TB training in Kenya: building capacity for care and prevention.

BACKGROUND: Devolution of healthcare services in Kenya resulted in a large number of newly recruited tuberculosis (TB) coordinators. We describe a unique collaboration between a national tuberculosis program (NTP), a local, and an international non-governmental organization to build human resource capacity in TB care and prevention. METHODS: From 2016 to 2021, the Kenya Division of National Tuberculosis, Leprosy and Lung Disease Program, Centre for Health Solutions-Kenya, and the International Union Against Tuberculosis and Lung Disease developed and conducted a series of 7-day training courses. A key focus of training was the introduction of TBData4Action, an approach involving the local use of routinely available data to strengthen decision-making and support supervision. RESULTS: Implementation outcomes included training 331 (96%) coordinators out of 344, representing all 47 counties, 37 national officers and 21 other stakeholders using the country-tailored curriculum, including hands-on group work by county teams and field practicals. Thirty-five national facilitators were identified and mentored as local faculty. Training costs were reduced by 75% compared with international alternatives. CONCLUSION: The collaboration resulted in the training of the majority of the coordinators in a standardized approach to TB care. A sustainable approach to capacity building in local data use was found feasible; the model could be adapted by other NTPs.

CONTEXTE: La décentralisation des services de santé au Kenya a conduit au recrutement d'un grand nombre de nouveaux coordinateurs TB. Nous décrivons une collaboration unique entre un programme national de lutte contre la TB (NTP), une organisation non gouvernementale locale et une organisation non gouvernementale internationale visant à renforcer les capacités humaines en matière de prévention et de soins de la TB. MÉTHODES: De 2016 à 2021, la division kényane du programme national de lutte contre la tuberculose, la lèpre et les maladies respiratoires, le Centre for Health Solutions-Kenya et l'Union internationale contre la tuberculose et les maladies respiratoires ont développé et dispensé une série de formations en 7 jours. La formation mettait l'accent sur l'introduction de l'approche TBData4Action, qui promeut une utilisation locale des données disponibles en routine afin de renforcer la prise de décision et d'épauler les activités de supervision. RÉSULTATS: Les résultats de la mise en place de cette formation comprenaient la formation de 331 (96%) coordinateurs sur 344, représentant l'ensemble des 47 pays, 37 administrateurs nationaux et 21 autres acteurs formés à l'aide du programme adapté aux besoins du pays concerné (dont travail de groupe pratique par les équipes nationales et travaux pratiques sur le terrain). Trente-cinq facilitateurs nationaux ont été identifiés et formés comme enseignants locaux. Les coûts de la formation ont été réduits de 75% par rapport aux alternatives internationales. CONCLUSION: La collaboration a permis de former la majorité des coordinateurs à l'aide d'une approche standardisée de soins de la TB. Une approche durable de renforcement des capacités en matière d'utilisation des données locales s'est avérée réalisable. Ce modèle peut être adapté à d'autres NTP.

Multi-locus sequence typing of African swine fever viruses from endemic regions of Kenya and Eastern Uganda (2011-2013) reveals rapid B602L central variable region evolution.

The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72 locus. Variation in the thymidine kinase locus is a novel additional tool for ASFV genotyping whose application for this purpose is described for the first time herein. We evaluated genetic variation at these four polymorphic loci in 39 ASFV isolates obtained from outbreaks in Kenya and a region of Eastern Uganda between 2011 and 2013. Analysis of the p72 and p54 loci revealed high genetic conservation among these isolates; all clustered within p72 genotype IX and were similar to isolates associated with earlier outbreaks in East Africa. The thymidine kinase gene of the Kenyan isolates in this study were distinct relative to Southern African isolates and synonymous substitutions were observed among viruses from central Kenya. Analysis of the CVR within the B602L gene revealed two previously unknown polymorphisms that were restricted to Western Kenya and Eastern Uganda. A novel variant was revealed within CVR subgroup XXIV and a novel CVR subgroup XXIVa that contains tetrameric repeat F which has previously only been associated with p72 genotype I, was also identified for the first time in East Africa. Phylogeographic analysis of isolates based on CVR polymorphisms revealed rapid evolution and dissemination of variants present within ASFV genotype IX in East Africa.

First Complete Genome Sequences of Porcine Bocavirus Strains from East Africa.

Here, we report the first complete genome sequences of two strains of porcine bocavirus (JOA_011 and JOA_015) detected in Uganda and Kenya, respectively. These data will help in understanding the molecular and evolutionary characteristics of the porcine bocaviruses in this region and the development of appropriate diagnostic and control tools.

Risk factors for rotavirus infection in pigs in Busia and Teso subcounties, Western Kenya.

We analysed data that were previously collected for molecular characterisation of rotavirus (RV) groups A and C in pigs from Teso and Busia subcounties in Kenya to determine risk factors for its infection. The data included records from 239 randomly selected piglets aged between 1 and 6 months raised in free range and backyard production systems. RV infection was confirmed by screening of fresh faecal samples by using reverse transcription polymerase chain reaction (RT-PCR); selected positive samples were subsequently sequenced and used for phylogenetic analysis. In this analysis, RV infection status was used as outcome variable, while the metadata collected at the time of sampling were used as predictors. A Bayesian hierarchical model which used integrated nested Laplace approximation (INLA) method was then fitted to the data. The model accounted for the spatial effect by using stochastic partial differential equations (SPDEs). Of the 239 samples screened, 206 were available for the analysis. Descriptive analyses showed that 27.7 % (57/206) of the samples were positive for rotaviruses groups A and C, 18.5 % were positive for group A rotaviruses, 5.3 % were positive for group C rotaviruses, while 3.9 % had co-infections from both groups of rotaviruses. The spatial effect was insignificant, and a simple (non-spatial) model showed that piglets (≤4 months) and those pigs kept in free range systems had higher risk of exposure to rotavirus infection as compared to older pigs (>4 months) and those tethered or housed, respectively. Intervention measures that will target these high-risk groups of pigs will be beneficial to farmers.

Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: predominance of P[8] genotype resembling human strains.

Viral enteritis is a serious problem accounting for deaths in neonatal animals and humans worldwide. The absence of surveillance programs and diagnostic laboratory facilities have resulted in a lack of data on rotavirus associated diarrheas in pigs in East Africa. Here we describe the incidence of group A rotavirus (RVA) infections in asymptomatic young pigs in East Africa. Of the 446 samples examined, 26.2% (117/446) were positive for RVA. More nursing piglets (78.7%) shed RVA than weaned (32.9%) and grower (5.8%) pigs. RVA incidence was higher in pigs that were either housed_free-range (77.8%) or tethered_free-range (29.0%) than those that were free-range or housed or housed-tethered pigs. The farms with larger herd size (>10 pigs) had higher RVA prevalence (56.5%) than farms with smaller herd size (24.1-29.7%). This study revealed that age, management system and pig density significantly (p<0.01) influenced the incidence of RVA infections, with housed_free-range management system and larger herd size showing higher risks for RVA infection. Partial (811-1604nt region) sequence of the VP4 gene of selected positive samples revealed that different genotypes (P[6], P[8] and P[13]) are circulating in the study area with P[8] being predominant. The P[6] strain shared nucleotide (nt) and amino acid (aa) sequence identity of 84.4-91.3% and 95.1-96.9%, respectively, with known porcine and human P[6] strains. The P[8] strains shared high nt and aa sequence identity with known human P[8] strains ranging from 95.6-100% to 92-100%, respectively. The P[13] strains shared nt and aa sequence identity of 83.6-91.7% and 89.3-96.4%, respectively, only with known porcine P[13] strains. No P[8] strains yielded RNA of sufficient quality/quantity for full genome sequencing. However analysis of the full genome constellation of the P[6], two P[13] and one untypeable strains revealed that the P[6] strain (Ke-003-5) genome constellation was G26-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1, P[13] strains (Ug-049 and Ug-453) had G5-P[13]-I5-R1-C1-M1-A8-N1-T7-E1-H1 while the untypeable strain (Ug-218) had G5-P[?]-I5-R1-C1-M1-A8-N1-T1-E1-H? In conclusion, P[6] and P[8] genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission. Further studies are required to determine the role of RVA in swine enteric disease burden and to determine the genetic/antigenic heterogeneity of the circulating strains for development of accurate diagnostic tools and to implement appropriate prophylaxis programs.

Comparison of African swine fever virus prevalence and risk in two contrasting pig-farming systems in South-west and Central Kenya.

We describe a horizontal survey of African swine fever virus (ASFV) prevalence and risk factors associated with virus infection in domestic pigs in two contrasting production systems in Kenya. A free range/tethering, low input production system in Ndhiwa District of South-western Kenya is compared with a medium input stall fed production system in Kiambu District of Central Kenya. Analysis of variance (ANOVA) of data derived from cluster analysis showed that number of animals, number of breeding sows and number of weaner pigs were a significant factor in classifying farms in Nhiwa and Kiambu. Analysis of blood and serum samples using a PCR assay demonstrated an average animal level positivity to ASFV of 28% in two independent samplings in South-western Kenya and 0% PCR positivity in Central Kenya. No animals were sero-positive in either study site using the OIE indirect-ELISA and none of the animals sampled exhibited clinical symptoms of ASF. The farms that contained ASFV positive pigs in Ndhiwa District were located in divisions bordering the Ruma National Park from which bushpig (Potamochoerus larvatus) incursions into farms had been reported. ASFV prevalence (P<0.05) was significantly higher at distances between 6 and 16km from the National Park than at distances closer or further away. One of the 8 bushpigs sampled from the park, from which tissues were obtained was PCR positive for ASFV. The data therefore indicated a potential role for the bushpig in virus transmission in South-western Kenya, but there was no evidence of a direct sylvatic virus transmission cycle in Central Kenya. ASF control strategies implemented in these areas will need to take these epidemiological findings into consideration.

Comparative evaluation of novel African swine fever virus (ASF) antibody detection techniques derived from specific ASF viral genotypes with the OIE internationally prescribed serological tests.

The presence of antibodies against African swine fever (ASF), a complex fatal notifiable OIE disease of swine, is always indicative of previous infection, since there is no vaccine that is currently used in the field. The early appearance and subsequent long-term persistence of antibodies combined with cost-effectiveness make antibody detection techniques essential in control programmes. Recent reports appear to indicate that the serological tests recommended by the OIE for ASF monitoring are much less effective in East and Southern Africa where viral genetic and antigenic diversity is the greatest. We report herein an extensive analysis including more than 1000 field and experimental infection sera, in which the OIE recommended tests are compared with antigen-specific ELISAs and immuno-peroxidase staining of cells (IPT). The antibody detection results generated using new antigen-specific tests, developed in this study, which are based on production of antigen fractions generated by infection and virus purification from COS-1 cells, showed strong concordance with the OIE tests. We therefore conclude that the lack of success is not attributable to antigenic polymorphism and may be related to the specific characteristics of the local breeds African pigs.