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phylogeny

  • Diversity of Dromedary Camel Coronavirus HKU23 in African Camels Revealed Multiple Recombination Events among Closely Related Betacoronaviruses of the Subgenus Embecovirus
    Genetic Diversity and Evolution
    Diversity of Dromedary Camel Coronavirus HKU23 in African Camels Revealed Multiple Recombination Events among Closely Related Betacoronaviruses of the Subgenus Embecovirus

    Genetic recombination is often demonstrated in coronaviruses and can result in host range expansion or alteration in tissue tropism. Here, we showed interspecies events of recombination of an endemic dromedary camel coronavirus, HKU23, with other clade A betacoronaviruses. Our results supported the possibility that the zoonotic pathogen MERS-CoV, which also cocirculates in the same camel species, may have undergone similar recombination...

    Ray T. Y. So, Daniel K. W. Chu, Eve Miguel, Ranawaka A. P. M. Perera, Jamiu O. Oladipo, Ouafaa Fassi-Fihri, Gelagay Aylet, Ronald L. W. Ko, Ziqi Zhou, Mo-Sheung Cheng, Sulyman A. Kuranga, François L. Roger, Veronique Chevalier, Richard J. Webby, Patrick C. Y. Woo, Leo L. M. Poon, Malik Peiris
  • Open Access
    Phylogeography of Lassa Virus in Nigeria
    Genetic Diversity and Evolution
    Phylogeography of Lassa Virus in Nigeria

    Lassa virus is the causative agent of Lassa fever, a viral hemorrhagic fever with a case fatality rate of approximately 30% in Africa. Previous studies disclosed a geographical pattern in the distribution of Lassa virus strains and a westward movement of the virus across West Africa during evolution. Our study provides a deeper understanding of the geography of genetic lineages and sublineages of the virus in Nigeria. In addition, we...

    Deborah U. Ehichioya, Simon Dellicour, Meike Pahlmann, Toni Rieger, Lisa Oestereich, Beate Becker-Ziaja, Daniel Cadar, Yemisi Ighodalo, Thomas Olokor, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Jacqueline Agbukor, Benevolence Ebo, John Aiyepada, Paulson Ebhodaghe, Blessing Osiemi, Solomon Ehikhametalor, Patience Akhilomen, Michael Airende, Rita Esumeh, Ekene Muoebonam, Rosemary Giwa, Anieno Ekanem, Ganiyu Igenegbale, George Odigie, Grace Okonofua, Racheal Enigbe, Edna Omonegho Yerumoh, Elisa Pallasch, Sabrina Bockholt, Liana E. Kafetzopoulou, Sophie Duraffour, Peter O. Okokhere, George O. Akpede, Sylvanus A. Okogbenin, Ikponmwosa Odia, Chris Aire, Nosa Akpede, Ekaete Tobin, Ephraim Ogbaini-Emovon, Philippe Lemey, Donatus I. Adomeh, Danny A. Asogun, Stephan Günther
  • Open Access
    Introduction and Dispersal of Sindbis Virus from Central Africa to Europe
    Genetic Diversity and Evolution
    Introduction and Dispersal of Sindbis Virus from Central Africa to Europe

    This study shows that only a single introduction of SINV into a new geographical area is required for spread and establishment, provided that the requisite vector(s) and reservoir(s) of epizootological and epidemiological importance are present. Furthermore, we present the first report of recombination between two strains of SINV in nature. Our study increases the knowledge on new introductions and dispersal of arboviruses in general...

    Jiaxin Ling, Teemu Smura, Jan O. Lundström, John H.-O. Pettersson, Tarja Sironen, Olli Vapalahti, Åke Lundkvist, Jenny C. Hesson
  • Intrahost Selection Pressure Drives Equine Arteritis Virus Evolution during Persistent Infection in the Stallion Reproductive Tract
    Genetic Diversity and Evolution
    Intrahost Selection Pressure Drives Equine Arteritis Virus Evolution during Persistent Infection in the Stallion Reproductive Tract

    EAV can persist in the reproductive tract of infected stallions, and consequently, long-term carrier stallions constitute its sole natural reservoir. Previous studies demonstrated that the ampullae of the vas deferens are the primary site of viral persistence in the stallion reproductive tract and the persistence is associated with a significant inflammatory response that is unable to clear the infection. This is the first study that...

    Bora Nam, Zelalem Mekuria, Mariano Carossino, Ganwu Li, Ying Zheng, Jianqiang Zhang, R. Frank Cook, Kathleen M. Shuck, Juliana R. Campos, Edward L. Squires, Mats H. T. Troedsson, Peter J. Timoney, Udeni B. R. Balasuriya
  • Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia
    Genetic Diversity and Evolution | Spotlight
    Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia

    The coevolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural experiments in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia, we show that...

    Peter J. Kerr, John-Sebastian Eden, Francesca Di Giallonardo, David Peacock, June Liu, Tanja Strive, Andrew F. Read, Edward C. Holmes
  • Open Access
    Comparison of Herpes Simplex Virus 1 Strains Circulating in Finland Demonstrates the Uncoupling of Whole-Genome Relatedness and Phenotypic Outcomes of Viral Infection
    Genetic Diversity and Evolution
    Comparison of Herpes Simplex Virus 1 Strains Circulating in Finland Demonstrates the Uncoupling of Whole-Genome Relatedness and Phenotypic Outcomes of Viral Infection

    Herpes simplex viruses (HSV) infect a majority of adults. Recent data have highlighted the genetic diversity of HSV-1 strains and demonstrated apparent genomic relatedness between strains from the same geographic regions. We used HSV-1 clinical isolates from Finland to test the relationship between viral genomic and geographic relationships, differences in specific genes, and characteristics of viral infection. We found that viral...

    Christopher D. Bowen, Henrik Paavilainen, Daniel W. Renner, Jussi Palomäki, Jenni Lehtinen, Tytti Vuorinen, Peter Norberg, Veijo Hukkanen, Moriah L. Szpara
  • Open Access
    Extensive Diversity of RNA Viruses in Australian Ticks
    Genetic Diversity and Evolution
    Extensive Diversity of RNA Viruses in Australian Ticks

    Each year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia burgdorferi sensu lato, in Australian ticks, the etiological basis of...

    Erin Harvey, Karrie Rose, John-Sebastian Eden, Nathan Lo, Thilanka Abeyasuriya, Mang Shi, Stephen L. Doggett, Edward C. Holmes
  • DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics
    Genetic Diversity and Evolution
    DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics
    Samantha James, Damien Donato, Jean-François Pouliquen, Manuel Ruiz-García, Anne Lavergne, Vincent Lacoste
  • Genetic Diversity and Evolution | Spotlight
    Discovery of a Highly Divergent Coronavirus in the Asian House Shrew from China Illuminates the Origin of the Alphacoronaviruses
    Wen Wang, Xian-Dan Lin, Yong Liao, Xiao-Qing Guan, Wen-Ping Guo, Jian-Guang Xing, Edward C. Holmes, Yong-Zhen Zhang
  • Genetic Diversity and Evolution
    High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia
    Mang Shi, Peter Neville, Jay Nicholson, John-Sebastian Eden, Allison Imrie, Edward C. Holmes

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