Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 19, Number 10—October 2013
Letter

Close Relative of Human Middle East Respiratory Syndrome Coronavirus in Bat, South Africa

Cite This Article

To the Editor: The severe acute respiratory syndrome (SARS) outbreak of 2002–03 and the subsequent implication of bats as reservoir hosts of the causative agent, a coronavirus (CoV), prompted numerous studies of bats and the viruses they harbor. A novel clade 2c betacoronavirus, termed Middle East respiratory syndrome (MERS)–CoV, was recently identified as the causative agent of a severe respiratory disease that is mainly affecting humans on the Arabian Peninsula (1). Extending on previous work (2), we described European Pipistrellus bat–derived CoVs that are closely related to MERS-CoV (3). We now report the identification of a South Africa bat derived CoV that has an even closer phylogenetic relationship with MERS-CoV.

During 2011–2012, fecal pellets were collected from 62 bats representing 13 different species in the KwaZulu-Natal and Western Cape Provinces of South Africa and stored in RNAlater solution (Life Technologies, Carlsbad, CA, USA). Details about the bat sample are available in the Technical Appendix. RNA was extracted by using the QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany). Screening for CoVs was done by nested reverse transcription PCR using broadly reactive oligonucleotide primers targeting a conserved region in the RNA-dependent RNA polymerase (RdRp) gene (online Technical Appendix). PCR results were positive for 5 (8%) of the 62 specimens. PCR amplicons for 4 positive specimens yielded alphacoronavirus sequences related to recently described bat alphacoronaviruses from South Africa (4). The other positive specimen, termed PML/2011, was from an adult female Neoromicia cf. zuluensis bat sampled in 2011; the specimen yielded a novel betacoronavirus (GenBank accession no. KC869678). Technical Appendix Figure 1 shows the distribution of this bat species.

To obtain better phylogenetic resolution, we extended the 398-nt RdRp fragment generated by the screening PCR to 816 nt, as described (5). PML/2011 differed from MERS-CoV by only 1 aa exchange (0.3%) in the translated 816-nt RdRp gene fragment. Thus, PML/2011 was much more related to MERS-CoV than any other known virus. The amino acid sequence of the next closest known relatives of MERS-CoV, from European Pipistrellus bats (3), differed from MERS-CoV by 1.8%. The amino acid sequences of viruses from Nycteris bats in Ghana (3) and the 2c prototype bat CoVs, HKU4 and HKU5, from China (6) differed by 5.5%–7.7% from MERS-CoV. The smaller 152- to 396-nt RdRp fragments of 2c bat CoVs from a Hypsugo savii bat in Spain (7), bat guano in Thailand (8), and a Nyctinomops bat in Mexico (9) showed no or only partial overlap with the 816-nt fragment generated in this study; thus, a direct comparison could not be done. However, in their respective RdRp fragments, these CoVs yielded amino acid sequence distances of 3.5%–8.0% and were thus probably more distant from MERS-CoV than the virus described here.

Figure

Thumbnail of Partial RNA-dependent RNA polymerase (RdRp) gene phylogeny, including the novel betacoronavirus from a Neoromicia zuluensis bat in South Africa (GenBank accession no. KC869678 for both partial RdRp and spike gene sequences). The Bayesian phylogeny was done on a translated 816-nt RdRp gene sequence fragment, as described (5). MrBayes V3.1 (http://mrbayes.sourceforge.net/) was used with a WAG substitution model assumption over 2,000,000 generations sampled every 100 steps, resulting i

Figure. . Partial RNA-dependent RNA polymerase (RdRp) gene phylogeny, including the novel betacoronavirus from a Neoromicia zuluensis bat in South Africa (GenBank accession no. KC869678 for both partial RdRp and spike gene...

A Bayesian phylogenetic analysis of the 816-nt RdRp sequence confirmed the close relationship between PML/2011 and MERS-CoV (Figure). Their phylogenetic relatedness was as close as that of SARS-CoV and the most closely related bat coronavirus known, Rs672 from a Rhinolophus sinicus bat (Figure). Like PML/2011 and MERS-CoV, Rs672 and SARS-CoV showed only 1 aa exchange in the translated 816-nt RdRp fragment. To confirm this relatedness, we amplified and sequenced a short 269-nt sequence encompassing the 3′-terminus of the spike gene for PML/2011 (oligonucleotide primers available upon request from the authors). A partial spike gene–based phylogeny using this sequence yielded the same topology as that using the partial RdRp sequence (Technical Appendix Figure 2). Again, PML/2011 was most closely related to MERS-CoV, showing only a 10.9% aa sequence distance in this gene, which encodes the glycoprotein responsible for CoV attachment and cellular entry. This distance was less than the 13.3% aa sequence distance between MERS-CoV and the European Pipistrellus CoVs (3) and less than the 20.5%–27.3% aa sequence distance between MERS-CoV and HKU5 and between MERS-CoV and HKU4 (6) in the same sequence fragment.

Our results further support the hypothesis that, like human CoV-229E and SARS-CoV, ancestors of MERS-CoV might exist in Old World insectivorous bats belonging to the family Vespertilionidae, to which the genera Neoromicia and Pipistrellus belong (3). Knowledge of the close relatedness of PML/2011 and MERS-CoV, which contrasts with the more distant relatedness of CoVs in bats from the Americas and Asia, enables speculations of an African origin for bat reservoir hosts of MERS-CoV ancestors. This hypothesis is limited by a global sampling bias, the small sample size, and the single clade 2c betacoronavirus detection in this study. Still, a putative transfer of MERS-CoV ancestors from Africa to the Arabian Peninsula would parallel the transfer of other viruses (e.g., the exportation of Rift Valley fever virus from East Africa, which led to a severe outbreak in Saudi Arabia in 2000) (10).

Studies of Vespertilionidae bats and potential intermediate hosts (e.g., carnivores and ungulates, such as camels) are urgently needed to elucidate the emergence of MERS-CoV. Such studies should focus on the Arabian Peninsula and Africa.

Top

Acknowledgments

We thank Tobias Bleicker, Sebastian Brünink, and Monika Eschbach-Bludau for technical assistance; Thomas Seifert, Sonja Matthee, and Conrad Mathee for invaluable help; and Anna-Marie Corman for assistance with geographic information processing.

This study was supported by the European Union FP7 projects EMPERIE (contract number 223498) and ANTIGONE (contract number 278976); the German Research Foundation (DFG grant DR 772/3-1, KA1241/18-1, to C.D.); the National Health Laboratory Service Research Trust (to W.P.); and the South African National Research Foundation (to W.P.).

Top

Ndapewa Laudika Ithete, Samantha Stoffberg, Victor Max Corman, Veronika M. Cottontail, Leigh Rosanne Richards, M. Corrie Schoeman, Christian Drosten, Jan Felix Drexler1Comments to Author , and Wolfgang Preiser1
Author affiliations: University of Stellenbosch/National Health Laboratory Service, Tygerberg, South Africa (N.L. Ithete, S. Stoffberg, W. Preiser); University of Bonn Medical Centre, Bonn, Germany (V.M. Corman, C. Drosten, J.F. Drexler); University of Ulm, Ulm, Germany (V.M. Cottontail); Durban Natural Science Museum, Durban, South Africa (L.R. Richards); University of KwaZulu Natal, Durban (M.C. Schoeman)

Top

References

  1. Zaki  AM, van Boheemen  S, Bestebroer  TM, Osterhaus  AD, Fouchier  RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:181420. DOIPubMedGoogle Scholar
  2. Reusken  CB, Lina  PH, Pielaat  A, de Vries  A, Dam-Deisz  C, Adema  J, Circulation of group 2 coronaviruses in a bat species common to urban areas in Western Europe. Vector Borne Zoonotic Dis. 2010;10:78591. DOIPubMedGoogle Scholar
  3. Annan  A, Baldwin  HJ, Corman  VM, Klose  SM, Owusu  M, Nkrumah  EE. Human betacoronavirus 2c EMC/2012–related viruses in bats, Ghana and Europe. Emerg Infect Dis. 2013;19:4569. DOIPubMedGoogle Scholar
  4. Geldenhuys  M, Weyer  J, Nel  LH, Markotter  W. Coronaviruses in South African bats. Vector Borne Zoonotic Dis. 2013;13:5169. DOIPubMedGoogle Scholar
  5. Drexler  JF, Gloza-Rausch  F, Glende  J, Corman  VM, Muth  D, Goettsche  M, Genomic characterization of severe acute respiratory syndrome–related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences. J Virol. 2010;84:1133649. DOIPubMedGoogle Scholar
  6. Woo  PC, Wang  M, Lau  SK, Xu  H, Poon  RW, Guo  R, Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features. J Virol. 2007;81:157485. DOIPubMedGoogle Scholar
  7. Falćon  A, Vazquez-Moron  S, Casas  I, Aznar  C, Ruiz  G, Pozo  F, Detection of alpha and betacoronaviruses in multiple Iberian bat species. Arch Virol. 2011;156:188390. DOIPubMedGoogle Scholar
  8. Wacharapluesadee  S, Sintunawa  C, Kaewpom  T, Khongnomnan  K, Olival  KJ, Epstein  JH. Group C betacoronavirus in bat guano fertilizer, Thailand. Emerg Infect Dis. 2013; Epub ahead of print.
  9. Anthony  SJ, Ojeda-Flores  R, Rico-Chavez  O, Navarrete-Macias  I, Zambrana-Torrelio  C, Rostal  MK, Coronaviruses in bats from Mexico. J Gen Virol. 2013;94:102838. DOIPubMedGoogle Scholar
  10. Bird  BH, Khristova  ML, Rollin  PE, Ksiazek  TG, Nichol  ST. Complete genome analysis of 33 ecologically and biologically diverse Rift Valley fever virus strains reveals widespread virus movement and low genetic diversity due to recent common ancestry. J Virol. 2007;81:280516. DOIPubMedGoogle Scholar

Top

Figure

Top

Cite This Article

DOI: 10.3201/eid1910.130946

1These authors contributed equally to this article.

Related Links

Top

Table of Contents – Volume 19, Number 10—October 2013

EID Search Options
presentation_01 Advanced Article Search – Search articles by author and/or keyword.
presentation_01 Articles by Country Search – Search articles by the topic country.
presentation_01 Article Type Search – Search articles by article type and issue.

Top

Comments

Please use the form below to submit correspondence to the authors or contact them at the following address:

Jan Felix Drexler, Institute of Virology, University of Bonn Medical Centre, 53127 Bonn, Germany

Send To

10000 character(s) remaining.

Top

Page created: September 16, 2013
Page updated: September 16, 2013
Page reviewed: September 16, 2013
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external