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BMC Research Notes

Open Access

Molecular epidemiological tracing of a cattle rabies outbreak lasting less than a month in Rio Grande do Sul in southern Brazil

  • Takuya Itou1Email author,
  • Toshiharu Fukayama1,
  • Nobuyuki Mochizuki1,
  • Yuki Kobayashi1,
  • Eduardo R. Deberaldini2,
  • Adolorata A. B. Carvalho2,
  • Fumio H. Ito3 and
  • Takeo Sakai1
BMC Research Notes20169:87

https://doi.org/10.1186/s13104-016-1898-5

Received: 5 August 2015

Accepted: 2 February 2016

Published: 12 February 2016

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 spontaneously in a small area of the Rio Grande do Sul State in southern Brazil. To investigate the epidemiological characteristics 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

BrazilCattle rabiesMolecular epidemiologyVampire bat

Background

Rabies is a fatal infectious disease that causes encephalomyelitis. Genetic diversity among rabies viruses (RABVs) depends on the host species and its geographic distribution. Rabies is endemic in Brazil, and RABVs have been isolated from a variety of mammalian hosts, including dogs, foxes, cats, cattle, and hematophagous, insectivorous and frugivorous bats [13]. Vampire bats, particularly 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 stable within a spatiotemporal context [5]. However, relatively little information currently exists on the molecular epidemiology of RABVs isolated from livestock in southern Brazil.

The incidence of vampire bat-transmitted cattle rabies cases is typically restricted to areas where the disease is endemic [57]. 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 epidemiological characteristics of this rabies outbreak in RS, the RABVs obtained in this area were subjected to phylogenetic analysis.

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 outbreak 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 analyzer (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 alignment 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 phylogenetic tree are listed in Additional file 2: Table S2.
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]. Abbreviation states in Brazil are as follows: GO Goiás; MG Minas Gerais; MS Mato Grosso do Sul; RJ Rio de Janeiro; SP São Paulo

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). Brazilian 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 homogeneity of epidemic RABVs in this outbreak.
Table 1

Rabies virus samples obtained from the Rio Grande do Sul

Sample name

Date of sampling

Site of occurrenceb

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

aNo information

bNumbers correspond to those in Fig. 1

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 collected 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 ancestor with RD1 lineage. RABVs in RD1 and RD2/3 lineages 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].
Fig. 2

Phylogenetic tree based on a partial N gene sequence (corresponding to 203–1420 nts of PV strain) of RABV samples from southern Brazil and surrounding countries. Black and gray circles indicate the interior branches with bootstrap values >90 and 90–70 %, respectively. 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

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 unable 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 reported by Carnieli Jr et al. and C-19 lineage identified by Kobayashi et al. [5, 13]. The distribution of RABV lineages in Brazil is known to be delimited by geomorphological 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 1998, has been endemic in the state of SP before epizootic 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 activity 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 measures 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 suddenly over the period of a month. There are several possible 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 isolated 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 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 outbreak 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

Declarations

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.

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).

Competing interests

The authors declare that they have no competing interests.

Open AccessThis 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.

Authors’ Affiliations

(1)
Nihon University Veterinary Research Center, Nihon University
(2)
Department of Preventive Veterinary Medicine, Faculty of Agriculture and Veterinary Science, UNESP
(3)
Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Zootechny, University of São Paulo

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Copyright

© Itou et al. 2016

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