ABSTRACT
Here, we report the genome sequence of strain UTPV1/AB belonging to the species Ungulate tetraparvovirus 1 (UTPV1). UTPV1/AB was isolated in the east of Ireland, directly from a nasal swab of a beef-suckler calf diagnosed with bovine respiratory disease on a farm in County Meath (longitude, 6°65′W; latitude, 53°52′N).
ANNOUNCEMENT
Ungulate tetraparvovirus 1 (UTPV1), previously classified as Bovine hokovirus (1), is a small, linear, single-stranded DNA (ssDNA) virus that belongs to the genus Tetraparvovirus, in the family Parvoviridae (2). The virus has been identified from domestic yaks in China (3) and in cattle feedlots by metagenomic sequencing (4). Here, we report an UTPV1 genome sequence isolated from Ireland.
The UTPV1/AB strain was collected and sequenced directly from a nasal swab of a 6-month-old Aberdeen-Angus suckler calf (189 days old; weight, 318 kg) diagnosed with bovine respiratory disease (BRD) in November 2019 during a large-scale research study (5).
Prior to nucleic acid extraction, 1× phosphate-buffered saline (PBS) was added to the nasal swab and vortexed, 300 μL was removed, and then bead beating and RNase and DNase treatment steps were performed (6). Nucleic acids were extracted using the QIAamp MinElute virus spin kit (Qiagen, Manchester, UK) with carrier RNA substituted with 5 mg/mL linear acrylamide (ThermoFisher). Double-stranded cDNA was synthesized, using the Maxima H minus double-stranded (ds) cDNA kit (ThermoFisher) with random hexamers and purified using the GeneJet PCR purification kit (ThermoFisher). The rapid PCR barcoding kit (SQK-RPB004) from Oxford Nanopore and NEBNext Ultra II Q5 master mix (New England BioLabs Inc.) were used to generate Nanopore sequencing libraries. The library was loaded on a spot-on flow cell (FLO-MIN106D R9) (Oxford Nanopore Technologies, Oxford, UK) and sequenced on a MinION Mk1C sequencer with high-accuracy base calling.
Nanopore reads were filtered using Nanofilt (v2.8.0), and host-derived reads were removed resulting in 2,349 reads of viral origin with a mean length of 2,578 bp (7). De novo assembly was carried out using Flye (v2.9) (8). The Nanopore long reads were used to polish the Flye assembly using a single Medaka (v1.4.3) pass. The final draft consensus assembly was annotated using Prokka (v1.14.6) (9). The UTPV1/AB sequence contained 5,227 nucleotides. According to BLASTN (10) analysis, the near-complete genome sequence showed the highest nucleotide identity (99.53%) with UTPV1 strain HK-B38, a nonstructural protein from China (accession no. JF504698.1). UTPV1/AB had a much lower nucleotide similarity with any of the described ungulate tetraparvovirus genome sequences found in GenBank, with the highest similarity for Ungulate tetraparvovirus 1 isolate Yak hokovirus at 90.34% (accession no. KT225725.1).
Multiple sequence alignment by the MUSCLE algorithm in MEGA11 (11, 12) of UTPV1/AB and 11 available UTPV1 genomes from GenBank was performed to infer phylogeny (Fig. 1). The phylogenetic analysis confirms that UTPV1/AB is closely related to UTPV1 strain HK-B38 and another UTPV1 isolate complete genome (accession no. MH814981.1) from China was also closely related. This UTPV1 complete genome was aligned against UTPV1/AB and their shared nucleotide identity was 99.56%.
FIG 1.
Phylogenetic tree of UTPV1/AB with Ovine HK-S01 as an outgroup to root the tree. Bootstrap values of >70% are displayed.
Two hypothetical proteins were identified from the analysis, and their amino acid sequences were searched against the nonreductant protein sequence database of BLASTP to determine their identity. Hypothetical protein 1 had the highest similarity, at 99.84%, to a UTPV1 nonstructural protein (accession no. ANN02913.1). Hypothetical protein 2 was most similar to a minor structural protein from UTPV1 with an amino acid identity of 99.89% (accession no. AEQ76794.1).
Data availability.
The genome sequence of UTPV1/AB has been deposited in GenBank under the accession number OP113956 and in the Sequence Read Archive under accession number SRR21529965.
ACKNOWLEDGMENT
We acknowledge funding support through the US-Ireland (Department of Agriculture, Food and the Marine [DAFM]) Tri-Partite grant (project number 2018US-IRL200).
Contributor Information
Bernadette Earley, Email: Bernadette.earley@teagasc.ie.
Jelle Matthijnssens, Katholieke Universiteit Leuven.
REFERENCES
- 1.Souza CK, Streck AF, Gonçalves KR, Pinto LD, Ravazzolo AP, de Barcellos DEDSN, Canal CW. 2016. Phylogenetic characterization of the first Ungulate tetraparvovirus 2 detected in pigs in Brazil. Braz J Microbiol 47:513–517. doi: 10.1016/j.bjm.2016.01.025. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Cotmore SF, Agbandje-McKenna M, Chiorini JA, Mukha DV, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Gatherer D, Davison AJ. 2014. The family Parvoviridae. Arch Virol 159:1239–1247. doi: 10.1007/s00705-013-1914-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Xu F, Pan Y, Wang M, Wu X, Tian L, Baloch AR, Zeng Q. 2016. First detection of ungulate tetraparvovirus 1 (bovine hokovirus 1) in domestic yaks in northwestern China. Arch Virol 161:177–180. doi: 10.1007/s00705-015-2638-1. [DOI] [PubMed] [Google Scholar]
- 4.Mitra N, Cernicchiaro N, Torres S, Li F, Hause BM. 2016. Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus. J Gen Virol 97:1771–1784. doi: 10.1099/jgv.0.000492. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Cuevas-Gómez I, McGee M, McCabe M, Cormican P, O’Riordan E, McDaneld T, Earley B. 2020. Growth performance and hematological changes of weaned beef calves diagnosed with respiratory disease using respiratory scoring and thoracic ultrasonography. J Anim Sci 98:skaa345. doi: 10.1093/jas/skaa345. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Esnault G, Earley B, Cormican P, Waters SM, Lemon K, Cosby SL, Lagan P, Barry T, Reddington K, McCabe MS. 2022. Assessment of rapid MinION Nanopore DNA virus meta-genomics using calves experimentally infected with bovine herpes virus-1. Viruses 14:1859. doi: 10.3390/v14091859. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34:2666–2669. doi: 10.1093/bioinformatics/bty149. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods 17:1103–1110. doi: 10.1038/s41592-020-00971-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 10.Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- 11.Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. doi: 10.1186/1471-2105-5-113. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. doi: 10.1093/molbev/msab120. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome sequence of UTPV1/AB has been deposited in GenBank under the accession number OP113956 and in the Sequence Read Archive under accession number SRR21529965.