Itou et al. BMC Res Notes (2016) 9:87 DOI 10.1186/s13104-016-1898-5 RESEARCH ARTICLE Molecular epidemiological tracing of a cattle rabies outbreak lasting less than a month in Rio Grande do Sul in southern Brazil Takuya Itou1*, Toshiharu Fukayama1, Nobuyuki Mochizuki1, Yuki Kobayashi1, Eduardo R. Deberaldini2, Adolorata A. B. Carvalho2, Fumio H. Ito3 and Takeo Sakai1 Abstract Background: Vampire bat-transmitted cattle rabies cases are typically encountered in areas where the disease is endemic. However, over the period of a month in 2009, an outbreak of cattle rabies occurred and then ended sponta- neously in a small area of the Rio Grande do Sul State in southern Brazil. To investigate the epidemiological character- istics of this rabies outbreak in Rio Grande do Sul, 26 nucleotide sequences of rabies virus (RABV) genomes that were collected in this area were analyzed phylogenetically. Results: Nucleotide sequence identities of the nucleoprotein gene and G–L intergenic region of the 26 RABVs were greater than 99.6 %. Phylogenetic analysis showed that all RABVs clustered with the vampire bat-related cattle RABV strains and that the RABVs were mainly distributed in southern Brazil. Conclusions: The findings of the present study suggested that a small population of rabid vampire bats carrying a single RABV strain produced a spatiotemporally restricted outbreak of cattle rabies in southern Brazil. Keywords: Brazil, Cattle rabies, Molecular epidemiology, Vampire bat © 2016 Itou et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/ zero/1.0/) applies to the data made available in this article, unless otherwise stated. Background Rabies is a fatal infectious disease that causes encephalo- myelitis. Genetic diversity among rabies viruses (RABVs) depends on the host species and its geographic distribu- tion. Rabies is endemic in Brazil, and RABVs have been isolated from a variety of mammalian hosts, including dogs, foxes, cats, cattle, and hematophagous, insectivo- rous and frugivorous bats [1–3]. Vampire bats, particu- larly Desmodus rotundus, are important vectors of rabies in Latin America. Rabies transmission from vampire bats to humans occurs frequently, primarily in the Amazonian regions of Brazil and Peru, and cattle rabies transmitted by vampire bats is also common in Brazil [4]. Vampire bat-related rabies is thus a serious problem from both animal and public health standpoints. Molecular and geographic epidemiological analyses of livestock rabies in northeastern, central and southeastern Brazil revealed that RABVs isolated from livestock were closely related to the virus strains found in vampire bat populations, and that the RABVs in these areas were sta- ble within a spatiotemporal context [5]. However, rela- tively little information currently exists on the molecular epidemiology of RABVs isolated from livestock in south- ern Brazil. The incidence of vampire bat-transmitted cattle rabies cases is typically restricted to areas where the disease is endemic [5–7]. However, between February and March 2009, an outbreak of cattle rabies occurred and ended spontaneously in a small region of Rio Grande do Sul State (RS) in southern Brazil. To investigate the epidemi- ological characteristics of this rabies outbreak in RS, the RABVs obtained in this area were subjected to phyloge- netic analysis. Open Access BMC Research Notes *Correspondence: itou.takuya@nihon-u.ac.jp 1 Nihon University Veterinary Research Center, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan Full list of author information is available at the end of the article http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/publicdomain/zero/1.0/ http://creativecommons.org/publicdomain/zero/1.0/ http://crossmark.crossref.org/dialog/?doi=10.1186/s13104-016-1898-5&domain=pdf Page 2 of 5Itou et al. BMC Res Notes (2016) 9:87 Methods An outbreak of cattle rabies occurred in a hilly area (<5  km radius) in the city of Nova Roma do Sul in Rio Grande do Sul State, southern Brazil (Fig.  1). This out- break occurred on a total of 19 cattle farms between February and March 2009, and ended spontaneously without any mitigation measures being implemented. Outbreaks of cattle rabies in this region had not been observed for at least 3 years before or after this outbreak. Brain specimens from these livestock were diagnosed as RABV-positive by an immunofluorescent antibody test and viral RNA was extracted from the brains of livestock using the QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany). Nucleoprotein (N) gene sequences from the Brazilian RABV samples were amplified by RT-PCR and determined using applied biosystems 3130 genetic ana- lyzer (ABI) using primers described previously [8, 9]. Information of primers used for RT-PCR and sequencing are shown in Additional file 1: Table S1. Multiple align- ment for the datasets of N and G–L genes were made by MAFFT program [10]. Neighbor-joining tree of N gene with 1000 bootstrap replicates was constructed with the p-distance using MEGA ver 6.10 [11]. The nucleotide sequences retrieved from GenBank to construct the phy- logenetic tree are listed in Additional file 2: Table S2. The geographic origins of the RABV sequences obtained from the Brazilian livestock were plotted at the municipal level in the federal states in which infection was observed using MapInfo Professional GIS software (ver. 8.0, MapInfo Japan K.K., Tokyo, Japan) and Google Earth (ver.6.0, Google, Mountain View, CA, USA). Bra- zilian maps were obtained from Brasil em Relevo— Embrapa Monitoramento por Satélite [12]. Results A total of 26 RNA samples were extracted from brains of rabid cattle from the 19 farms surveyed in this study (Fig.  1; Table  1). The PCR amplified sequences of the 1424-nt N-mRNA region and 578-nt G–L region were determined for all 26 RABV samples [GenBank: AB685222–AB685247 and LC057591–LC057616] (Table  1). The results from N gene sequences showed that, with the exception of BRbv1289, the nucleotide and amino acid sequence identities of the RS RABVs were 100 %. Between BRbv1285, which was selected among the 25 identical RABV RNAs as the representative sequence, and BRbv1289, nucleotide and amino acid sequence identities were more than 99.9 and 100  %, respectively. To validate the genomic homogeneity among the RABV samples, the variable G–L intergenic 578-bp region (position: 4929–5514 of PV) was additionally analyzed. The nucleotide sequence identity was more than 99.6 % among all 26 RABVs, showing the quite high homogene- ity of epidemic RABVs in this outbreak. Phylogenetic analysis based on a partial N sequence (position: 203–1420 of PV) revealed that 26 RABV samples formed a monophyletic cluster in vampire bat- related RABV lineage (Fig.  2). Comparison with RABVs obtained from neighboring countries, indicated that these 26 RABVs formed a sub-cluster with RABVs col- lected in the states of Sao Paulo (SP) and Rio de Janeiro (RJ) in Brazil. In addition to this sub-cluster, there are two another sub-clusters consisted of RABV samples collected in the state of SP and neighboring areas. These lineages were named the lineages of RD1, RD2/3, and Old strains by Carnieli et al. [13]. RS strains belonged to the lineage of Old strains and shared a common ances- tor with RD1 lineage. RABVs in RD1 and RD2/3 line- ages were distributed in mountain range located in the boundary of the states of SP, Minas Gerais, and RJ, while Old strains were isolated from towns in the interior of the state of SP [13]. Using a 203-bp segment (position: 109–311 of PV) of the N gene, Kobayashi et al. reported the existence of at least 24 RABV genetic variants among the vampire bat- transmitted rabies cases in cattle in Brazil [5]. Using the same 203-bp segment, our analysis revealed that the 26 RS RABVs of the present study correlate with the C-19 lineage described by Kobayashi et  al. [5] (Additional file 3: Figure S1). Samples belonging to the C-19 lineage were distributed in the states of RS, Goiás, Mato Grosso do Sul, SP and RJ, which are the southeastern regions of Brazil [5]. Discussion Nucleoprotein gene and G–L intergenic segments from the 26 RABV samples collected in early spring of 2009 from separate farms in a restricted region of Nova Roma do Sul, RS, were sequenced and subjected to phylogenetic analysis. The genetic analysis revealed that the nucleotide and amino acid sequences were almost identical among the 26 RABVs and shared a common ancestor, suggesting the RABV strain was transmitted from a small population of rabid vampire bats infected with RABV, which may be derived from a single introduction, to a cattle population grazing in Nova Roma do Sul. Generally, vampire bat-transmitted RABVs were restricted to specific geographic areas because of the vampire bat ecology. The phylogenetic analysis described here revealed that all of the livestock RABVs in RS were derived from vampire bat rabies. Although we were una- ble to investigate the prevalence of rabid vampire bats in this area, the findings of the present study revealed that the 26 RABVs correspond with the “Old strains” lineage Page 3 of 5Itou et al. BMC Res Notes (2016) 9:87 reported by Carnieli Jr et al. and C-19 lineage identified by Kobayashi et al. [5, 13]. The distribution of RABV line- ages in Brazil is known to be delimited by geomorpholog- ical boundaries, such as mountain ranges and rivers [14]. The reason why the C-19 lineage consists of RABVs from Brazil and none from Argentina may be thus because a very large river, the Uruguay River, separates the Brazil and Argentina. However, the C-19 lineage is distributed over larger areas. Since the “Old strains” lineage, which was made up basically of the isolates collected before Uruguay Argen�na SP RS Brazil RJ MGMS GO 3 km Nova Roma do Sul Fig. 1 Location of farms infected with cattle rabies in Nova Roma do Sul, the state of Rio Grande do Sul (RS). Numbers on the map correspond with the site numbers given in Table 1. Star-shaped symbols indicate the states, where RABVs belonging to C-19 lineage were distributed [5]. Abbrevia- tion states in Brazil are as follows: GO Goiás; MG Minas Gerais; MS Mato Grosso do Sul; RJ Rio de Janeiro; SP São Paulo Page 4 of 5Itou et al. BMC Res Notes (2016) 9:87 1998, has been endemic in the state of SP before epizo- otic of RD2/RD3 were observed [13], suggesting that RABVs in Old strains lineages may have gradually spread in southern Brazil, including the state of RS. The typical distribution range of D. rotundas activ- ity around a roost is about 10 km2 [15]; the range of this outbreak was approximately 80 km2. In extensive random surveys conducted in Trinidad and Brazil, the prevalence of the virus among vampire bats in the field was 0.46– 0.75 % (see Baer) [16]. Further, no rabies outbreaks have been reported in the past 3 years in this region, and the outbreak ended without any specific prevention meas- ures being implemented for cattle rabies. Although the non-migratory, vampire bats have distribution ranges of between 10 and 20 km2 [17], it has been suggested that the vampire bats may need to fly over longer distances to feed and that they share roosts with other bat species; indeed, this may explain how the RABV could spread over a short period of time [18]. However, the cattle rabies cases described in the present study ended sud- denly over the period of a month. There are several pos- sible reasons why the activities of the vampire bats may have been limited and why this outbreak of cattle rabies ended suddenly. The affected area was geographically iso- lated by a river valley that may have limited the feeding activities and distribution of the bats. It is also possible that the size of the vampire bat population in the region may have been too small to act as reservoir for RABV. Taken together, it is considered that this outbreak was caused by small population of vampire bats that were vectors of the RABV lineage that is distributed mainly in southern Brazil. It is considered that the relatively Table 1 Rabies virus samples obtained from  the Rio Grande do Sul a No information b Numbers correspond to those in Fig. 1 Sample name Date of sampling Site of occur- renceb GenBank accession # N gene G–L intergenic BRbv1285 28/02/2009 1 AB685222 LC057591 BRbv1286 08/03/2009 2 AB685223 LC057592 BRbv1287 18/03/2009 3 AB685224 LC057593 BRbv1288 28/02 2009 4 AB685225 LC057594 BRbv1289 28/02/2009 5 AB685226 LC057595 BRbv1290 28/02/2009 6 AB685227 LC057596 BRbv1291 23/02/2009 1 AB685228 LC057597 BRbv1292 11/03/2009 7 AB685229 LC057598 BRbv1293 13/03/2009 8 AB685230 LC057599 BRbv1294 06/03/2009 6 AB685231 LC057600 BRbv1297 08/03/2009 9 AB685232 LC057601 BRbv1298 09/03/2009 10 AB685233 LC057602 BRbv1299 12/03/2009 1 AB685234 LC057603 BRbv1301 18/02/2009 11 AB685235 LC057604 BRbv1302 13/03/2009 12 AB685236 LC057605 BRbv1303 18/03/2009 3 AB685237 LC057606 BRbv1304 18/03/2009 13 AB685238 LC057607 BRbv1305 23/02/2009 2 AB685239 LC057608 BRbv1306 –a 14 AB685240 LC057609 BRbv1307 12/03/2009 15 AB685241 LC057610 BRbv1308 27/02/2009 16 AB685242 LC057611 BRbv1309 02/03/2009 17 AB685243 LC057612 BRbv1310 23/02/2009 18 AB685244 LC057613 BRbv1311 25/02/2009 19 AB685245 LC057614 BRbv1312 28/02/2009 5 AB685246 LC057615 BRbv1313 04/03/2009 9 AB685247 LC057616 BRbv1289 BRbv1285(25) T. brasiliensis USA 0.005 Brazil PB, PE Brazil GO Brazil SP (RD1) Brazil SP(Old strains), RJ, RS Argen�na Argen�na Brazil MT Uruguay Brazil SP(RD2/3), MG Colombia Fig. 2 Phylogenetic tree based on a partial N gene sequence (corre- sponding to 203–1420 nts of PV strain) of RABV samples from south- ern Brazil and surrounding countries. Black and gray circles indicate the interior branches with bootstrap values >90 and 90–70 %, respec- tively. RABV samples in RS were indicated by red text. The numbers in parenthesis show the number of other strains with 100 % identical sequence to the indicated strain. Abbreviation states in Brazil are as follows: GO Goiás; MG Minas Gerais; MT Mato Grosso; PB Paraiba; PE Pernambico; RJ Rio de Janeiro; SP São Paulo. RABV sequence from Tadarida brasiliensis was used as outgroup Page 5 of 5Itou et al. BMC Res Notes (2016) 9:87 restricted range of bats contributed to the sudden end of the outbreak before it could spread to other regions. Conclusions Segments of N gene and G–L intergenic region sequences from 26 RABV samples that were collected in early spring from separate farms in small region of Nova Roma do Sul, Rio Grande do Sul, in 2009, were subjected to phylogenetic analysis. The N gene and G–L region sequence analysis revealed that the 26 RABVs had almost identical nucleotide and amino acid sequences. The out- break was likely caused by a small population of vampire bats that were infected with a single strain of the RABV lineage found mainly in southern Brazil that invaded the area of the study site. Abbreviation RABV: rabies virus. Authors’ contributions ERD and AASBC collected epidemiological samples and information in the field. TI, TF and NM drafted the manuscript. TF conducted the RT-PCR and sequencing analyses. TI, NM, YK, FHI and TS contributed to study design, management, coordination, and drafting of the manuscript. All authors read and approved the final manuscript. Author details 1 Nihon University Veterinary Research Center, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan. 2 Department of Preventive Veterinary Medicine, Faculty of Agriculture and Veterinary Science, UNESP, Via de Acesso Prof. Paulo Donato Castellane, Jaboticabal, Sao Paulo 14884-900, Brazil. 3 Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Zootechny, University of São Paulo, Av. Prof. Dr. Orlando Marques de paiva, 87, Cidade Universtiátria, Sao Paulo, São Paulo 05508-000, Brazil. Acknowledgements This study was supported in part by a Grant-in-Aid for Scientific Research (24580453) from the Japan Society for the Promotion of Science and the Strategic Research Base Development Program, “International joint research and training of young researchers for zoonosis control in a globalized world”, and a matching fund subsidy from the Ministry of Education, Culture, Sports, Science and Technology of Japan (S0991023 and S1491007). Additional files Additional file 1. Primers used for RT-PCR and sequencing. Additional file 2. Nucleotide sequences RABV N gene retrieved from GenBank. Additional file 3. Phylogenetic tree based on nucleoprotein gene 203 nts (corresponding 107–311 nts of PV strain) using Brazilian RABV isolates. The 24 lineages classified by Kobayashi et al. [5] and RS RABV samples in this study were compared. All RS samples belonged to C-19 lineage main- tained in Southwestern Brazil. The symbols for each lineage correspond to the results by Kobayashi et al. [5]. Competing interests The authors declare that they have no competing interests. Received: 5 August 2015 Accepted: 2 February 2016 References 1. Ito M, Arai YT, Itou T, Sakai T, Ito FH, Takasaki T, Kurane I. Genetic characterization and geographic distribution of rabies virus isolates in Brazil: identification of two reservoirs, dogs and vampire bats. Virology. 2001;284:214–22. 2. Sato G, Kobayashi Y, Shoji Y, Sato T, Itou T, Ito FH, Santos HP, Brito CJ, Sakai T. Molecular epidemiology of rabies from Maranhão and surrounding states in the northeastern region of Brazil. Arch Virol. 2006;151:2243–51. 3. Kobayashi Y, Sato G, Kato M, Itou T, Cunha EM, Silva MV, Mota CS, Ito FH, Sakai T. Genetic diversity of bat rabies viruses in Brazil. Arch Virol. 2007;152:1995–2004. 4. Kobayashi Y, Ogawa A, Sato G, Sato T, Itou T, Samara SI, Carvalho AA, Nociti DP, Ito FH, Sakai T. Geographical distribution of vampire bat-related cattle rabies in Brazil. J Vet Med Sci. 2006;68:1097–100. 5. Kobayashi Y, Sato G, Mochizuki N, Hirano S, Itou T, Carvalho AA, Albas A, Santos HP, Ito FH, Sakai T. Molecular and geographic analyses of vampire bat-transmitted cattle rabies in central Brazil. BMC Vet Res. 2008;4:44. 6. Condori-Condori RE, Streicker DG, Cabezas-Sanchez C, Velasco-Villa A. Enzootic and epizootic rabies associated with vampire bats, peru. Emerg Infect Dis. 2013;19(9):1463–9. 7. Torres C, Lema C, Dohmen FG, Beltran F, Novaro L, Russo S, Freire MC, Velasco-Villa A, Mbayed VA, Cisterna DM. Phylodynamics of vampire bat- transmitted rabies in Argentina. Mol Ecol. 2014;23:2340–52. 8. Hirano S, Itou T, Carvalho AA, Ito FH, Sakai T. Epidemiology of vampire bat-transmitted rabies virus in Goiás, central Brazil: re-evaluation based on G–L intergenic region. BMC Res Notes. 2012;3:288. 9. Mochizuki N, Kobayashi Y, Sato G, Hirano S, Itou T, Ito FH, Sakai T. Deter- mination and molecular analysis of the complete genome sequence of two wild-type rabies viruses isolated from a haematophagous bat and a frugivorous bat in Brazil. J Vet Med Sci. 2011;73:759–66. 10. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. 11. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9. 12. Brasil em Relevo—Embrapa Monitoramento por Satélite http://www. relevobr.cnpm.embrapa.br/. Accessed 13 May 2015. 13. Carnieli P Jr, Castilho JG, Fahl Wde O, Véras NM, Timenetsky Mdo C. Genetic characterization of rabies virus isolated from cattle between 1997 and 2002 in an epizootic area in the state of São Paulo, Brazil. Virus Res. 2009;144:215–24. 14. Mochizuki N, Kawasaki H, Silva ML, Afonso JA, Itou T, Ito FH, Sakai T. Molecular epidemiology of livestock rabies viruses isolated in the north- eastern Brazilian states of Paraíba and Pernambuco from 2003–2009. BMC Res Notes. 2012;5:32. 15. Arellano-Sota C. Biology, ecology, and control of the vampire bat. Rev Infect Dis. 1988;10(Suppl 4):S615–9. 16. Baer GM. Vampire bat and bovine paralytic rabies. In: Baer GM, editor. Natural History of Rabies. 2nd ed. Boston: CRC Press; 1991. p. 389–403. 17. Lord RD. Seasonal reproduction of vampire bats and its relation to sea- sonality of bovine rabies. J Wildl Dis. 1992;28:292–4. 18. Romijn PC, van der Heide R, Cattaneo CA, Silva Rde C, van der Poel WH. Study of lyssaviruses of bat origin as a source of rabies for other animal species in the State of Rio De Janeiro, Brazil. Am J Trop Med Hyg. 2003;69:81–6. http://dx.doi.org/10.1186/s13104-016-1898-5 http://dx.doi.org/10.1186/s13104-016-1898-5 http://dx.doi.org/10.1186/s13104-016-1898-5 http://www.relevobr.cnpm.embrapa.br/ http://www.relevobr.cnpm.embrapa.br/ Molecular epidemiological tracing of a cattle rabies outbreak lasting less than a month in Rio Grande do Sul in southern Brazil Abstract Background: Results: Conclusions: Background Methods Results Discussion Conclusions Authors’ contributions References