Yatinder Singh Binepal - Academia.edu (original) (raw)
Papers by Yatinder Singh Binepal
Journal of Medical Entomology, Mar 1, 1991
During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Provin... more During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Province, Kenya, 61,347 mosquitoes (1,287 pools) collected in CO 2-baited light traps yielded seven viral isolates. Five isolates of RVF virus were recovered from 18,831 Culex zombaensis Theobald and one from 14,439 Mansonia africana (Theobald). One isolate of a Bunyamwera group virus was recovered from 1,175 Aedes quasiunivittatus (Theobald).
Veterinary Record, Mar 31, 2023
A vet who made a substantial contribution to tropical veterinary virology.
Viruses
The avian gamma-coronavirus infectious bronchitis virus (AvCoV, IBV; Coronaviridae family) causes... more The avian gamma-coronavirus infectious bronchitis virus (AvCoV, IBV; Coronaviridae family) causes upper respiratory disease associated with severe economic losses in the poultry industry worldwide. Here, we report for the first time in Kenya and the Eastern African region two novel AvCoVs, designated IBV/ck/KE/1920/A374/2017 (A374/17) and AvCoV/ck/KE/1922/A376/2017 (A376/17), inadvertently discovered using random nontargeted next-generation sequencing (NGS) of cloacal swabs collected from indigenous chickens. Despite having genome organization (5′UTR-[Rep1a/1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3′UTR), canonical conservation of essential genes and size (~27.6 kb) typical of IBVs, the Kenyan isolates do not phylogenetically cluster with any genotypes of the 37 IBV lineages and 26 unique variants (UVs). Excluding the spike gene, genome sequences of A374/17 and A376/17 are only 93.1% similar to each other and 86.7–91.4% identical to genomes of other AvCoVs. All five non-spike genes of the ...
Advances in Virology, Jan 30, 2023
Rift Valley fever virus (RVFV) is a high-priority zoonotic pathogen with the ability to cause mas... more Rift Valley fever virus (RVFV) is a high-priority zoonotic pathogen with the ability to cause massive loss during its outbreak within a very short period of time. Lack of a highly sensitive, instant reading diagnostic method for RVFV, which is more suitable for on-site testing, is a big gap that needs to be addressed. Te aim of this study was to develop a novel one-step reverse transcription loop-mediated isothermal amplifcation (RT-LAMP) method for the rapid detection of RVFV. To achieve this, the selected RVFV M segment nucleotide sequences were aligned using Multiple Sequence Comparison by Log-Expectation (MUSCLE) software in MEGA11 version 11.0.11 program to identify conserved regions. A 211 pb sequence was identifed and six diferent primers to amplify it were designed using NEB LAMP Primer design tool version 1.1.0. Te specifcity of the designed primers was tested using primer BLAST, and a primer set, specifc to RVFV and able to form a loop, was selected. In this study, we developed a single-tube test based on calorimetric RT-LAMP that enabled the visual detection of RVFV within 30 minutes at 65°C. Diagnostic sensitivity and specifcity of the newly developed kit were compared with RVFV qRT-PCR, using total RNA samples extracted from 118 blood samples. Te colorimetric RT-LAMP assay had a sensitivity of 98.36% and a specifcity of 96.49%. Te developed RT-LAMP was found to be tenfold more sensitive compared to the RVFV qRT-PCR assay commonly used in the confrmatory diagnosis of RVFV.
International Journal of Animal Science and Technology, 2021
Vaccination of flocks against Newcastle disease virus (NDV) outbreaks is the main approach for co... more Vaccination of flocks against Newcastle disease virus (NDV) outbreaks is the main approach for controlling the spread of Newcastle disease (ND). Nevertheless, NDV outbreaks have been reported in vaccinated chickens. In this study, we determined the prevalence of NDV among vaccinated indigenous chickens (ICs) and examined the relationship of the disease with the weather (temperature, rainfall, humidity, and wind speed) at the time of sample collection, production system, and the presence of other species. The genetic diversity of the NDV matrix and fusion genes was also inferred. A total of 1,210 swabs were collected between 2017 and 2018 from ICs that were vaccinated or unvaccinated against NDV in free-range and semifree-range production systems. We collected 650 swabs each from the oropharynx and cloaca of ICs in 68 households within the Bomet, Baringo, Kilifi, Nakuru, Kakamega, and Machakos counties in Kenya. NDV matrix genes were detected using reverse transcription-polymerase chain reaction, and amplicons of matrix and fusion genes were sequenced using a capillary sequencer from the pooled samples. Among the vaccinated ICs, the prevalence of NDV was 78.5% (p=0.045). There were significant relationships between the presence of NDV and vaccination history of the ICs (p=0.034), the type of production system for ICs (p=0.004) and the months of sample collection (p < 0.0001). However, no significant relationship was found between the presence of NDV and the interaction between ICs and other birds. The presence of matrix and fusion genes in samples from vaccinated flocks indicated the presence of both virulent and low-virulence strains of NDV. These findings highlight the significant presence of NDV among vaccinated ICs and suggest the possibility of inadequate vaccination and viral shedding post-vaccination as the drivers of infections.
Infection, Genetics and Evolution, 2019
, et al., Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influe... more , et al., Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets, Infection, Genetics and Evolution(2018),
Tropical Animal Health and Production, 2019
Newcastle disease (ND) is a major constraint to Kenya’s poultry production, which is comprised of... more Newcastle disease (ND) is a major constraint to Kenya’s poultry production, which is comprised of approximately 80% indigenous chickens (ICs; caged and free-range system) and 20% exotic chickens (intensive system). This study analyzed cases reported as suspected ND in Kenya between 2005 and 2015. Of the suspected 332 ND reported cases from the three production systems in 27 locations within six Kenyan Agro-Ecological Zones (AEZs), 140 diagnosed as infected with avian orthoavulavirus 1 (AOaV-1; formerly Newcastle disease virus) were present in every year in all AEZs. The numbers of AOaV-1-positive cases differed significantly (p < 0.05) between the production systems across the years depending on the season, climate, and location. In the free-range system, both ambient temperatures and season associated significantly (p = 0.001 and 0.02, respectively) with the number of cases, while in the intensive and caged systems, the positive cases correlated significantly with season and rel...
Journal of Genetic Engineering and Biotechnology, 2017
In this study, indigenous chickens were collected from eight different regions in Kenya and kept ... more In this study, indigenous chickens were collected from eight different regions in Kenya and kept at InCIP-Egerton University. These were studied using eighteen microsatellite markers to determine genetic variation. Statistics related to genetic variation were estimated using GenA-LEx6. Mean percentage polymorphic loci (PPL) was 96.71% and 4% genetic variance (p ! 0.003) was seen between the eight populations. MCW0123 marker had the highest genetic variance of 13% among populations (p ! 0.003) at 95% CI. Mean He ranged from 0.351 ± 0.031 (SIB) to 0.434 ± 0.022 (BM) with a grand mean He of 0.399 ± 0.011 across the populations using the microsatellite markers. Nei's genetic distance ranged from 0.016 (SIB and WP) to 0.126 (NR and SIB). DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. This study found a lot of genetic variation and relatedness within and among populations. Based on the phylogenetic tree result, it is concluded that the clustering of the chicken populations in the present study is not based on geographical proximity. The microsatellite markers used in this study were suitable for the measurement of the genetic biodiversity and relationship of Kenyan chicken populations. These results can therefore serve as an initial step to plan the conservation of indigenous chickens in Kenya.
Journal of Medical Entomology, 1991
During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Provin... more During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Province, Kenya, 61,347 mosquitoes (1,287 pools) collected in CO 2-baited light traps yielded seven viral isolates. Five isolates of RVF virus were recovered from 18,831 Culex zombaensis Theobald and one from 14,439 Mansonia africana (Theobald). One isolate of a Bunyamwera group virus was recovered from 1,175 Aedes quasiunivittatus (Theobald).
Journal of Virological Methods, 2014
Arthropod-Borne Animal Diseases Research Unit, Agricultural Research Service, United States Depar... more Arthropod-Borne Animal Diseases Research Unit, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA Biotechnology Building, ARC-Onderstepoort Veterinary Institute, P/Bag X5, Onderstepoort 0110, South Africa National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, 1015 Arlington Street, Winnipeg, Manitoba, Canada Biotechnology Center, Kenya Agricultural Research Institute, Off Waiyaki Way, P.O. Box 57811-00200, City Square, Nairobi, Kenya Department Veterinary Tropical Diseases, Veterinary Faculty, University of Pretoria, P/Bag X4, Onderstepoort 0110, South Africa Special Viral Pathogens Laboratory, Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases, A Division of the National ealth Laboratory Service, Private Bag X4, Sandringham 2131, South Africa
Journal of Virological Methods, 2013
Outbreaks of Rift Valley fever in Kenya, Madagascar, Mauritania, and South Africa had devastating... more Outbreaks of Rift Valley fever in Kenya, Madagascar, Mauritania, and South Africa had devastating effects on livestock and human health. In addition, this disease is a food security issue for endemic countries. There is growing concern for the potential introduction of RVF into non-endemic countries. A number of single-gene target amplification assays have been developed for the rapid detection of RVF viral RNA. This paper describes the development of an improved amplification assay that includes two confirmatory target RNA segments (L and M) and a third target gene, NSs, which is deleted in the Clone 13 commercial vaccine and other candidate vaccines. The assay also contains an exogenous RNA control added during the PCR setup for detection of amplification inhibitors. The assay was evaluated initially with samples from experimentally infected animals, after which clinical veterinary and human samples from endemic countries were tested for further evaluation. The assay has a sensitivity range of 66.7-100% and a specificity of 92.0-100% depending on the comparison. The assay has an overall sensitivity of 92.5%, specificity of 95% and a positive predictive value of 98.7%. The single-tube assay provides confirmation of the presence of RVFV RNA for improved confidence in diagnostic results and a "differentiate infected from vaccinated animals" (DIVA)-compatible marker for RVFV NSs-deleted vaccines, which is useful for RVF endemic countries, but especially important in non-endemic countries.
Journal of Tropical Microbiology and Biotechnology, 2008
Veterinary Record, Aug 1, 1999
C. K. Ngichabe, BVM, MSc, PhD, Y. S. Binepal, BVM, MSc, PhD, J. W. Njiru, HNDMLT, Kenya Agricultu... more C. K. Ngichabe, BVM, MSc, PhD, Y. S. Binepal, BVM, MSc, PhD, J. W. Njiru, HNDMLT, Kenya Agricultural Research Institute, National Veterinary Research Centre Muguga, PO Box 32, Kikuyu, Kenya V. M. Carn, BVM, MRCVS, PhD, Institute for Animal Health, Pirbright Laboratory, Pirbright, Woking, Surrey GU24 ONF CAPRIPOXVIRUSES are economically important viruses of livestock causing pox in sheep, goats and cattle, and are characterised by pyrexia, skin and internal papular eruptions, and enlargement of superficial lymph nodes. The animals lose condition and productivity while young ones usually die (Burdin and Pyridie 1959, Weiss 1968, Prozesky and Bernard 1982, Davies 1991). The annual revenue lost following outbreaks in Kenya is approximately 180 million Ksh (Upton 1980). The disease caused by capripoxviruses is endemic in Asia, Africa and the Middle East. Control measures, including slaughter, ring vaccination and the imposition of quarantine, depend entirely on confirmatory diagnosis in the laboratory. This involves virus isolation followed by serological tests such as fluorescent antibody and serum neutralisation. However, the serological tests are limited in their application because they are dependent on cell culture techniques, resulting in delays ofup to two weeks for the virus cytopathic effect (cpe) to develop (Plowright and Ferris 1958). Some strains grow very poorly in these cell cultures and may require several blind passages before the cpe develops, and further delays in diagnosis frequently involve contamination of cell cultures by bacteria, fungi and yeast. These difficulties have prompted the development of the immunocapture ELISA (icELISA) based on a detection antibody raised against a capripoxvirus recombinant antigen (Chand 1992). This paper reports the results of the evaluation and potential application of the test in the routine diagnosis of capripoxvirus diseases. Fifty-six test samples, comprising 41 biopsy supernatants from capripox clinical cases, eight different batches oflumpy skin disease vaccine and seven non-capripox clinical case samples, were prepared as described by Carn (1995) and tested directly on icELISA. Parallel aliquots were inoculated onto prepubertal lamb testis cell cultures to isolate the virus. The capture antibody (a rabbit anti-capripoxvirus polyclonal antiserum) and the detector antiserum (a guinea pig antibody against the recombinant capripoxvirus 32 kDa antigen) were prepared as described by Carn and others (1994). To determine the test detection threshold level, capripoxvirus (Kedong strain) was grown in prepubertal lamb testis cells and harvested when the cpe was approximately 95 per cent. Ten-fold virus dilutions were titrated in tissue culture microtitre plates as previously described (Plowright and Ferris 1958) and infectivity titres (TCID50) were calculated according to the method described by Karber (1931). The virus had a titre of 106 TCID50/50 iil. Ten-fold dilutions of the same virus ranging from logl0 10-1 to log10 10-7 were made and titrated in the icELISA at eight wells per dilution. The icELISA test was carried out as described by Carn (1995). ELISA plates (Nunc Maxisorp) were coated with 100 i1l capture antibody in coating buffer (0.05M carbonate/bicarbonate, pH 9.6) at a predetermined dilution of 1:100. The plates were incubated at 4°C overnight and then washed four times in phosphate buffered saline (PBS). Test samples (50 [Il) were added to appropriate wells in duplicate, and titrated by cJ
Journal of Biology Agriculture and Healthcare, 2013
The diagnosis of Nairobi Sheep Disease relies on the inoculation of tissue culture, Baby Hamster ... more The diagnosis of Nairobi Sheep Disease relies on the inoculation of tissue culture, Baby Hamster kidney (BHK-21), with suspensions of infected samples followed by identification of the virus using indirect Immunofluorescent assay. These tests have a number of drawbacks including low specificity; visual reading of results which requires highly skilled expertise and tissue culture facilities therefore development of capture Enzyme linked Immuno Sorbent assay (ELISA) would improve the diagnosis of NSD in infected sheep. Nairobi Sheep Disease Virus (NSDV) was isolated, purified and titrated to determine the best working titer for immunization of animals. The purified virus subjected to IIFA test and fluorescence indicated the presence of NSDV. The animals immunized were rabbits and goat which were used for production of antibodies for C-ELISA test. C-ELISA was setup using anti-goat sera as the primary antibody, purified NSDV as antigen and anti-rabbit sera as the secondary antibody. A 1:400 dilution was established as best dilution for true positive and negative samples. The diagnostic specificity and specificity of the developed C-ELISA was estimated. False positive samples were picked by IIFA, which was confirmed by tissue culture technique. The level of agreement between developed C-ELISA and IIFA used as a gold test was 95%, and the Kappa index was 0.86. The perfect agreement indicated by Kappa values is a sign that both tests can be used. However, C-ELISA is a better test in that it is more flexible and less subjective. The sensitivity and specificity of C-ELISA was estimated at 80% and 100% respectively. The results showed high diagnostic specificity of developed C-ELISA which could be adapted to test a large number of samples over short periods of time. The test is useful during outbreaks of NSD without need for tissue culture facilities.
The Kenya Veterinarian, 2011
The surveillance of Rift Valley Fever (RVF) was carried out in the risk areas of Kenya by monitor... more The surveillance of Rift Valley Fever (RVF) was carried out in the risk areas of Kenya by monitoring free range/migratory and sedentary farm sheep and goat herds for antibodies to RVF virus (RVFV). A total of 986 serum samples were collected and analyzed from farms in Molo, (where no outbreaks has ever been previously reported), Naivasha, (an RVF-endemic area and where the first case of RVF was reported in Kenya), Kajiado, (where there had been reports of an RVF-like disease) and Shompole, (a chief transmigratory livestock-route and market on the Kenya/Tanzania border). Of the total sera tested, 16.9% (164/966), 8.4% (81/966) and 4.1% (39/966) were found to be positive by IgG-sandwich enzyme-linked immunosorbent assay (ELISA), IgM-capture ELISA and serum neutralization (SN) tests respectively. On average, the percentages of sera testing positive for antibodies from sedentary farm herds (Molo, Nakuru and Naivasha) were higher than those from the free-range herds (Kajiado, Namanga, Ma...
Journal of Virology, 2008
Rift Valley fever (RVF) virus historically has caused widespread and extensive outbreaks of sever... more Rift Valley fever (RVF) virus historically has caused widespread and extensive outbreaks of severe human and livestock disease throughout Africa, Madagascar, and the Arabian Peninsula. Following unusually heavy rainfall during the late autumn of 2006, reports of human and animal illness consistent with RVF virus infection emerged across semiarid regions of the Garissa District of northeastern Kenya and southern Somalia. Following initial RVF virus laboratory confirmation, a high-throughput RVF diagnostic facility was established at the Kenyan Central Veterinary Laboratories in Kabete, Kenya, to support the real-time identification of infected livestock and to facilitate outbreak response and control activities. A total of 3,250 specimens from a variety of animal species, including domesticated livestock (cattle, sheep, goats, and camels) and wildlife collected from a total of 55 of 71 Kenyan administrative districts, were tested by molecular and serologic assays. Evidence of RVF inf...
Infectio, Genetics & Evolution, 2019
Poultry production plays an important role in the economy and livelihoods of rural households in ... more Poultry production plays an important role in the economy and livelihoods of rural households in Kenya. As part of a surveillance program, avian influenza virus (AIV)-specific real-time RT-PCR (RRT-PCR) was used to screen 282 oropharyngeal swabs collected from chickens at six live bird markets (LBMs) and 33 backyard poultry farms in Kenya and 8 positive samples were detected. Virus was isolated in eggs from five samples, sequenced, and identified as H9N2 low pathogenic AIV (LPAIV) G1 lineage, with highest nucleotide sequence identity (98.6-99.9%) to a 2017 Ugandan H9N2 isolate. The H9N2 contained molecular markers for mammalian receptor specificity, implying their zoonotic potential. Virus pathogenesis and transmissibility was assessed by inoculating low and medium virus doses of a representative Kenyan H9N2 LPAIV isolate into experimental chickens and exposing them to naïve uninfected chickens at 2 -days post inoculation (dpi). Virus shedding was determined at 2/4/7 dpi and 2/5 days post placement (dpp), and seroconversion determined at 14 dpi/12 dpp. None of the directly-inoculated or contact birds exhibited any mortality or clinical disease signs. All directly-inoculated birds in the low dose group shed virus during the experiment, while only one contact bird shed virus at 2 dpp. Only two directly-inoculated birds that shed high virus titers seroconverted in that group. All birds in the medium dose group shed virus at 4/7 dpi and at 5 dpp, and they all seroconverted at 12/14 dpp. This is the first reported detection of H9N2 LPAIV from Kenya and it was shown to be infectious and transmissible in chickens by direct contact and represents a new disease threat to poultry and potentially to people.
Journal of Medical Entomology, Mar 1, 1991
During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Provin... more During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Province, Kenya, 61,347 mosquitoes (1,287 pools) collected in CO 2-baited light traps yielded seven viral isolates. Five isolates of RVF virus were recovered from 18,831 Culex zombaensis Theobald and one from 14,439 Mansonia africana (Theobald). One isolate of a Bunyamwera group virus was recovered from 1,175 Aedes quasiunivittatus (Theobald).
Veterinary Record, Mar 31, 2023
A vet who made a substantial contribution to tropical veterinary virology.
Viruses
The avian gamma-coronavirus infectious bronchitis virus (AvCoV, IBV; Coronaviridae family) causes... more The avian gamma-coronavirus infectious bronchitis virus (AvCoV, IBV; Coronaviridae family) causes upper respiratory disease associated with severe economic losses in the poultry industry worldwide. Here, we report for the first time in Kenya and the Eastern African region two novel AvCoVs, designated IBV/ck/KE/1920/A374/2017 (A374/17) and AvCoV/ck/KE/1922/A376/2017 (A376/17), inadvertently discovered using random nontargeted next-generation sequencing (NGS) of cloacal swabs collected from indigenous chickens. Despite having genome organization (5′UTR-[Rep1a/1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3′UTR), canonical conservation of essential genes and size (~27.6 kb) typical of IBVs, the Kenyan isolates do not phylogenetically cluster with any genotypes of the 37 IBV lineages and 26 unique variants (UVs). Excluding the spike gene, genome sequences of A374/17 and A376/17 are only 93.1% similar to each other and 86.7–91.4% identical to genomes of other AvCoVs. All five non-spike genes of the ...
Advances in Virology, Jan 30, 2023
Rift Valley fever virus (RVFV) is a high-priority zoonotic pathogen with the ability to cause mas... more Rift Valley fever virus (RVFV) is a high-priority zoonotic pathogen with the ability to cause massive loss during its outbreak within a very short period of time. Lack of a highly sensitive, instant reading diagnostic method for RVFV, which is more suitable for on-site testing, is a big gap that needs to be addressed. Te aim of this study was to develop a novel one-step reverse transcription loop-mediated isothermal amplifcation (RT-LAMP) method for the rapid detection of RVFV. To achieve this, the selected RVFV M segment nucleotide sequences were aligned using Multiple Sequence Comparison by Log-Expectation (MUSCLE) software in MEGA11 version 11.0.11 program to identify conserved regions. A 211 pb sequence was identifed and six diferent primers to amplify it were designed using NEB LAMP Primer design tool version 1.1.0. Te specifcity of the designed primers was tested using primer BLAST, and a primer set, specifc to RVFV and able to form a loop, was selected. In this study, we developed a single-tube test based on calorimetric RT-LAMP that enabled the visual detection of RVFV within 30 minutes at 65°C. Diagnostic sensitivity and specifcity of the newly developed kit were compared with RVFV qRT-PCR, using total RNA samples extracted from 118 blood samples. Te colorimetric RT-LAMP assay had a sensitivity of 98.36% and a specifcity of 96.49%. Te developed RT-LAMP was found to be tenfold more sensitive compared to the RVFV qRT-PCR assay commonly used in the confrmatory diagnosis of RVFV.
International Journal of Animal Science and Technology, 2021
Vaccination of flocks against Newcastle disease virus (NDV) outbreaks is the main approach for co... more Vaccination of flocks against Newcastle disease virus (NDV) outbreaks is the main approach for controlling the spread of Newcastle disease (ND). Nevertheless, NDV outbreaks have been reported in vaccinated chickens. In this study, we determined the prevalence of NDV among vaccinated indigenous chickens (ICs) and examined the relationship of the disease with the weather (temperature, rainfall, humidity, and wind speed) at the time of sample collection, production system, and the presence of other species. The genetic diversity of the NDV matrix and fusion genes was also inferred. A total of 1,210 swabs were collected between 2017 and 2018 from ICs that were vaccinated or unvaccinated against NDV in free-range and semifree-range production systems. We collected 650 swabs each from the oropharynx and cloaca of ICs in 68 households within the Bomet, Baringo, Kilifi, Nakuru, Kakamega, and Machakos counties in Kenya. NDV matrix genes were detected using reverse transcription-polymerase chain reaction, and amplicons of matrix and fusion genes were sequenced using a capillary sequencer from the pooled samples. Among the vaccinated ICs, the prevalence of NDV was 78.5% (p=0.045). There were significant relationships between the presence of NDV and vaccination history of the ICs (p=0.034), the type of production system for ICs (p=0.004) and the months of sample collection (p < 0.0001). However, no significant relationship was found between the presence of NDV and the interaction between ICs and other birds. The presence of matrix and fusion genes in samples from vaccinated flocks indicated the presence of both virulent and low-virulence strains of NDV. These findings highlight the significant presence of NDV among vaccinated ICs and suggest the possibility of inadequate vaccination and viral shedding post-vaccination as the drivers of infections.
Infection, Genetics and Evolution, 2019
, et al., Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influe... more , et al., Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets, Infection, Genetics and Evolution(2018),
Tropical Animal Health and Production, 2019
Newcastle disease (ND) is a major constraint to Kenya’s poultry production, which is comprised of... more Newcastle disease (ND) is a major constraint to Kenya’s poultry production, which is comprised of approximately 80% indigenous chickens (ICs; caged and free-range system) and 20% exotic chickens (intensive system). This study analyzed cases reported as suspected ND in Kenya between 2005 and 2015. Of the suspected 332 ND reported cases from the three production systems in 27 locations within six Kenyan Agro-Ecological Zones (AEZs), 140 diagnosed as infected with avian orthoavulavirus 1 (AOaV-1; formerly Newcastle disease virus) were present in every year in all AEZs. The numbers of AOaV-1-positive cases differed significantly (p < 0.05) between the production systems across the years depending on the season, climate, and location. In the free-range system, both ambient temperatures and season associated significantly (p = 0.001 and 0.02, respectively) with the number of cases, while in the intensive and caged systems, the positive cases correlated significantly with season and rel...
Journal of Genetic Engineering and Biotechnology, 2017
In this study, indigenous chickens were collected from eight different regions in Kenya and kept ... more In this study, indigenous chickens were collected from eight different regions in Kenya and kept at InCIP-Egerton University. These were studied using eighteen microsatellite markers to determine genetic variation. Statistics related to genetic variation were estimated using GenA-LEx6. Mean percentage polymorphic loci (PPL) was 96.71% and 4% genetic variance (p ! 0.003) was seen between the eight populations. MCW0123 marker had the highest genetic variance of 13% among populations (p ! 0.003) at 95% CI. Mean He ranged from 0.351 ± 0.031 (SIB) to 0.434 ± 0.022 (BM) with a grand mean He of 0.399 ± 0.011 across the populations using the microsatellite markers. Nei's genetic distance ranged from 0.016 (SIB and WP) to 0.126 (NR and SIB). DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. This study found a lot of genetic variation and relatedness within and among populations. Based on the phylogenetic tree result, it is concluded that the clustering of the chicken populations in the present study is not based on geographical proximity. The microsatellite markers used in this study were suitable for the measurement of the genetic biodiversity and relationship of Kenyan chicken populations. These results can therefore serve as an initial step to plan the conservation of indigenous chickens in Kenya.
Journal of Medical Entomology, 1991
During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Provin... more During an outbreak of Rift Valley fever (RVF) in livestock near Lake Naivasha, Rift Valley Province, Kenya, 61,347 mosquitoes (1,287 pools) collected in CO 2-baited light traps yielded seven viral isolates. Five isolates of RVF virus were recovered from 18,831 Culex zombaensis Theobald and one from 14,439 Mansonia africana (Theobald). One isolate of a Bunyamwera group virus was recovered from 1,175 Aedes quasiunivittatus (Theobald).
Journal of Virological Methods, 2014
Arthropod-Borne Animal Diseases Research Unit, Agricultural Research Service, United States Depar... more Arthropod-Borne Animal Diseases Research Unit, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA Biotechnology Building, ARC-Onderstepoort Veterinary Institute, P/Bag X5, Onderstepoort 0110, South Africa National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, 1015 Arlington Street, Winnipeg, Manitoba, Canada Biotechnology Center, Kenya Agricultural Research Institute, Off Waiyaki Way, P.O. Box 57811-00200, City Square, Nairobi, Kenya Department Veterinary Tropical Diseases, Veterinary Faculty, University of Pretoria, P/Bag X4, Onderstepoort 0110, South Africa Special Viral Pathogens Laboratory, Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases, A Division of the National ealth Laboratory Service, Private Bag X4, Sandringham 2131, South Africa
Journal of Virological Methods, 2013
Outbreaks of Rift Valley fever in Kenya, Madagascar, Mauritania, and South Africa had devastating... more Outbreaks of Rift Valley fever in Kenya, Madagascar, Mauritania, and South Africa had devastating effects on livestock and human health. In addition, this disease is a food security issue for endemic countries. There is growing concern for the potential introduction of RVF into non-endemic countries. A number of single-gene target amplification assays have been developed for the rapid detection of RVF viral RNA. This paper describes the development of an improved amplification assay that includes two confirmatory target RNA segments (L and M) and a third target gene, NSs, which is deleted in the Clone 13 commercial vaccine and other candidate vaccines. The assay also contains an exogenous RNA control added during the PCR setup for detection of amplification inhibitors. The assay was evaluated initially with samples from experimentally infected animals, after which clinical veterinary and human samples from endemic countries were tested for further evaluation. The assay has a sensitivity range of 66.7-100% and a specificity of 92.0-100% depending on the comparison. The assay has an overall sensitivity of 92.5%, specificity of 95% and a positive predictive value of 98.7%. The single-tube assay provides confirmation of the presence of RVFV RNA for improved confidence in diagnostic results and a "differentiate infected from vaccinated animals" (DIVA)-compatible marker for RVFV NSs-deleted vaccines, which is useful for RVF endemic countries, but especially important in non-endemic countries.
Journal of Tropical Microbiology and Biotechnology, 2008
Veterinary Record, Aug 1, 1999
C. K. Ngichabe, BVM, MSc, PhD, Y. S. Binepal, BVM, MSc, PhD, J. W. Njiru, HNDMLT, Kenya Agricultu... more C. K. Ngichabe, BVM, MSc, PhD, Y. S. Binepal, BVM, MSc, PhD, J. W. Njiru, HNDMLT, Kenya Agricultural Research Institute, National Veterinary Research Centre Muguga, PO Box 32, Kikuyu, Kenya V. M. Carn, BVM, MRCVS, PhD, Institute for Animal Health, Pirbright Laboratory, Pirbright, Woking, Surrey GU24 ONF CAPRIPOXVIRUSES are economically important viruses of livestock causing pox in sheep, goats and cattle, and are characterised by pyrexia, skin and internal papular eruptions, and enlargement of superficial lymph nodes. The animals lose condition and productivity while young ones usually die (Burdin and Pyridie 1959, Weiss 1968, Prozesky and Bernard 1982, Davies 1991). The annual revenue lost following outbreaks in Kenya is approximately 180 million Ksh (Upton 1980). The disease caused by capripoxviruses is endemic in Asia, Africa and the Middle East. Control measures, including slaughter, ring vaccination and the imposition of quarantine, depend entirely on confirmatory diagnosis in the laboratory. This involves virus isolation followed by serological tests such as fluorescent antibody and serum neutralisation. However, the serological tests are limited in their application because they are dependent on cell culture techniques, resulting in delays ofup to two weeks for the virus cytopathic effect (cpe) to develop (Plowright and Ferris 1958). Some strains grow very poorly in these cell cultures and may require several blind passages before the cpe develops, and further delays in diagnosis frequently involve contamination of cell cultures by bacteria, fungi and yeast. These difficulties have prompted the development of the immunocapture ELISA (icELISA) based on a detection antibody raised against a capripoxvirus recombinant antigen (Chand 1992). This paper reports the results of the evaluation and potential application of the test in the routine diagnosis of capripoxvirus diseases. Fifty-six test samples, comprising 41 biopsy supernatants from capripox clinical cases, eight different batches oflumpy skin disease vaccine and seven non-capripox clinical case samples, were prepared as described by Carn (1995) and tested directly on icELISA. Parallel aliquots were inoculated onto prepubertal lamb testis cell cultures to isolate the virus. The capture antibody (a rabbit anti-capripoxvirus polyclonal antiserum) and the detector antiserum (a guinea pig antibody against the recombinant capripoxvirus 32 kDa antigen) were prepared as described by Carn and others (1994). To determine the test detection threshold level, capripoxvirus (Kedong strain) was grown in prepubertal lamb testis cells and harvested when the cpe was approximately 95 per cent. Ten-fold virus dilutions were titrated in tissue culture microtitre plates as previously described (Plowright and Ferris 1958) and infectivity titres (TCID50) were calculated according to the method described by Karber (1931). The virus had a titre of 106 TCID50/50 iil. Ten-fold dilutions of the same virus ranging from logl0 10-1 to log10 10-7 were made and titrated in the icELISA at eight wells per dilution. The icELISA test was carried out as described by Carn (1995). ELISA plates (Nunc Maxisorp) were coated with 100 i1l capture antibody in coating buffer (0.05M carbonate/bicarbonate, pH 9.6) at a predetermined dilution of 1:100. The plates were incubated at 4°C overnight and then washed four times in phosphate buffered saline (PBS). Test samples (50 [Il) were added to appropriate wells in duplicate, and titrated by cJ
Journal of Biology Agriculture and Healthcare, 2013
The diagnosis of Nairobi Sheep Disease relies on the inoculation of tissue culture, Baby Hamster ... more The diagnosis of Nairobi Sheep Disease relies on the inoculation of tissue culture, Baby Hamster kidney (BHK-21), with suspensions of infected samples followed by identification of the virus using indirect Immunofluorescent assay. These tests have a number of drawbacks including low specificity; visual reading of results which requires highly skilled expertise and tissue culture facilities therefore development of capture Enzyme linked Immuno Sorbent assay (ELISA) would improve the diagnosis of NSD in infected sheep. Nairobi Sheep Disease Virus (NSDV) was isolated, purified and titrated to determine the best working titer for immunization of animals. The purified virus subjected to IIFA test and fluorescence indicated the presence of NSDV. The animals immunized were rabbits and goat which were used for production of antibodies for C-ELISA test. C-ELISA was setup using anti-goat sera as the primary antibody, purified NSDV as antigen and anti-rabbit sera as the secondary antibody. A 1:400 dilution was established as best dilution for true positive and negative samples. The diagnostic specificity and specificity of the developed C-ELISA was estimated. False positive samples were picked by IIFA, which was confirmed by tissue culture technique. The level of agreement between developed C-ELISA and IIFA used as a gold test was 95%, and the Kappa index was 0.86. The perfect agreement indicated by Kappa values is a sign that both tests can be used. However, C-ELISA is a better test in that it is more flexible and less subjective. The sensitivity and specificity of C-ELISA was estimated at 80% and 100% respectively. The results showed high diagnostic specificity of developed C-ELISA which could be adapted to test a large number of samples over short periods of time. The test is useful during outbreaks of NSD without need for tissue culture facilities.
The Kenya Veterinarian, 2011
The surveillance of Rift Valley Fever (RVF) was carried out in the risk areas of Kenya by monitor... more The surveillance of Rift Valley Fever (RVF) was carried out in the risk areas of Kenya by monitoring free range/migratory and sedentary farm sheep and goat herds for antibodies to RVF virus (RVFV). A total of 986 serum samples were collected and analyzed from farms in Molo, (where no outbreaks has ever been previously reported), Naivasha, (an RVF-endemic area and where the first case of RVF was reported in Kenya), Kajiado, (where there had been reports of an RVF-like disease) and Shompole, (a chief transmigratory livestock-route and market on the Kenya/Tanzania border). Of the total sera tested, 16.9% (164/966), 8.4% (81/966) and 4.1% (39/966) were found to be positive by IgG-sandwich enzyme-linked immunosorbent assay (ELISA), IgM-capture ELISA and serum neutralization (SN) tests respectively. On average, the percentages of sera testing positive for antibodies from sedentary farm herds (Molo, Nakuru and Naivasha) were higher than those from the free-range herds (Kajiado, Namanga, Ma...
Journal of Virology, 2008
Rift Valley fever (RVF) virus historically has caused widespread and extensive outbreaks of sever... more Rift Valley fever (RVF) virus historically has caused widespread and extensive outbreaks of severe human and livestock disease throughout Africa, Madagascar, and the Arabian Peninsula. Following unusually heavy rainfall during the late autumn of 2006, reports of human and animal illness consistent with RVF virus infection emerged across semiarid regions of the Garissa District of northeastern Kenya and southern Somalia. Following initial RVF virus laboratory confirmation, a high-throughput RVF diagnostic facility was established at the Kenyan Central Veterinary Laboratories in Kabete, Kenya, to support the real-time identification of infected livestock and to facilitate outbreak response and control activities. A total of 3,250 specimens from a variety of animal species, including domesticated livestock (cattle, sheep, goats, and camels) and wildlife collected from a total of 55 of 71 Kenyan administrative districts, were tested by molecular and serologic assays. Evidence of RVF inf...
Infectio, Genetics & Evolution, 2019
Poultry production plays an important role in the economy and livelihoods of rural households in ... more Poultry production plays an important role in the economy and livelihoods of rural households in Kenya. As part of a surveillance program, avian influenza virus (AIV)-specific real-time RT-PCR (RRT-PCR) was used to screen 282 oropharyngeal swabs collected from chickens at six live bird markets (LBMs) and 33 backyard poultry farms in Kenya and 8 positive samples were detected. Virus was isolated in eggs from five samples, sequenced, and identified as H9N2 low pathogenic AIV (LPAIV) G1 lineage, with highest nucleotide sequence identity (98.6-99.9%) to a 2017 Ugandan H9N2 isolate. The H9N2 contained molecular markers for mammalian receptor specificity, implying their zoonotic potential. Virus pathogenesis and transmissibility was assessed by inoculating low and medium virus doses of a representative Kenyan H9N2 LPAIV isolate into experimental chickens and exposing them to naïve uninfected chickens at 2 -days post inoculation (dpi). Virus shedding was determined at 2/4/7 dpi and 2/5 days post placement (dpp), and seroconversion determined at 14 dpi/12 dpp. None of the directly-inoculated or contact birds exhibited any mortality or clinical disease signs. All directly-inoculated birds in the low dose group shed virus during the experiment, while only one contact bird shed virus at 2 dpp. Only two directly-inoculated birds that shed high virus titers seroconverted in that group. All birds in the medium dose group shed virus at 4/7 dpi and at 5 dpp, and they all seroconverted at 12/14 dpp. This is the first reported detection of H9N2 LPAIV from Kenya and it was shown to be infectious and transmissible in chickens by direct contact and represents a new disease threat to poultry and potentially to people.