Isolates of Zaire ebolavirus from wild apes reveal genetic lineage and recombinants

^†Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon;
^‡Department of Biology and Center for Disease Ecology, Emory University, 1510 Clifton Road, Atlanta, GA 30322;
^§Muséum National d'Histoire Naturelle/Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5202, 75005 Paris, France;
^¶Wildlife Conservation Society, 2300 Southern Boulevard, Bronx, NY 10460;
^‖Institut de Recherches pour le Développement, UR178, Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; and
^††Institut de Recherche pour le Développement, UR178, Mahidol University at Salaya, Phutthamonthon 4, Nakhonpathom 73170, Thailand

Edited by Rita R. Colwell, University of Maryland, College Park, MD, and approved August 30, 2007 (received for review May 2, 2007)

Abstract

Over the last 30 years, Zaire ebolavirus (ZEBOV), a virus highly pathogenic for humans and wild apes, has emerged repeatedly in Central Africa. Thus far, only a few virus isolates have been characterized genetically, all belonging to a single genetic lineage and originating exclusively from infected human patients. Here, we describe the first ZEBOV sequences isolated from great ape carcasses in the Gabon/Congo region that belong to a previously unrecognized genetic lineage. According to our estimates, this lineage, which we also encountered in the two most recent human outbreaks in the Republic of the Congo in 2003 and 2005, diverged from the previously known viruses around the time of the first documented human outbreak in 1976. These results suggest that virus spillover from the reservoir has occurred more than once, as predicted by the multiple emergence hypothesis. However, the young age of both ZEBOV lineages and the spatial and temporal sequence of outbreaks remain at odds with the idea that the virus simply emerged from a long-established and widespread reservoir population. Based on data from two ZEBOV genes, we also demonstrate, within the family Filoviridae, recombination between the two lineages. According to our estimates, this event took place between 1996 and 2001 and gave rise to a group of recombinant viruses that were responsible for a series of outbreaks in 2001–2003. The potential for recombination adds an additional level of complexity to unraveling and potentially controlling the emergence of ZEBOV in humans and wildlife species.

Footnotes

^§§To whom correspondence should be addressed. E-mail: eric.leroy{at}ird.fr
Author contributions: E.M.L. designed research; T.J.W., P. Rouquet, P. Reed, P.Y., X.P., and E.M.L. performed research; P. Rouquet, P. Reed, X.P., and E.M.L. contributed new reagents/analytic tools; T.J.W., R.B., A.H., L.A.R., J.-P.G., and E.M.L. analyzed data; and T.J.W., R.B., and E.M.L. wrote the paper.
↵ ^‡‡Present address: Division of Environmental and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database [accession nos. EU051634 and EU051647 (Etoumbi_may05), EU051635 and EU051648 (Mbandza_nov03), EU051630 and EU051649 (GOR1_Lossi_dec02), EU051631 (GOR2_Lossi_dec02), EU051632 (GOR_Ekata_nov01), EU051633 (CH_Lossi_feb03), EU051636 (GOR_Mbandza_jun03), EU051637 (GOR1_odz_june05), EU051638 and EU051650 (GOR_odz_jun05), EU51639 (Mayibout_96), EU05164 (Mendemba_A_oct01), EU051641 (Mendemba_B_oct01) EU051642 (Etakangaye_dec01), EU051643 (Olloba_dec01), EU051645 (Mvoula_jan03), EU051644 (Entsiami_jan03), and EU051646 (Yembelengoye_jan03)].
This article contains supporting information online at www.pnas.org/cgi/content/full/0704076104/DC1.
Abbreviations:

CP,

codon position;

ML,

maximum likelihood;

RC,

Republic of the Congo;

ZEBOV,

Zaire ebolavirus.