Dalton, Desire Lee

Du Plessis, Morne

Loots, Angelika K.

Mitchell, Emily

Venter, Estelle H.

English

Canine distemper virus causes global multihost infectious disease. Thisreport details complete genome sequences of three vaccine and two new wild-typestrains. The wild-type strains belong to the South African lineage, and all three vaccine strains to the America 1 lineage. This constitutes the first genomic sequences of this virus from South Africa

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Genome Sequences of Three VaccineStrains and Two Wild-Type CanineDistemper Virus Strains from a RecentDisease Outbreak in South AfricaAngelika K. Loots,a,b Morné Du Plessis,a,c Desiré Lee Dalton,a,d Emily Mitchell,aEstelle H. Venterb,eNational Zoological Gardens of South Africa, Gauteng, South Africaa; Department of Veterinary TropicalDiseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africab; Department ofBiotechnology, University of the Western Cape, Cape Town, South Africac; Department of Zoology, Universityof Venda, Thohoyandou, South Africad; College of Public Health, Medical and Veterinary Sciences, James CookUniversity, Townsville, Queensland, AustraliaeABSTRACT Canine distemper virus causes global multihost infectious disease. Thisreport details complete genome sequences of three vaccine and two new wild-typestrains. The wild-type strains belong to the South African lineage, and all three vac-cine strains to the America 1 lineage. This constitutes the first genomic sequences ofthis virus from South Africa.Canine distemper virus (CDV) (family Paramyxoviridae) is an enveloped, nonseg-mented, single-stranded, negative-sense RNA virus responsible for the diseasecanine distemper (CD), which has a high mortality rate in domestic and wild carnivorehosts (1–3). Vaccination has proven to be an effective intervention strategy against CDVin domestic hosts (3, 4); however, there is still a lack of quantitative data on the effectsof a CDV vaccine in wildlife (5).The RNA genome is 15,690 nucleotides (nt) long and consists of 6 genes that encodefor a single envelope-associated protein [matrix (M)], 2 glycoproteins [the hemagglu-tinin (H) and fusion (F) proteins], 2 transcriptase-associated proteins [phosphoprotein(P) and large (L) protein], and a nucleocapsid (N) protein (6). The organization of themajor genes was 3=-N-P-M-F-H-L-5=, each separated by untranslated regions (7). Onlyone serotype of CDV has been recognized, with several cocirculating genotypes basedon H-gene variation clustering into the lineages America 1 and 2; Asia 1 and 2;Europe–South America 1; Europe wildlife; South America 2 and 3; Arctic; Rockborn-like;and Africa and Africa 2 (8–11).Here, we report the complete genome of the three CDV strains (CDV_Buc,CDV_Nobi, and CDV_OVI) commonly found in vaccines and two wild-type strains (WT01and WT02) from a recent CDV outbreak in South Africa. Both WT01 and WT02 wereobtained from lung tissue collected from an infected African wild dog (Lycaon pictus),in Northern Cape Province, South Africa, and spotted hyena (Crocuta crocut), in Lim-popo Province, South Africa, respectively. Samples were cultured and passaged be-tween one and three times on VerodogSLAM cells grown in 25 cm2 tissue culture flasks(12). Viral RNA was extracted using Trizol (Invitrogen). Sequence-independent whole-genome reverse transcription-PCR amplification was used to prepare templates, whichwere sequenced on an Illumina MiSeq sequencer using the TruSeq sample preparationkit (Illumina). Data quality was assessed using FastQC version 0.11.2 software (http://www.bioinformatics.babraham.ac.uk). Paired sequence reads were analyzed with CLCGenomics Workbench version 6 (CLC bio, Aarhus, Denmark). Full-length genomesequences were assembled using a combination of mapping and de novo assembly.Received 9 May 2017 Accepted 16 May2017 Published 6 July 2017Citation Loots AK, Du Plessis M, Dalton DL,Mitchell E, Venter EH. 2017. Genomesequences of three vaccine strains and twowild-type canine distemper virus strains from arecent disease outbreak in South Africa.Genome Announc 5:e00603-17. https://doi.org/10.1128/genomeA.00603-17.Copyright © 2017 Loots et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Desiré Lee Dalton,desire@nzg.ac.za.VIRUSEScrossmVolume 5 Issue 27 e00603-17 genomea.asm.org 1 on July 17, 2017 by guesthttp://genomea.asm.org/Downloaded from The genomes of WT01, WT02, CDV_Buc, CDV_OVI, and CDV_Nobi are 15,690 nt,15,649 nt, 15,673 nt, 15,670 nt, and 15,649 nt, respectively. Amino acid lengths of thesix proteins encoded by each of the four genomes were 522 (N), 506 (P), 334 (M), 662(F), 604 (H), and 2,183 (L). Multiple sequence alignments and Bayesian phylogeneticanalysis according to the H-gene revealed that WT01 and WT02 belong to the SouthAfrican lineage. The three vaccine strains were grouped in the America 1 lineage, whichis consistent with other known vaccine strain groupings.The two wild-type CDV strains constitute the first report of genomic sequences inSouth Africa. Data suggest the formulation of new and updated vaccines, consideringthe level of genetic variability obtained. These data contribute to the knowledge ofCDV, which may be beneficial in determining effective preventative, diagnostic, andcontrol measures for CD in South Africa.Accession number(s). The genome sequences of WT01, WT02, CDV_Buc, CDV_Nobi,and CDV_OVI have been deposited in GenBank under the accession numbers KY971528,KY971532, KY971529, KY971530, and KY971531, respectively.ACKNOWLEDGMENTSThis study was supported by the National Zoological Gardens of South Africa andfunded by the National Research Foundation (NRF) Professional Development Program.We acknowledge wildlife veterinarian Peter Caldwell (Old Chapel Veterinary Clinic,Tshwane) for his invaluable contribution in collecting samples, as well as the TswaluKalahari Reserve for their permission to collect samples and data for this study. KarenEbersohn and Peter Coetzee are recognized for their assistance in the laboratory andthe Agricultural Research Council’s Biotechnology Platform for sequencing on theMiSeq.REFERENCES1. Appel MJG. 1987. Canine distemper virus, p 133–159. In Appel MJG (ed),Virus infections of carnivores. Elsevier Science, New York, NY.2. Beineke A, Baumgärtner W, Wohlsein P. 2015. Cross-species transmissionof canine distemper virus—an update. One Health 1:49 –59. https://doi.org/10.1016/j.onehlt.2015.09.002.3. Bronson E, Deem SL, Sanchez C, Murray S. 2007. Serologic response to acanarypox-vectored canine distemper virus vaccine in the giant panda(Ailuropoda melanoleuca). J Zoo Wildl Med 38:363–366. https://doi.org/10.1638/1042-7260(2007)038[0363:SRTACC]2.0.CO;2.4. Sadler RA, Ramsay E, Mcaloose D, Rush RCVP, Wilkes RP. 2016. Evaluationof two canine distemper virus vaccines in captive tigers (Panthera tigris).J Zoo Wildl Med 47:558 –563. https://doi.org/10.1638/2015-0223.1.5. Loots AK, Mitchell E, Dalton DL, Kotzé A, Venter EH. 2017. Advances incanine distemper virus pathogenesis research: a wildlife perspective. JGen Virol 98:311–321. https://doi.org/10.1099/jgv.0.000666.6. Diallo A. 1990. Morbillivirus group: genome organisation and pro-teins. Vet Microbiol 23:155–163. https://doi.org/10.1016/0378-1135(90)90145-L.7. Sidhu MS, Husar W, Cook SD, Dowling PC, Udem SA. 1993. Caninedistemper terminal and intergenic non-protein coding nucleotidesequences: completion of the entire CDV genome sequence. Virology193:66 –72. https://doi.org/10.1006/viro.1993.1103.8. Ke GM, Ho CH, Chiang MJ, Sanno-Duanda B, Chung CS, Lin MY, Shi YY,Yang MH, Tyan YC, Liao PC, Chu PY. 2015. Phylodynamic analysis of thecanine distemper virus hemagglutinin gene. BMC Vet Res 11:164.https://doi.org/10.1186/s12917-015-0491-9.9. Panzera Y, Sarute N, Iraola G, Hernández M, Pérez R. 2015. Molecularphylogeography of canine distemper virus: geographic origin and globalspreading. Mol Phylogenet Evol 92:147–154. https://doi.org/10.1016/j.ympev.2015.06.015.10. Martinez-Gutierrez M, Ruiz-Saenz J. 2016. Diversity of susceptible hostsin canine distemper virus infection: a systematic review and data syn-thesis. BMC Vet Res 12:78. https://doi.org/10.1186/s12917-016-0702-z.11. Harder TC, Osterhaus AD. 1997. Canine distemper virus—a morbillivirusin search of new hosts? Trends Microbiol 5:120 –124. https://doi.org/10.1016/S0966-842X(97)01010-X.12. von Messling V, Svitek N, Cattaneo R. 2006. Receptor (SLAM [CD150])recognition and the V protein sustain swift lymphocyte-based invasionof mucosal tissue and lymphatic organs by a morbillivirus. J Virol 80:6084 – 6092. https://doi.org/10.1128/JVI.00357-06.Loots et al.Volume 5 Issue 27 e00603-17 genomea.asm.org 2 on July 17, 2017 by guesthttp://genomea.asm.org/Downloaded from 

Genome Sequences of Three Vaccine Strains and Two Wild-Type Canine Distemper Virus Strains from a Recent Disease Outbreak in South Africa

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Genome Sequences of Three Vaccine Strains and Two Wild-Type Canine Distemper Virus Strains from a Recent Disease Outbreak in South Africa

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