Genetic diversity of ruminant Pestivirus strains collected in Northern Ireland between 1999 and 2011 and the role of live ruminant imports

Abstract

Background: The genus pestivirus within the family Flaviviridae includes bovine viral diarrhoea virus (BVDV) types 1 and 2, border disease virus (BDV) and classical swine fever virus. The two recognised genotypes of BVDV are divided into subtypes based on phylogenetic analysis, namely a-p for BVDV-1 and a-c for BVDV-2.

Methods: Three studies were conducted to investigate the phylogenetic diversity of pestiviruses present in Northern Ireland. Firstly, pestiviruses in 152 serum samples that had previously tested positive for BVDV between 1999 and 2008 were genotyped with a RT-PCR assay. Secondly, the genetic heterogeneity of pestiviruses from 91 serum samples collected between 2008 and 2011 was investigated by phylogenetic analysis of a 288 base pair portion of the 5' untranslated region (UTR). Finally, blood samples from 839 bovine and 4,437 ovine animals imported in 2010 and 2011 were tested for pestiviral RNA. Analysis of animal movement data alongside the phylogenetic analysis of the strains was carried out to identify any links between isolates and animal movement.

Results: No BVDV-2 strains were detected. All of the 152 samples in the first study were genotyped as BVDV-1. Phylogenetic analysis indicated that the predominant subtype circulating was BVDV-1a (86 samples out of 91). The remaining five samples clustered close to reference strains in subtype BVDV-1b. Out of the imported animals, 18 bovine samples tested positive and 8 inconclusive (Ct ≥36), while all ovine samples were negative. Eight sequences were obtained and were defined as BVDV-1b. Analysis of movement data between herds failed to find links between herds where BVDV-1b was detected.

Conclusion: Given that only BVDV-1a was detected in samples collected between 1968 and 1999, this study suggests that at least one new subtype has been introduced to Northern Ireland between 1999 and 2011 and highlights the potential for importation of cattle to introduce new strains.

Keywords: 5’untranslated region; Bovine viral diarrhoea virus; Importation; Phylogenetic analysis.

Fig. 1

Phylogenetic typing of 27 selected (excluding identical strains) Panel II isolates in the 5’UTR. Reference strains are marked with a circle and the accession numbers for these strains on NCBI Genbank are as follows: BVDV-1a- NADL (M31182), Singer (L32875), Oregon C24V (AB019678); BVDV-1b- Draper (L32880), Osloss (M96687); BVDV-1c- Bega (AF049221), Manasi (EU159702); BVDV-1d- F-Au (AF298065), 16-111-Fr (AF298056); BVDV-1e- 10-84-Fr (AF2980054), 3186 V6 (AF298062); BVDV-1f- J-Au (AF298076), W-Au (AF298073); BVDV-1 g- A-Au (AF298064), L-Au (AF298069); BVDV-1 h- G-Au (AF298066), KM-SK (AF298068); BVDV-1i- 23-15 (AF298059); BVDV-1j- KS86-1-ncp (AB078950), Deer (AB040132); BVDV-1 k- Suwa (AF117699), Rebe (AF299317); BVDV-1 m- ZM-95 (AF526381), TY05 (GU120242); BVDV-1n- Shitara-02-06 (AB359930), So CP-75 (AB359929); BVDV-1o- IS25CP-01 (AB359931), AQGN96B15 (AB300691); BVDV-1p- BJ0702 (GU120248), BJ0703 (GU120249); BVDV-2- 890 (BVU18059). GenBank accession numbers for the 5’ regions sequenced for this paper are KP999051-KP999149

Fig. 2

Phylogenetic subtree with all BVDV-1b detected strains in Panels II and III and a Dutch BVDV-1b strain. Reference strains are marked with a circle. Accession numbers for these as per Fig. 1 and Dutch BVDV-1b-98 (AF098156)

Fig. 3

Phylogenetic circle showing the relationship between the 91 samples in Panel II and previous Northern Ireland (NI), Republic of Ireland (ROI) and Great Britain (GB) strains. Relevant reference strains are marked with a dot, previously reported strains from NI and ROI marked with a triangle and previously reported GB strains are marked with a diamond. The accession numbers for these strains on NCBI Genbank are as follows: DG H851 98 (AJ312908) (ROI), DG 125 85 (AJ312909) (NI), DG 4796 94 (AJ312910) (NI), DG B551 98 (AJ312911) (ROI), DG K869 98 (AJ312912) (ROI), DG 2703D 99 (AJ312913) (NI), DG 80/1 ncp 82 (AJ312914) (NI), DG 2586X 99 (AJ312915) (NI), DG 2750A 99 (AJ312916) (NI), DG 985 84 (AJ312917) (NI), DG 371 89 (AJ312918 (NI)), DG L1000 98 (AJ312919) (ROI), DG 4771 94 (AJ312920) (NI), DG 8087 99 (AJ312921) (NI), DG L322 98 (AJ312922) (ROI), DG H686 98 (AJ312923) (ROI), DG 819 85 (AJ312924) (NI), DG 252 84 (AJ312925) (NI), DG 383 76 (AJ312926) (NI), DG 1 77 (AJ312927) (NI), DG Ln 68 (AJ312928) (NI), DG 80/1 cp 82 (AJ312929) (NI), DG 2430 95 (AJ312930) (NI), DG 4898 94 (AJ312931) (NI), DG 3114 93 (AJ312932) (NI), Strong 416 (JQ920052), Strong 463 (JQ920074), Strong 2175 (JQ920096), Strong 2405 (JQ920208), Strong 2475 (JQ920250)