Skip to main content

Bat Astrovirus in Mozambique


Astroviruses (AstVs) are responsible for infection of a large diversity of mammalian and avian species, including bats, aquatic birds, livestock and humans. We investigated AstVs circulation in bats in Mozambique and Mayotte, a small island in the Comoros Archipelago located between east Africa and Madagascar. Biological material was collected from 338 bats and tested for the presence of the AstV RNA-dependent RNA-polymerase gene with a pan-AstV semi-nested polymerase chain reaction assay. None of the 79 samples obtained from Mayotte bats (Pteropus seychellensis comorensis and Chaerephon pusillus) tested positive; however, 20.1% of bats sampled in Mozambique shed AstVs at the time of sampling and significant interspecific variation in the proportion of positive bats was detected. Many AstVs sequences obtained from a given bat species clustered in different phylogenetic lineages, while others seem to reflect some level of host-virus association, but also with AstVs previously reported from Malagasy bats. Our findings support active circulation of a large diversity of AstVs in bats in the western Indian Ocean islands, including the southeastern African coast, and highlight the need for more detailed assessment of its risk of zoonotic transmission to human populations.

Astroviruses (AstVs) are small non-enveloped RNA viruses, transmitted via the fecal-oral route. They have been detected from over 80 vertebrate host species [1], and represent a significant source of morbidity and economic losses. Worldwide, AstVs account for 2 to 9% of all acute non-bacterial gastroenteritis in children [2]; they are also responsible for diseases in livestock, poultry and domestic pets [3]. In wild animals, AstVs have been mostly detected in bats [4] and in aquatic birds [5], although detection in other host types have been reported, such as in marine mammals [6] and non-human primates [7].

Current knowledge on the epidemiology of AstVs in African bats is limited [8, 9]. In a previous study, we detected high genetic diversity of AstVs in Malagasy bats [10]. Detection of AstVs on other islands of the western Indian Ocean has not been reported. The goal of this study was to investigate AstV circulation in bats in Mozambique and on Mayotte, a small island in the Comoros archipelago located between east Africa and Madagascar.

Biological material was collected on Mayotte at several locations (Bandrele, Chiconi, Coconi, Kwale, Mangajou, Passamainty, Sohoabe, Tsoundzou), in November–December 2014, and in Mozambique (Inhassoro district) in February and May 2015. Bats were captured using mist nets and harp traps. On Mayotte, rectal swabs were obtained with sterile rayon-tipped applicators (Puritan, Guilford, ME, USA) from 21 Pteropus seychellensis comorensis, and droppings were collected from 58 Chaerephon pusillus. Swabs and droppings were placed in 1.5 mL of Virus Transport Media (VTM; [10]), and were immediately frozen in liquid nitrogen. In Mozambique, one rectal and one buccal swab were collected for each sampled bat. The two swabs were then placed in the same tube, containing 1.5 mL of VTM, and were immediately frozen in liquid nitrogen. Sampled bat species and number of tested samples are presented in Table 1.

Table 1 Family, species day roosts, and number of bats sampled and tested for the presence of Astroviruses, in Mozambique

RNA extraction was performed with the QIAamp Viral RNA Mini Kit (QIAGEN, Valencia, CA, USA). Reverse transcription was performed on 10 μL of RNA using the ProtoScript II Reverse Transcriptase and Random Primer 6 (New England BioLabs, Ipswich, MA, USA) using a previously published protocol [10]. cDNAs were tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene using a pan-AstV semi-nested polymerase chain reaction (PCR) assay [10, 11]. PCRs were performed with the GoTaq G2 Hot Start Green Master Mix (Promega, Madison, WI, USA) in an Applied Biosystems 2720 Thermal Cycler (Thermo Fisher Scientific, Waltham, MA, USA). Electrophoresis were performed on 1.5% agarose gels stained with 2% GelRed (Biotium, Hayward, CA, USA). Chi square tests were conducted to investigate the effect of the host species, sampling period (month), and sex, on the probability of successful detection of AstV RdRp genes. Statistical analyses were conducted with R, version 3.2.3 [12].

PCR products of the expected size were submitted for direct Sanger sequencing (Genoscreen, Lille, France). The 31 sequences obtained in this study were aligned with 112 reference AstV RdRp partial nucleotide sequences, with CLC Sequence Viewer version 7.7.1 (CLC Bio, Aarhus, Denmark). A maximum-likelihood analysis was performed Phylogenetic trees were constructed by maximum likelihood with the software PhyML 3.1 [13]. The evolutionary model was selected by Model Generator 0.85 (GTR + I + Г, I = 0.10, α = 0.71; [14]), and nodal supports were assessed with 1000 bootstrap replicates. A Bayesian Markov Chain Monte Carlo coalescent analysis was also performed, with the program BEAST, version 1.8.4 [15], and the Shapiro-Rambaut-Drummond-2006 (SRD06) nucleotide substitution model [16]. A strict molecular clock and a constant population size were selected. The analysis was performed with a chain length of 60 million generations sampled every 1000 iterations, with first 10% trees discarded as burn-in. The maximum clade credibility tree was visualized with FigTree, version 1.4.3 (

None of the 79 samples collected on Mayotte tested positive for the presence of AstV. Although this negative result may be affected by the relatively small sample size and differences in sampling protocols (swabs vs droppings), it may also suggest temporal variation in AstVs shedding and circulation in bat populations, as previously documented [17]. Additional studies are thus needed before concluding that AstVs do not circulate in Mayotte bats.

In Mozambique, 52 of the 259 bats tested positive for the presence of AstV RdRp (mean detection rate ± 95% confidence interval: 20.1% ± 4.9%). This detection rate was similar to other studies using the same PCR assay, including the one we reported on Malagasy bats (22.5% ± 6.1%; [10]). For the Mozambique samples, five of the ten bat species tested positive (Table 1 and Additional file 1 for details), with significant variation between species (χ2 = 104, P < 0.001). A high detection rate was found in Triaenops afer (68.6% ± 12.7%), as compared to other species (Table 1). Significant variation was also found between the two sampling sessions (χ2 = 9, P < 0.005) with a higher detection rate in May (25.3% ± 6.5%) than in February (10.1% ± 6.3%), in particular for T. afer (χ2 = 13, P < 0.001; 20% ± 24.7% in February, and 80.5% ± 12.1% in May). This variation may be associated with factors related with bat population dynamics facilitating or limiting virus transmission (e.g. population size, density, age structure, body condition [18, 19]). No significant difference was found in AstV detection rate between males and females (χ2 = 0.4, P < 0.5).

High genetic diversity was detected among AstVs sequences obtained from Mozambican bats (pairwise distance up to 45%), without strong support for host family or species restriction (Fig. 1 and Additional file 2 for details), as commonly described for bat AstVs [8, 10, 11, 20, 21]. Most of the detected viruses clustered in large phylogenetic lineages, in particular for Triaenops afer and Hipposideros caffer, although statistical support was limited. Sequences of AstVs detected in Nycteris thebaica and Mops condylurus were mostly highly divergent and not included in larger genetic lineages comprising viruses of same bat family or the same geographic area (Fig. 1).

Fig. 1
figure 1

Maximum Likelihood (ML) consensus tree derived from 143 Astrovirus (AstV) RNA-dependent RNA-polymerase partial nucleotide sequences (380 bp). Colored circles indicate nodes with bootstrap values > 70 in the ML tree, or posterior probabilities higher than 0.7 in the maximum clade credibility tree. Sequence names in bold indicate bat AstVs detected in this study, and were colored according to the bat family. Scale bar indicates mean number of nucleotide substitutions per site

The limited genetic information available for AstVs in public databases [1], as well as the high saturation of their genome [22], considerably affects the resolution of phylogenetic trees. Current understanding of the long-time evolutionary history of Astroviridae therefore remains limited. In addition, ecological factors involved in AstV infection in bats need to be better assessed. High temporal dynamics of viral infection has been documented before [17], and the risk of spillover to other hosts, including humans, has also been demonstrated to coincide with changes in bat behavior and population structure [23]. The high propensity of AstVs for host shifts highlight the need for a better assessment of zoonotic transmission risk to human populations, particularly in relationship to some unique aspects of bat immunology and ecology.





Polymerase chain reaction


RNA-dependent RNA-polymerase


Virus Transport Media


  1. Mendenhall IH, Smith GJD, Dhanasekaran V. Ecological drivers of virus evolution: Astrovirus as a case study. J Virol. 2015;89:6978–81.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Bosch A, Pinto RM, Guix S. Human Astroviruses. Clin Microbiol Rev. 2014;27:1048–74.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. De Benedictis P, Schultz-Cherry S, Burnham A, Cattoli G. Astrovirus infections in humans and animals - molecular biology, genetic diversity, and interspecies transmissions. Infect. Genet. Evol. 2011;11:1529–44.

    Article  PubMed  CAS  Google Scholar 

  4. Fischer K, dos Reis VP, Balkema-buschmann A. Bat Astroviruses: towards understanding the transmission dynamics of a neglected virus family. Viruses. 2017;9:34.

    Article  PubMed Central  Google Scholar 

  5. Chu DKW, Leung CYH, Perera HKK, Ng EM, Gilbert M, Joyner PH, et al. A novel group of avian astroviruses in wild aquatic birds. J Virol. 2012;86:13772–8.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Rivera R, Nollens HH, Venn-Watson S, Gulland FMD, Wellehan JFX. Characterization of phylogenetically diverse astroviruses of marine mammals. J Gen Virol. 2010;91:166–73.

    Article  PubMed  CAS  Google Scholar 

  7. Karlsson EA, Small CT, Freiden P, Feeroz MM, Matsen FA, San S, et al. Non-human primates harbor diverse mammalian and avian Astroviruses including those associated with human infections. PLoS Pathog. 2015;11:e1005225.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Rougeron V, Suquet E, Maganda GD, Jiolle D, Mombo IM, Bourgarel M, et al. Characterization and phylogenetic analysis of new bat astroviruses detected in Gabon, Central Africa. Acta Virol. 2016;60:386–92.

    Article  PubMed  CAS  Google Scholar 

  9. Waruhiu C, Ommeh S, Obanda V, Agwanda B, Gakuya F, Ge XY, et al. Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses. Virol Sin. 2017;32:101–14.

    Article  PubMed  CAS  Google Scholar 

  10. Lebarbenchon C, Ramasindrazana B, Joffrin L, Bos S, Lagadec E, Le MG, et al. Astroviruses in bats, Madagascar. Emerg Microbes Infect. 2017;6:e58.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Chu DKW, Poon LLM, Guan Y, Peiris JSM. Novel astroviruses in insectivorous bats. J Virol. 2008;82:9107–14.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. R Core Team R. A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2015.

    Google Scholar 

  13. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.

    Article  PubMed  CAS  Google Scholar 

  14. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 2006;6:29.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007;7:214.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Shapiro B, Rambaut A, Drummond AJ. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 2006;23:7–9.

    Article  PubMed  CAS  Google Scholar 

  17. Drexler JF, Corman VM, Wegner T, Tateno AF, Zerbinati RM, Gloza-Rausch F, et al. Amplification of emerging viruses in a bat colony. Emerg Infect Dis. 2011;17:449–56.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Seltmann A, Corman V, Rasche A, Drosten C, Czirjak G, Bernard H, et al. Seasonal fluctuations of Astrovirus, but not coronavirus shedding in bats inhabiting human-modified tropical forests. EcoHealth. 2017;14:272–84.

    Article  PubMed  Google Scholar 

  19. Mendenhall IH, Skiles MM, Neves ES, Borthwick SA, Low DHW, Liang B, et al. Influence of age and body condition on astrovirus infection of bats in Singapore: an evolutionary and epidemiological analysis. One Heal. 2017;4:27–33.

    Article  Google Scholar 

  20. Kemenesi G, Dallos B, Gorfol T, Boldogh S, Estok P, Kurucz K, et al. Molecular survey of RNA viruses in hungarian bats: discovering novel astroviruses, coronaviruses, and caliciviruses. Vector Borne Zoonotic Dis. 2014;14:846–55.

    Article  PubMed  Google Scholar 

  21. Lacroix A, Duong V, Hul V, San S, Davun H, Omaliss K, et al. Diversity of bat astroviruses in Lao PDR and Cambodia. Infect. Genet. Evol. 2017;47:41–50.

    Article  PubMed  CAS  Google Scholar 

  22. Lukashov VV, Goudsmit J. Evolutionary relationships among Astroviridae. J. Gen. Virol. 2002;83:1397–405.

    Article  PubMed  CAS  Google Scholar 

  23. Plowright RK, Foley P, Field HE, Dobson AP, Foley JE, Eby P, et al. Urban habituation, ecological connectivity and epidemic dampening: the emergence of Hendra virus from flying foxes (Pteropus spp.). Proc Biol Sci. 2011;278:3703–12.

    Article  PubMed  PubMed Central  Google Scholar 

Download references


We thank Koussay Dellagi and Hervé Pascalis for the development and the management of the ‘partenariat Mozambique-Réunion dans la recherche en santé: pour une approche intégrée d’étude des maladies infectieuses à risque épidémique (MoZaR)’ research program.


Field research was funded by the ‘Partenariat Mozambique-Réunion dans la recherche en santé: pour une approche intégrée d’étude des maladies infectieuses à risque épidémique (MoZaR)’ (Fond Européen de Développement Régional, Programme Opérationnel de Coopération Territoriale) and by the ‘Centre National de la Recherche Scientifique’ (Projets Exploratoires Premier Soutien BATMAN). Molecular analyses were funded by tutorship institutions of the UMR PIMIT. LJ is supported by a ‘Région Réunion, European Regional Development Funds (FEDER 2014-2020)’ PhD fellowship. BR’s post-doctoral fellowship was supported by the ‘Run Emerge’ European Union’s Seventh Framework Program (FP7/2007–2013; Grant agreement NO 263958), the ‘Fonds de Coopération Régionale, Prefecture de La Réunion’ and The Field Museum of Natural History, Chicago, through the Ralph and Marian Falk Medical Research Trust. CL is supported by a ‘Chaire mixte: Université de La Réunion – INSERM’. The funding agencies did not have any involvement in the study design, implementation or publishing of this study, and the research presented herein represents the opinions of the authors but not necessarily the opinions of the funding agencies.

Availability of data and materials

Sequences generated in this study have been deposited in GenBank under the accession numbers MH013965 to MH013995.

Author information

Authors and Affiliations



CL conceived and designed the study. EL, GLM, and BR collected biological material on Mayotte. SMG, GLM, ADS, and MCS collected biological material in Mozambique. FH and LJ performed the molecular analyses. FH and CL analyzed the data and wrote the paper. ESG and PM contributed to the project management between French and Mozambican institutions and to the first draft of the paper. All authors edited, read, and approved the final manuscript.

Corresponding author

Correspondence to Camille Lebarbenchon.

Ethics declarations

Ethics approval

All procedures have been evaluated and approved by an ethic committee (Agreement number A974 001; Comité d’éthique du CYROI number 114; Cyclotron Reunion Océan Indien, Sainte Clotilde, Reunion Island), and authorized by the French Ministry of Education and Research (Reference numbers 03584.01 and APAFIS#2638-2015110616208322v1). On Mayotte, research permits were issued by the ‘Direction de l’Environnement, de l’Aménagement et du Logement’ (Arreté n°158/DEAL/SEPR/2014). In Mozambique, research permits were issued by the Museum of Natural History (Ref. 01/MHN/E.27/2015) and the Ministry of Health (N°S/N/SDI/0233/15).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Additional files

Additional file 1:

Detailed results of Astrovirus detection in samples from Mozambique. (ODS 30 kb)

Additional file 2:

List of the bat families and species included in the phylogenetic tree. (PDF 44 kb)

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, 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 ( applies to the data made available in this article, unless otherwise stated.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hoarau, F., Le Minter, G., Joffrin, L. et al. Bat Astrovirus in Mozambique. Virol J 15, 104 (2018).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: