Journal of General Virology (2009), 90, 2669–2678 DOI 10.1099/vir.0.014183-0 Isolation of a novel species of flavivirus and a new strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda Shelley Cook,1 Gregory Moureau,2 Ralph E. Harbach,1 Louis Mukwaya,3 Kim Goodger,1 Fred Ssenfuka,3 Ernest Gould,2,4 Edward C. Holmes5 and Xavier de Lamballerie2 Correspondence 1Natural History Museum, Cromwell Road, London SW7 5BD, UK Shelley Cook 2Unite´ des Virus Emergents UMR190 ‘Emergence des Pathologies Virales’, Universite´ de la [email protected] Me´diterrane´e et Institut de Recherche pour le De´veloppement, Marseille, France 3Mosquito Research Programme, Uganda Virus Research Institute, PO Box 49, Entebbe, Uganda 4Centre for Ecology and Hydrology Oxford, Mansfield Road, Oxford OX1 3SR, UK 5Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA The genus Flavivirus, which contains approximately 70 single-stranded, positive-sense RNA viruses, represents a unique model for studying the evolution of vector-borne disease, as it includes viruses that are mosquito-borne, tick-borne or have no known vector. Both theoretical work and field studies suggest the existence of a large number of undiscovered flaviviruses. Recently, the first isolation of cell fusing agent virus (CFAV) was reported from a natural mosquito population in Puerto Rico, and sequences related to CFAV have been discovered in mosquitoes from Thailand. CFAV had previously been isolated from a mosquito cell line in 1975 and represented the only known ‘insect-only’ flavivirus, appearing to replicate in insect cells alone. A second member of the ‘insect-only’ group, Kamiti River virus (KRV), was isolated from Kenyan mosquitoes in 2003. A third tentative member of the ‘insect-only’ group, Culex flavivirus (CxFV), was first isolated in 2007 from Japan and further strains have subsequently been reported from the Americas. We report the discovery, isolation and characterization of two novel ‘insect-only’ flaviviruses from Entebbe, Uganda: a novel lineage tentatively designated Nakiwogo virus (NAKV) and a new strain of CxFV. The individual mosquitoes from which these strains were isolated, identified retrospectively by using a reference molecular phylogeny generated using voucher specimens from the region, were Mansonia africana nigerrima and Culex quinquefasciatus, Received 8 June 2009 respectively. This represents the first isolation, to our knowledge, of a novel insect-only flavivirus Accepted 30 July 2009 from a Mansonia species and the first isolation of a strain of CxFV from Africa. INTRODUCTION (ii) presumed to be limited to vertebrates alone; and (iii) appear to be restricted to insects alone (‘insect-only’ The genus Flavivirus represents a unique model for flaviviruses). In addition, the genus includes pathogens of studying the evolution of vector-borne disease because it significant importance to human health, including dengue includes viruses that are: (i) arthropod-borne, infecting a virus and yellow fever virus (YFV). Cell fusing agent virus range of vertebrate hosts through mosquito or tick bites; (CFAV), first isolated from a Stegomyia aegypti (as Aedes aegypti) cell line [Stollar & Thomas, 1975; nomenclature for The GenBank/EMBL/DDBJ accession numbers for the COI gene the aedine mosquitoes follows Reinert (2000) and Reinert sequences from mosquito species obtained during this study are et al. (2004, 2006, 2008)] and characterized by Cammisa- GQ165759–GQ165807, that for Culex flavivirus Uganda is GQ165808, Parks et al. (1992), previously represented the only known that for Nakiwogo virus is GQ165809 and that for cell fusing agent virus ‘insect-only’ flavivirus, appearing to replicate uniquely in strain Rio Piedras is GQ165810. insect cells (Kuno, 2007). In recent years, Cook et al. (2006) Three supplementary tables listing primer sequences used, flaviviral reported the first isolation of CFAV, from a natural abbreviation codes and accession numbers, and mosquito accession numbers and Barcode of Life Datasystem (BOLD) reference numbers mosquito population in Puerto Rico. The virus was found are available with the online version of this paper. in several different species and in mosquitoes of both sexes. 014183 G 2009 SGM Printed in Great Britain 2669 S. Cook and others Two strains of a second member of the ‘insect-only’ group, mosquitoes representing species found at sampling locations were designated Kamiti River virus (KRV), were isolated from retained as voucher specimens for the development of molecular Neomelaniconion mcintoshi mosquitoes from Kenya identification protocols. Mosquitoes were sampled from a variety of locations (Fig. 1), using different methods to maximize species {Crabtree et al., 2003; Sang et al., 2003; these authors diversity. Centers for Disease Control (CDC) fan-augmented light stated that KRV was isolated from ‘Ae. macintoshi’ from traps were supplemented with dry ice for approximately 8 h trapping flooded dambos in Central Province, Kenya. However, periods between dusk and dawn and placed at various heights in Aedes (Ochlerotatus) macintoshi (Marks) [Ochlerotatus urban, rural and forest environments. Modified backpack aspirators macintoshi in the classification of Reinert et al. (2008)] is and hand-held aspirators were used to sample resting mosquitoes. an Australian mosquito, and the species in this case is Specimens were placed on dry ice immediately upon collection at the actually the Rift Valley fever vector Neomelaniconion sampling sites. Upon arrival at the laboratory, samples were sorted on a chill table according to trap, location and sex and placed in mcintoshi (Huang) (originally named Aedes mcintoshi), individual wells in microtitre plates before storage at 280 uC. whose larvae are frequently found in dambos}. Taken together with theoretical work that suggested the existence Sample preparation, nucleic acid extraction and RT-PCR of over 2000 unknown mosquito-borne flaviviruses (Pybus screening. Whole mosquitoes were homogenized individually as et al., 2002), as well as the discovery of DNA sequences described previously (Cook et al., 2006). Samples of 65 ml from five related to flaviviruses in the genomes of St. aegypti and individual mosquitoes were pooled for RNA extraction. Total nucleic Stegomyia albopicta, which probably resulted from integ- acid (NA) extraction was conducted via the MagNApure LC System using a Culture Cells kit and standard manufacturer’s protocol ration events following infection of each mosquito species (Roche Diagnostics), or using a Biorobot EZ1, with Virus Mini kit by a virus (or viruses) related to the CFAV group, it was v2.0 (Qiagen). proposed that further ‘insect-only’ flaviviruses were likely A5ml aliquot of each pooled RNA extraction was used in a one-step to be discovered in natural mosquito populations (Crochu real-time QuantiTect SYBR-Green RT-PCR assay, according to et al., 2004). Indeed, sequences related to CFAV been Moureau et al. (2007), with primers PF1S and PF2R-bis (see discovered have more recently in St. aegypti mosquitoes Supplementary Table S1, available in JGV Online). Second-round from Thailand (Kihara et al., 2007). A third member of the PCR on 2.5 ml cDNA, using primers PF3S and PF2R-bis, used the ‘insect-only’ group, Culex flavivirus (CxFV), was first following conditions: 94 uC for 2 min; 40 cycles of 94 uC for 30 s, isolated in 2007 from Culex tritaeniorhynchus and Culex 50 uC for 45 s and 72 uC for 1 min; followed by a final extension of quinquefasciatus in Japan and Indonesia (Hoshino et al., 72 uC for 7 min and cooling to 20 uC for 2 min. To avoid any potential contamination, positive cDNA samples from first-round 2007). Further strains have subsequently been isolated RT-PCR were manipulated separately from all other samples for from Cx. quinquefasciatus in Guatemala (Morales-Betoulle second-round PCR. Negative controls comprising both NA extrac- et al., 2008) and Mexico (Farfan-Ale et al., 2009), and from tions from non-infected mosquitoes and reactions in which water Cx. quinquefasciatus and Culex restuans in Texas, USA, and replaced RNA were performed through all stages. Positive controls Trinidad (Kim et al., 2009). Finally, flavivirus RNA has also comprised Rio Bravo, Japanese encephalitis and Montana myotis recently been discovered in phlebotomine sandflies from leukoencephalitis viruses (RBV, JEV and MMLV, respectively). Algeria (Moureau et al., 2009). Second-round PCR products were analysed visually by electrophor- esis through ethidium bromide-stained 2 % agarose gels under UV We now report the discovery, isolation and characterization light. Products were purified by using a QIAquick Spin PCR of two novel flaviviruses of the ‘insect-only’ group from the Purification kit (Qiagen). Amplicons were sequenced on both strands Entebbe area of Uganda: a novel lineage, tentatively with an ABI 377 automated sequencer (Applied Biosystems). designated Nakiwogo virus (NAKV), and a new strain of For those samples that gave positive results using the primer set CxFV. The individual mosquitoes from which these strains PF1S–2Rbis–3S on RNA extractions from pooled mosquitoes, NA were isolated, identified retrospectively from a backbone were re-extracted from the original individual mosquito homogenates phylogeny generated using the ‘barcode’ region of voucher by using a Biorobot EZ1, with Virus Mini kit v2.0 according to the specimens from the area, were specimens of Mansonia manufacturer’s instructions (Qiagen).