bovine Viral Diarrhoea Virus Eradication in Aus­tralia and New Zealand. Pathogens 7(1):14. doi:10.3390/pathogens7010014.

Ridpath JF. 2005. Classification and Molecular Biology. In: SM In: Goyal, e Ridpath Julia F, editors, Bovine viral diarrhea virus: diagnosis, management, and control. Iowa USA, John Wiley & Sons, 1st edition. p. 65–80.

Saepulloh M, Sendow I, et al. 2015. Identification and characterization of bovine viral diarrhea virus from Indonesian cattle. J. Vet 16(1):1–7.

Vilcek S, Durkovic B, Kolesárová M, Greiser­Wilke I, Pa­ ton D. 2004. Genetic diversity of international bovine viral diarrhoea virus (BVDV) isolates: identification of a new BVDV­1 genetic group. Vet Res. 35(5):609– 615. doi:10.1051/vetres:2004036.

Vilcek S, Durkovic B, Kolesarova M, Paton D. 2005. Genetic diversity of BVDV: conse­quences for classification and molecular epi­demiology. Prev Vet Med. 72(1­2):31–35. doi:10.1016/j.prevetmed.2005.08.004.

Wiyono A, Ronohardjo P, Graydon R, Daniels P. 1989. Diare ganas sapi: 1. Kejadian penyakit pada sapi Bali bibit asal Sulawesi Selatan yang baru tiba di Kaliman­ tan Barat. Penyakit Hewan 21(38):77–83.

Wuryastuti H, Wasito R, Sugiyono. 2018. Genotypes and biotypes variation of bovine viral diarrhea virus from persistently infected dairy cattle in Java, Indonesia. Integr J Vet Biosci 3(2):1–7.

Wuryastuti H, Putro PP, Wasito R, Maes RK. 2015. Ge­netic Variability of Bovine Viral Diarrhea Virus in Persistently Infected Cattle in Central Java, Indone­sia. Merit Res J Microbiol Biol Sci. 3(3):031–036.

Yeşilbağ K, Alpay G, Becher P. 2017. Variabil­ity and global distribution of subgenotypes of bovine viral diarrhea virus. Viruses 9(6):128. doi:10.3390/v9060128.

Yeşilbağ K, Förster C, Ozyiğit MO, Alpay G, Tuncer P, Thiel HJ, König M. 2014. Characterization of bovine viral diarrhoea virus (BVDV) isolates from an outbreak with haemorrhagic enteritis and se­vere pneumonia. Vet Microbiol. 169(1­2):42–49. doi:10.1016/j.vetmic.2013.12.005.


Article Metrics

Abstract views : 2322 | views : 2697


  • There are currently no refbacks.

Copyright (c) 2020 The Author(s)

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.