Genome sequencing and phylogenetic reconstruction reveal a potential fourth rhinovirus species and its worldwide distrib
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BRIEF REPORT
Genome sequencing and phylogenetic reconstruction reveal a potential fourth rhinovirus species and its worldwide distribution Kim Tien Ng1,2 · Yutaka Takebe3,4 · Adeeba Kamarulzaman1 · Kok Keng Tee3,5 Received: 13 July 2020 / Accepted: 14 September 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract Genome sequences of members of a potential fourth rhinovirus (RV) species, provisionally denoted as rhinovirus A clade D, from patients with acute respiratory infection were determined. Bayesian coalescent analysis estimated that clade D emerged around the 1940s and diverged further around 2006-2007 into two distinctive sublineages (RV-A8-like and RV-A45-like) that harbored unique “clade-defining” substitutions. Similarity plots and bootscan mapping revealed a recombination breakpoint located in the 5ʹ-UTR region of members of the RV-A8-like sublineage. Phylogenetic reconstruction revealed the distribution of clade D viruses in the Asia Pacific region and in Europe, underlining its worldwide distribution. Rhinoviruses (RVs), the primary viral etiologic agents of acute respiratory tract infections, contribute significantly to the global health burden through increased medical expenses and loss of productivity [1]. On average, RVs cause 2-4 episodes of respiratory infections in adults and 8-12 episodes in children each year [2]. More importantly, recent reports have highlighted the involvement of RV in lower respiratory tract infections [3, 4]. Likewise, fatal respiratory tract infections associated with RV outbreaks have become increasingly evident [5, 6]. In addition, several recent studies have shown that individuals with underlying respiratory conditions may experience severe RV-associated complications, as observed in the exacerbation of asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis [7–9]. Handling Editor: Tim Skern. * Kok Keng Tee [email protected] 1
Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
2
Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
3
Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
4
AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku‑ku, Tokyo, Japan
5
School of Healthcare and Medical Sciences, Sunway University, Bandar Sunway, Selangor Darul Ehsan, Malaysia
There are currently three confirmed RV species in the genus Enterovirus: Rhinovirus A, Rhinovirus B and Rhinovirus C. Each species includes multiple genetically distinct types that have diverged via rapid evolution [10]. In the present population-based RV molecular epidemiological study, we describe nine genome sequences of members of a potential fourth species of RV, provisionally denoted as rhinovirus A clade D [11], detected in patients with acute respiratory illnesses in Kuala Lumpur, Malaysia, between 2012 and 2014. Im
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