Emerging Infectious Diseases
Emerg Infect Dis. Mar 2009; 15(3): 482–485.
Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya
Suxiang Tong, Christina Conrardy, Susan Ruone, Ivan V. Kuzmin, Xiling Guo, Ying Tao, Michael Niezgoda, Lia Haynes, Bernard Agwanda, Robert F. Breiman, Larry J. Anderson, and Charles E. Rupprecht
Diverse coronaviruses have been identified in bats from several continents but not from Africa. We identified group 1 and 2 coronaviruses in bats in Kenya, including SARS-related coronaviruses. The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans.
The 2003 outbreak of severe acute respiratory syndrome (SARS) generated renewed interest in coronaviruses (CoV) and the source for the SARS CoV that caused the outbreak in humans. Serologic studies demonstrated that the virus had not previously circulated in human populations to any large extent and suggested a source of zoonotic. A likely natural viral reservoir for the virus was not identified until horseshoe bats (Rhinolophus spp.) in several regions in the People’s Republic of China were demonstrated to harbor SARS-like CoVs. Subsequently, a number of other SARS-like CoVs, as well as CoVs from antigenic groups I and II, were identified from bats in Asia, Europe, and North America, and coronavirus antibodies were detected in African bat species. It is not surprising that a growing number of CoVs have been detected in bats.
To date, >60 viral species have been detected in bats because their biodiversity (second only to rodents), high population densities, wide distribution, and ability to fly over long distances allow them to harbor and easily spread multiple infectious agents. Bats have long been known as natural hosts for lyssaviruses and more recently have been recognized as potential reservoirs for emerging human pathogens, including Ebola, Marburg, Nipah, and Hendra viruses in addition to SARS-CoV.
Given the association of bats with emerging infectious diseases, field surveys were performed during July–August 2006 in the southern portion of Kenya (Figure 1). The selection of sites was based on preliminary data regarding bat roost locations and observations of bats in the field during the survey. Attempts were made to collect specimens from 10–20 animals of each species present in each location. Bats were captured manually and by using mist nets and hand nets; adults and subadults of both sexes were captured. Each bat was measured, sexed, and identified to the genus or species level when possible. Blood samples and oral and fecal swabs were collected; the animals were then euthanized in compliance with field protocol. Blood, fecal swabs, and selected tissue samples were transported on dry ice from the field and stored at –80°C.
Map of Kenya showing the locations of 17 bat collection sites.
Fecal swabs (n = 221; Table) were screened for the presence of CoV RNA using 2 semi-nested reverse transcription–PCR (RT-PCR) assays. (...)
Of 221 bat fecal swabs examined, 41 (19%) were positive by at least 1 of the 2 seminested RT-PCR assays (Table). One specimen had 2 distinct CoV sequences, each amplified by 1 of the 2 PCR assays, giving a total of 42 distinct CoV sequences. To characterize the overall diversity of CoV sequences, in this study a phylogenetic tree of the 121-bp fragment of RdRp was generated from 39 coronaviruses from bats in Kenya and 47 selected human and animal coronaviruses from the National Center for Biotechnology Information database based on the Bayesian Monte Carlo Markov Chain method. Three of the 42 sequences were not of sufficiently high quality to include in this tree. Some nodes had low Bayesian posterior probabilities. Longer sequences from these viruses are needed to refine their phylogenetic relationships.
Results of detection of CoV RNA in fecal swabs of bats from Kenya*
coronavirus; SARS, severe acute respiratory syndrome.
The American Journal of Tropical Medicine and HygienePublished online May 27, 2014 , doi: 10.4269/ajtmh.13-0664 Am J Trop Med Hyg 2014 vol. 91 no. 2 258-266
Short Report: Molecular Detection of Adenoviruses, Rhabdoviruses, and Paramyxoviruses in Bats from Kenya
Christina Conrardy, Ying Tao, Ivan V. Kuzmin, Michael Niezgoda, Bernard Agwanda, Robert F. Breiman, Larry J. Anderson, Charles E. Rupprecht, and Suxiang Tong
We screened 217 bats of at least 20 species from 17 locations in Kenya during July and August of 2006 for the presence of adenovirus, rhabdovirus, and paramyxovirus nucleic acids using generic reverse transcription polymerase chain reaction (RT-PCR) and PCR assays. Of 217 bat fecal swabs examined, 4 bats were adenovirus DNA-positive, 11 bats were paramyxovirus RNA-positive, and 2 bats were rhabdovirus RNA-positive. Three bats were coinfected by two different viruses. By sequence comparison and phylogenetic analysis, the Kenya bat paramyxoviruses and rhabdoviruses from this study may represent novel viral lineages within their respective families; the Kenya bat adenoviruses could not be confirmed as novel, because the same region sequences from other known bat adenovirus genoomparison were lacking. Our study adds to previous evidence that bats carry diverse, potentially zoonotic viruses and may be coinfected with more than one virus.
Over one-half of all known human pathogens originated from animals, and over 75% of emerging infectious diseases identified in the last three decades were zoonotic. The threat of veterinary pathogens to human health continues to grow because of increasing population density and urbanization, global movement of people and animals, and deforestation accompanied by increased proximity of human and wildlife habitats. Recent emerging infectious diseases have been concentrated in tropical Africa, Latin America, and Asia, with outbreaks usually occurring within populations living near wild animals. Identification of animal reservoirs from which zoonosis may emerge and detection and characterization of pathogens in these reservoirs will facilitate timely implementation of control strategies for new zoonotic infections. Therefore, pathogen discovery studies in animal reservoirs represent an integral part of public health surveillance.
Bats have long been known as natural hosts for lyssaviruses, and more recently, they have been recognized as potential reservoirs for emerging human pathogens, including henipaviruses, filoviruses, and severe acute respiratory syndrome (SARS) related coronaviruses. Novel viruses are documented in bats every year, which has drawn increasing attention to these mammalian reservoirs that are uniquely associated with a variety of known and potential zoonotic pathogens. In this study, we report the detection of nucleic acids of adenoviruses, rhabdoviruses, and paramyxoviruses in bats from Kenya.
Field sampling of bats was implemented in Kenya for zoonotic surveillance within the framework of the Global Disease Detection Program of the Centers for Disease Control and Prevention. Detailed information on bat capture and handling is described elsewhere. [see above: Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya] In this study, fecal swabs (N = 217) collected during July and August of 2006 from apparently healthy bats representing 21 species in 13 genera from 17 locations within Kenya were screened for the presence of adenovirus, polyomavirus, rhabdovirus, and paramyxovirus nucleic acids using generic reverse transcription polymerase chain reaction (RT-PCR) and PCR assays. (...)
Of 217 fecal swabs tested (Table 1), adenovirus DNA was detected in 4 samples from Chaerephon sp. (N = 2) and Otomops martiensseni (N = 2); paramyxovirus RNA was detected in 11 samples from Cardioderma cor (N = 1), Chaerephon sp. (N = 1), O. martiensseni (N = 5), Rousettus aegyptiacus (N = 2), Miniopterus minor (N = 1), and M. natalensis (N = 1); and rhabdovirus RNA was detected in 2 samples from Chaerephon sp. (N = 1) and M. africanus (N = 1). Three bats harbored viruses from two different viral families. One O. martiensseni bat was coinfected with a paramyxovirus and a polyomavirus previously described. Another O. martiensseni bat was coinfected with an adenovirus and a paramyxovirus. One Chaerephon sp. bat was coinfected with a rhabdovirus and a polyomavirus 9 Additional specimens of lung, kidney, liver, and/or brain tissues from nine bats that had paramyxovirus RNA-positive fecal swabs were also tested for paramyxovirus RNA. Four bats (KY149, KY151, KY166, and KY291) tested positive on kidney tissues, and one bat (KY159) tested positive on kidney, lung, and liver tissues. The KY159 bat kidney and lung tissues were coinfected with two different types of paramyxoviruses. One sequence was the same as identified in the fecal swab (KY159a), and the other sequence represented a rubula-related virus (KY159b). These findings support an assumption for an active viral infection rather than simple transit of ingested infected material through the digestive tract of the bat. In addition, positive identification of paramyxovirus RNA in these tissues may stem from infection at these sites or possible viremia.
Positive PCR results per bat species and geographical locations
We detected distinct viral DNA and RNA from the families Adenoviridae, Rhabdoviridae, and Paramyxoviridae in Kenya bats using generic family and/or genus RT-PCR and PCR assays. Although the limited length of genome sequences and the low Bayesian posterior probabilities do not provide reliable phylogenetic comparisons and taxonomic inferences, the magnitude of the genetic distance (85% or less nucleotide identity in highly conserved genomic regions) between the Kenya bat paramyxoviruses and rhabdoviruses from this study and other known paramyxoviruses and rhabdoviruses might be suggestive of their being novel viral lineages within their respective families. The Kenya bat adenoviruses could not be confirmed as novel, because many bat adenoviruses have recently been described that are also related to canine adenovirus types 1 and 2, and we were unable to obtain sequences from the same region of the genome for direct comparison.
Our findings also show that Kenya bats maintain as much genetic diversity in paramyxoviruses as bats in other geographic locations. The concurrent detection of both RNA and DNA viruses in apparently healthy bats supports evidence that bats may be carriers of more than one virus. Of note, many bats that tested positive for adenovirus, paramyxovirus, and polyomavirus were O. martiensseni from Suswa Cave. Suswa Cave houses one of the largest known colonies of O. martiensseni and has an extensive history of guano mining and tourist visits.23 Anthropogenic activities, including guano mining, cave tourism, hunting, and consumption of bats, likely increase the chance of zoonotic infection spillovers from these bats.2 Studying viral diversity in bats and their biology will help understanding and response to novel emerging viruses. (....)
eLife 2014;10.7554/eLife.04395. Published September 8, 2014
Mapping the zoonotic niche of Ebola virus disease in Africa
David M Pigott, Nick Golding, Adrian Mylne, Zhi Huang, Andrew J Henry, Daniel J Weiss, Oliver J Brady, Moritz U G Kraemer, David L Smith, Catherine L Moyes, Samir Bhatt, Peter W Gething, Peter W Horby, Isaac I Bogoch, John S Brownstein, Sumiko R Mekaru, Andrew J Tatem, Kamran Khan, Simon I HayCorresponding Author
Areas where Ebola virus infection in animals is likely (colour scale ranging from red for most likely, through yellow to blue for least likely).
Areas where Ebola virus infection in animals is likely (colour scale ranging from red for most likely, through yellow to blue for least likely). The borders of all African countries are outlined in grey.
Areas where Ebola virus infection in animals is likely (colour scale ranging from red for most likely, through yellow to blue for least likely). The borders of African countries containing areas likely to be at risk are outlined.
Areas where Ebola virus infection in animals is likely (colour scale ranging from red for most likely, through yellow to blue for least likely). The borders of African countries where Ebola virus outbreaks have started are outlined.