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Bat epidemiology research and study
natural history - ecologyepizootiology

Bat epidemiology
Epidemiology bat research and study: chiropterology.com
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Emerging Infectious Diseases

Emerg Infect Dis. Mar 2009; 15(3): 482–485.
doi:  10.3201/eid1503.081013
 
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

Abstract
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.

The Study
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.

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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*

Bat species

Geographic location

PCR results, no. positive/no. tested

Clusters

Cardioderma cor

15

0/10



12


1/3


BtCoVA970-like


Chaerophon sp.

6

1/14

BtHKU7-like


17

6/19

BtHKU7-like, BtKY18-like, SARSCoV-like


3


0/5



Chaerophon pumilus

3

2/3

HCoV229E-like


11


0/4



Coleura afra

11

0/1



14


0/1



Eidolon helvum

4

6/10

BtKY18-like

Epomophorus wahlbergi

9

0/3


Hipposideros commersoni


14


1/10


BtHKU9-like


Hipposideros ruber

2

0/4



5


0/2



Lissonycteris angolensis

5

0/10


Miniopterus africanus

10

1/8

BtCoV1A-like

Miniopterus inflatus

5

7/12

BtCoV1A-like, BtHKU8-like

Miniopterus minor

13

1/16

BtCoV1A-like

Miniopterus natalensis

1

1/7

BtCoV1A-like

Neoromicia tenuipinnis

6

0/4


Otomops martinsseni

7

2/19

BtHKU7-like

Pipistrellus sp.

8

0/1


Rhinolophus hildebrandtii


10


0/4



Rhinolophus sp.

14

0/1



13

0/1



8


0/5



Rousettus aegyptiacus

1

2/10

BtKY18-like


2

2/9

BtCoVA970-like, BtHKU9-like


16

6/9

BtCoVA970-like, BtHKU9-like


13


2/11


BtHKU9-like


Taphozous hildegardeae

14

0/3


Taphozous sp.


11


0/2



Total


41/221 (19%)


*CoV, coronavirus; SARS, severe acute respiratory syndrome.

(...)

Conclusions
These data demonstrate that the CoV diversity in bats previously detected in Asia, Europe, and North America is also present, possibly to a greater extent, in Africa. The extent of this diversity among CoVs may be shown more clearly through additional studies in bats, and increased demonstration of CoV diversity in bats may require a reconsideration of how they should be grouped. The frequency and diversity of CoV detections in bats, now in multiple continents, demonstrate that bats are likely an important source for introduction into other species globally. Understanding the extent and diversity of CoV infection in bats provides a foundation for detecting new disease introductions that may, like SARS, present a public health threat.

 
The American Journal of Tropical Medicine and Hygiene
Published 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

Abstract.
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.

Introduction
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.
 
Study
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

Bat species/location

Number of bats tested

Adenovirus

Paramyxovirus

Rhabdovirus

Polyomavirus*

Cardioderma cor
 Kisumu 1       1
 Panga Yambo cave 10   1    
 Tsavolite goldmine 3        
Chaerephon sp.
 Kisumu 13 1   1 5
 Moi University 16 1 1   2
 Asembo Bay 6        
Chaerephon pumilus
 Marungu 5        
 Shimoni cave 1        
Coleura afra
 Marungu 1        
 Shimoni cave 1        
Eidolon helvum
 Vihiga District 9       1
Epomophorus wahlbergi
 Nairobi 3        
Hipposideros commersoni
 Shimoni cave 9       1
Hipposideros ruber
 Kakamega cave 2        
 Makingeny cave 4        
Lissonycteris angolensis
 Kakamega cave 11       1
 Kisumu 1       1
Miniopterus africanus
 Chyulu National Park 9     1 1
Miniopterus inflatus
 Kakamega cave 10        
Miniopterus natalensis
 Kitum cave 8   1    
Miniopterus minor
 Three caves 16   1    
Otomops martiensseni
 Suswa cave 19 2 5   6
Pipistrellus sp.
 Nairobi 1        
 Kisumu 4        
Rhinolophus sp.
 Three caves 1        
 Shimoni cave 1        
 No information 2        
Rhinolophus clivosus
 Nairobi 5        
Rhinolophus hildebrandtii
 Chyulu National Park 4        
Rousettus aegyptiacus
 Three caves 11       3
 Kitum cave 10   1    
 Makingeny cave 9        
 Watamu cave 6   1   1
Taphozous nudiventris
 Marungu 2        
Taphozous hildegarde
 Shimoni cave 3        
Total 217 4 11 2 23

Conclusion
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
 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). David M Pigott et al: Mapping the zoonotic niche of Ebola virus disease in Africa.  eLife 2014;10.7554/eLife.04395. Published September 8, 2014
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. David M Pigott et al: Mapping the zoonotic niche of Ebola virus disease in Africa.  eLife 2014;10.7554/eLife.04395. Published September 8, 2014
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. David M Pigott et al: Mapping the zoonotic niche of Ebola virus disease in Africa.  eLife 2014;10.7554/eLife.04395. Published September 8, 2014
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. David M Pigott et al: Mapping the zoonotic niche of Ebola virus disease in Africa.  eLife 2014;10.7554/eLife.04395. Published September 8, 2014
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.

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Bat epidemiology
Bat research and study epidemiology : chiropterology.com
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natural history - ecologyepizootiology - epidemiology

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Ebola virus disease (EVD) aka Ebola hemorrhagic fever (EHF) [ICD-10 A98.4] by dr Z Halat, Medical Epidemiology Consultant