Recent Emergence and Spread of an Arctic-Related Phylogenetic Lineage of Rabies Virus in Nepal

• Main Authors: Pant, Ganesh, Lavenir, Rachel, Wong, Frank, Certoma, Andrea, Larrous, Florence, Bhatta, Dwij, Bourhy, Hervé, Stevens, Vittoria, Dacheux, Laurent
• Other Authors: Rabies Vaccine Production Laboratory, Rabies Vaccine laboratory, Centre Collaborateur de l'OMS pour la Rage - Dynamique des lyssavirus et adaptation à l'hôte (CC-OMS), Institut Pasteur Paris (IP), Centre National de Référence de la Rage-Dynamique des Lyssavirus et adaptation à l'hôte (CNR), Australian Animal Health Laboratory (AAHL), CSIRO Health and Biosecurity Australia, Commonwealth Scientific and Industrial Research Organisation Canberra (CSIRO)-Commonwealth Scientific and Industrial Research Organisation Canberra (CSIRO), Central Department of Microbiology, Tribhuvan University, This research was supported by the European Union Seventh Framework Programme (FP7/2007–2013) PREDEMICS grant#278433. We are grateful to the Institut de Veille Sanitaire (InVS) for financial support. The Crawford Fund, Victorian Division, Australia is acknowledged for their generous support that enabled technical exchange visits by G. Pant to the Australian Animal Health Laboratory, European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2013
• Subjects: [SDV]Life Sciences [q-bio]; [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology; Arctic; Greenland; Indian
• Online Access: https://hal-pasteur.archives-ouvertes.fr/pasteur-01430500; https://hal-pasteur.archives-ouvertes.fr/pasteur-01430500/document; https://hal-pasteur.archives-ouvertes.fr/pasteur-01430500/file/Pant_PLOSNTD_2013.pdf; https://doi.org/10.1371/journal.pntd.0002560.s002

International audience Rabies is a zoonotic disease that is endemic in many parts of the developing world, especially in Africa and Asia. However its epidemiology remains largely unappreciated in much of these regions, such as in Nepal, where limited information is available about the spatiotemporal dynamics of the main etiological agent, the rabies virus (RABV). In this study, we describe for the first time the phylogenetic diversity and evolution of RABV circulating in Nepal, as well as their geographical relationships within the broader region. A total of 24 new isolates obtained from Nepal and collected from 2003 to 2011 were full-length sequenced for both the nucleoprotein and the glycoprotein genes, and analysed using neighbour-joining and maximum-likelihood phylogenetic methods with representative viruses from all over the world, including new related RABV strains from neighbouring or more distant countries (Afghanistan, Greenland, Iran, Russia and USA). Despite Nepal's limited land surface and its particular geographical position within the Indian subcontinent, our study revealed the presence of a surprising wide genetic diversity of RABV, with the coexistence of three different phylogenetic groups: an Indian subcontinent clade and two different Arctic-like sub-clades within the Arctic-related clade. This observation suggests at least two independent episodes of rabies introduction from neighbouring countries. In addition, specific phylogenetic and temporal evolution analysis of viruses within the Arctic-related clade has identified a new recently emerged RABV lineage we named as the Arctic-like 3 (AL-3) sub-clade that is already widely spread in Nepal.