DISPATCHESDistinct Lineages of Bufavirus inWild Shrews and Nonhuman PrimatesMichihito Sasaki, Yasuko Orba,Paulina D. Anindita, Akihiro Ishii, Keisuke Ueno, 1Bernard M. Hang’ombe, Aaron S. Mweene,Kimihito Ito, Hirofumi SawaViral metagenomic analysis identified a new parvovirus genomein the intestinal contents of wild shrews in Zambia.Related viruses were detected in spleen tissues from wildshrews and nonhuman primates. Phylogenetic analysesshowed that these viruses are related to human bufaviruses,highlighting the presence and genetic diversity of bufavirusesin wildlife.Bufavirus (BuV), a recently described parvovirus, wasinitially discovered in the feces of a child with diarrheain Burkina Faso in 2012 (1). Thereafter, BuV was identifiedin fecal samples from children and adults with gastroenteritisin Bhutan, Finland, and the Netherlands in 2014 (2–4),respectively. Genome sequences and phylogenetic analysesrevealed that BuV comprised at least 3 genotypes andwas distinct from all other known members of the Parvoviridaefamily (1,2). The International Committee on Taxonomyof Viruses assigned BuV as a new species of thegenus Protoparvovirus in the subfamily Parvovirinae (5).Whether BuV is an etiologic agent of human gastroenteritisremains unclear, but knowledge about its distribution andgenetic divergence in humans is accumulating. However,whether BuV infection exists in wildlife remains unanswered.Through use of metagenomics, we previously describedthe enteric virome of wild shrews of the Crociduragenus sampled at Mpulungu, Zambia, in 2012 (6). Fromthis sequence dataset (GenBank/EMBL/DDBJ accessionno. DRA002561), we identified sequence reads related toBuV. Here, we describe the genome of this new parvovirus.The StudyWe determined the nearly complete genome sequence ofBuV, which we named Mpulungu BuV (MpBuV), by fillinggenome gaps with primer walking and rapid amplificationof cDNA ends (GenBank/EMBL/DDBJ accession no.AB937988). The MpBuV genome comprises 4,613 nt andAuthor affiliations: Hokkaido University, Sapporo, Japan(M. Sasaki, Y. Orba, P.D. Anindita, A. Ishii, K. Ueno, K. Ito,H. Sawa); University of Zambia, Lusaka, Zambia(B.M. Hang’ombe, A.S. Mweene)DOI: http://dx.doi.org/10.3201/eid2107.141969encodes open reading frames of the nonstructural protein(NS) 1 and the viral capsid protein (VP) 1 and VP2 (onlineTechnical Appendix Figure, http://wwwnc.cdc.gov/EID/article/21/7/14-1969-Techapp1.<strong>pdf</strong>). blastp (http://blast.ncbi.nlm.nih.gov) searches showed that the MpBuV NS1,VP1, and VP2 proteins were closely related to those of humanBuVs and the WUHARV parvovirus (E-value = 0.0).WUHARV parvovirus, identified in rhesus monkeys experimentallyinfected with simian immunodeficiency virusunder laboratory conditions in the United States, was foundto be a closely related to human BuVs (7).In MpBuV, NS1 shares 52.5% aa identity with NS1of human BuV (GenBank accession no. JX027296). Wefound that the amino acid sequence identity of VP1 betweenMpBuV and human BuV is 52.3%, whereas that ofVP2 is 51.4%. Similar to human BuV, MpBuV showedpotential splicing signals in the VP1 coding region. Wealso identified the parvovirus-conserved amino acid motifsin NS1, VP1, and VP2 of MpBuV (online TechnicalAppendix Figure) (8–12). Phylogenetic analysis was performedas described previously (6). A Bayesian phylogenetictree was generated on the basis of the full-lengthNS1 proteins of MpBuV, human BuVs, and representativeparvoviruses. MpBuV clustered with human BuVsand WUHARV parvovirus (online Technical AppendixFigure). According to the species demarcation criteria ofthe International Committee on Taxonomy of Viruses,each parvovirus species encodes an NS1 protein sharing
Bufavirus in Wild Shrews and Nonhuman PrimatesTable. Sample information and nested PCR screening results for bufavirus, ZambiaAnimal,* species (common name) Location Year PCR positive/totalPrimatePapio cynocephalus (yellow baboon) Mfuwe 2009 2/50P. ursinus (Chacma baboon) Livingstone 2010–2011 1/50Chlorocebus pygerythrus (vervet monkey) Mfuwe 2009 0/50Livingstone 2010–2011 0/39ShrewCrocidura hirta (lesser red musk shrew) Livingstone 2011 0/2Mpulungu 2012 5/22Namwala 2012 0/2Mazabuka 2013 0/4Solwezi 2013 0/2C. luna (moonshine shrew) Mpulungu 2012 0/1Solwezi 2013 12/16RodentMastomys natalensis (African soft-furred rat) Livingstone 2011 0/35Mpulungu 2012 0/28Namwala 2012 0/29Mazabuka 2013 0/57Solwezi 2013 0/56Other species† Livingstone 2011 0/9Mpulungu 2012 0/20Namwala 2012 0/34Mazabuka 2013 0/16Solwezi 2013 0/14Total 20/536*For this analysis, the template DNA was prepared from the spleen tissues of the animals indicated.†Other species from the genera.Aethomys, Arvicanthis, Cricetomys, Gerbilliscus, Grammomys, Graphiurus, Lemniscomys, Mus, Paraxerus, Pelomys,Rattus, Saccostomus, and Steatomys.5′-GTTGGAGGTACACATGGATGAGGA-3′).We detected the MpBuV genome in 5 (22%) of the 23samples from the intestinal contents of individual shrewscaptured in Mpulungu. We then tested for the presence ofMpBuV in the lung, spleen, liver, and kidney tissues of theshrews that were PCR positive for MpBuV by screening ofintestinal contents. The MpBuV genome was detected in 5spleen and 4 liver samples from the 5 shrews.This discovery of MpBuV urged us to further investigateBuVs and related parvoviruses in wildlife. We designeddegenerate primers for nested PCR screening onthe basis of a multiple sequence alignment of the NS1 genefrom human BuV, WUHARV parvovirus and MpBuV asfollows: BuV-F1 (position 190–215 in MpBuV genome,5′-TCAAWRTMACCTGGAAAGACTACAGA-3′) andBuV-R1 (position 1503 1534, 5′-TCATTGGTTGTCAT-KAYWACTGGAGTTGGTTC-3′) for the first PCR round,and BuV-F2 (position 980–1006, containing an equimolarmixture of 5′-AGAAAAATGGATGCTCCAAGATCCA-GA-3′ and 5′-AGAAAAATGGATGCTTGGTGAWCCW-GA-3′) and BuV-R2 (position 1444 1465, 5′-ATTGCTTG-GCCACTCATGATKG-3′) for the second PCR round.PCRs were performed by using Tks Gflex DNA polymeraseand the annealing temperatures were set at 50°C and 55°Cfor the first and second PCR round, respectively.We screened 536 spleen tissue specimens from wildlife.The specimens from 3 nonhuman primate species,2 shrew species, and 14 rodent genera from 6 locationsin Zambia were used for different research projects, asreported previously (13,14). All our sampling activitieswere conducted with the permission of the Zambia WildlifeAuthority (Act No. 12 of 1998). We chose spleen tissuefor nested PCR screening because specimens of intestinalcontents were unavailable for almost all of the animals wesampled. As we described, MpBuV was detected in spleensamples in addition to samples of intestinal contents fromthe same animals.Nested PCR screening for BuVs detected MpBuVfrom 5 shrews in Mpulungu; these were the same animalsthat were PCR-positive for MpBuV by using a specificprimer set targeting MpBuV. Nested PCR was also positivein 3 primates and 12 shrews (Table). The PCR ampliconswith expected size (≈480 bp) were subjected to directsequence analysis. A Bayesian phylogenetic analysis wasperformed as described by using the partial nucleotide sequencesobtained for the NS1 gene with the exception ofthe primer sequences (434–440 bp) and the correspondinggenome regions of known protoparvoviruses and amdoviruses.The BuVs detected clustered with human BuVs andthe WUHARV parvovirus and are distinguishable fromother protoparvoviruses (Figure). The BuVs detected canbe divided into MpBuV and 3 other strains; we have tentativelynamed these Solwezi BuV, Mfuwe BuV, and LivingstoneBuV (Figure). Solwezi BuV, which shares 79%nt sequence identity with MpBuV, was identified in 12shrews (Crocidura luna) in Solwezi. Mfuwe BuV and LivingstoneBuV were identified in 2 yellow baboons (Papiocynocephalus) in Mfuwe and a chacma baboon (P. ursinus)Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 21, No. 7, July 2015 1231
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