ABSTRACT
Bartonella spp. are intracellular bacteria associated with several re-emerging human diseases. Small mammals play a significant role in the maintenance and spread of Bartonella spp. Despite the high small mammal biodiversity in South Africa, there is limited epidemiological information regarding Bartonella spp. in these mammals. The main aim of this study was to determine the prevalence and genetic diversity of Bartonella spp. from wild small mammals from 15 localities in 8 provinces of South Africa. Small mammals (n = 183) were trapped in the Eastern Cape, Free State, Gauteng, Limpopo, Mpumalanga, Northern Cape, North West, and Western Cape provinces of South Africa between 2010 and 2018. Heart, kidney, liver, lung, and spleen were harvested for Bartonella DNA screening, and prevalence was determined based on the PCR amplification of partial fragments of the 16S-23S rRNA intergenic spacer (ITS) region, gltA, and rpoB genes. Bartonella DNA was detected in Aethomys chrysophilus, Aethomys ineptus, Gerbillurus spp., Lemniscomys rosalia, Mastomys coucha, Micaelamys namaquensis, Rhabdomys pumilio, and Thallomys paedulcus. An overall prevalence of 16.9% (31/183, 95% CI: 12.2%-23%) was observed. Bartonella elizabethae, Bartonella grahamii, and Bartonella tribocorum were the zoonotic species identified, while the remaining sequences were aligned to uncultured Bartonella spp. with unknown zoonotic potential. Phylogenetic analyses confirmed five distinct Bartonella lineages (I-V), with lineage IV displaying strong M. coucha host specificity. Our results confirm that South African wild small mammals are natural reservoirs of a diverse assemblage of Bartonella spp., including some zoonotic species with high genetic diversity, although prevalence was relatively low.IMPORTANCESmall mammals play a significant role in the maintenance and spread of zoonotic pathogens such as Bartonella spp. Despite the high small mammal biodiversity in southern Africa including South Africa, there is limited epidemiological information regarding Bartonella spp. in these mammals across the country. Results from our study showed the liver and spleen had the highest positive cases for Bartonella spp. DNA among the tested organs. Bartonella elizabethae, B. grahamii, and B. tribocorum were the three zoonotic species identified and five distinct Bartonella lineages (I-V) were confirmed through phylogenetic analyses. To the best of our knowledge, this study presents the first extensive nuclear diversity investigation of Bartonella spp. in South African small mammals in South Africa.
ABSTRACT
Although rabies is endemic in Malawi, there have been no studies in which rabies virus was systematically investigated and characterized in multiple animal hosts in that country. In order to provide molecular epidemiological data on rabies virus in Malawi, 683 suspected rabies case reports from 2008 to 2021 were examined, and 46 (dog = 40, cow = 5, and cat = 1) viable rabies-positive brain samples archived at the Central Veterinary Laboratory (CVL), Lilongwe, Malawi, were analyzed genetically. The results showed an increase in the submission of brain samples from 2008 to 2010, with the highest number of submissions observed in 2020. Of the 683 case reports analyzed for the period under review, 38.1% (260/683) (CI: 34.44 - 41.84) were confirmed by direct fluorescent antibody test. Among the confirmed cases, 65.4% (170/260) (CI: 59.23 - 71.09) were canine rabies. Further, phylogenetic analysis revealed that sequences from different animal hosts clustered together within the Africa 1b lineage, suggesting that the strains circulating in livestock are similar to those in domestic dogs. This finding supports the hypothesis that canine rabies is spilling over to livestock and emphasizes the need for further studies to provide data for effective control of rabies in Malawi.
Subject(s)
Dog Diseases , Rabies virus , Rabies , Female , Cattle , Animals , Dogs , Rabies virus/genetics , Rabies/epidemiology , Rabies/veterinary , Phylogeny , Malawi/epidemiology , Molecular Epidemiology , Dog Diseases/epidemiology , LivestockABSTRACT
This study assessed the knowledge, attitudes and practices of livestock farmers in Namibia's Khomas region and animal health practitioners (veterinarians and animal health technicians) in the whole country concerning neosporosis and toxoplasmosis. Structured questionnaires were used, and a total of 63 farmers and 51 animal health practitioners responded out of an estimated 560 farmers in the Khomas region and 300 veterinarians and veterinary technicians in the country. Only 15.9% of the livestock farmers (n = 63) had heard about neosporosis or toxoplasmosis or knew how animals get infected (p < 0.0001). Only 5% of the farmers knew the risks associated with keeping dogs and cats concerning neosporosis and toxoplasmosis, respectively (p < 0.0001). None of the 51 animal health practitioners routinely requested Neospora caninum or Toxoplasma gondii laboratory tests in cases of cattle, sheep or goat abortions. Although all animal health practitioners indicated they routinely interacted with livestock farmers, none regularly discussed neosporosis or toxoplasmosis. Only 3.9% of animal health practitioners (n = 51) indicated that they had ever discussed either neosporosis or toxoplasmosis at a farmers' gathering (p < 0.0001), and only 21.6% had talked to at least one cat owner about toxoplasmosis in the previous 12 months (p < 0.0001). The authors concluded that farmers in the Khomas region were generally unaware of neosporosis and toxoplasmosis but could change their attitudes and practices if educated. The animal health practitioners lacked a deeper understanding and appreciation of the two diseases, which is required to cultivate enough confidence to educate farmers. Sharing this research and other relevant information on the two diseases at farmers' meetings, veterinary congresses, journals and newsletters could help educate farmers and animal health practitioners. Such platforms are likely to succeed because both these groups use these forums to get new information.
Subject(s)
Cat Diseases , Coccidiosis , Dog Diseases , Goat Diseases , Neospora , Toxoplasma , Toxoplasmosis, Animal , Pregnancy , Female , Animals , Cattle , Sheep , Cats , Dogs , Humans , Namibia/epidemiology , Cat Diseases/epidemiology , Farmers , Health Knowledge, Attitudes, Practice , Coccidiosis/veterinary , Seroepidemiologic Studies , Dog Diseases/epidemiology , Goats , Goat Diseases/epidemiology , Goat Diseases/prevention & controlABSTRACT
Tick-borne pathogens are an emerging public health threat worldwide. However, information on tick-borne viruses is scanty in sub-Saharan Africa. Here, by RT-PCR, 363 ticks (Amblyomma, Hyalomma and Rhipicephalus) in the Namwala and Livingstone districts of Zambia were screened for tick-borne phleboviruses (TBPVs). TBPVs (L gene) were detected in 19 (5.2%) Rhipicephalus ticks in Namwala. All the detected TBPVs were Shibuyunji viruses. Phylogenetically, they were closely related to American dog tick phlebovirus. This study highlights the possible role of Rhipicephalus ticks as the main host of Shibuyunji virus and suggests that these viruses may be present outside the area where they were initially discovered.
Subject(s)
Amblyomma/virology , Phlebotomus Fever/epidemiology , Phlebovirus/isolation & purification , Rhipicephalus/virology , Tick-Borne Diseases/epidemiology , Animals , Genetic Variation/genetics , Phlebotomus Fever/transmission , Phlebotomus Fever/virology , Phlebovirus/genetics , Phylogeny , Prevalence , Sequence Analysis, DNA , Tick-Borne Diseases/virology , Zambia/epidemiologyABSTRACT
We detected West Nile virus (WNV) nucleic acid in crocodiles (Crocodylus niloticus) in Zambia. Phylogenetically, the virus belonged to lineage 1a, which is predominant in the Northern Hemisphere. These data provide evidence that WNV is circulating in crocodiles in Africa and increases the risk for animal and human transmission.
Subject(s)
Alligators and Crocodiles , West Nile Fever , West Nile virus , Animals , Humans , West Nile Fever/epidemiology , West Nile Fever/veterinary , West Nile virus/genetics , Zambia/epidemiologyABSTRACT
Although canine parvovirus (CPV) causes severe gastroenteritis in dogs globally, information on the molecular epidemiology of the virus is lacking in many African countries. Here, 32 fecal samples collected from diarrheic dogs in Zambia were tested for CPV infection using molecular assays. CPV was detected in 23 samples (71.9%). Genetic characterization revealed the predominance of CPV-2c (91.3%). This finding differs from previous reports in Africa, which indicated that CPV-2a and CPV-2b were most prevalent. Phylogenetically, most Zambian CPVs formed a distinct cluster. This is the first report on the molecular characterization of CPV in Zambia.
Subject(s)
Diarrhea/veterinary , Dog Diseases/virology , Parvoviridae Infections/veterinary , Parvovirus, Canine/genetics , Parvovirus, Canine/isolation & purification , Amino Acid Sequence , Animals , Capsid Proteins/chemistry , Capsid Proteins/metabolism , Diarrhea/epidemiology , Diarrhea/virology , Dog Diseases/epidemiology , Dogs , Parvoviridae Infections/epidemiology , Parvoviridae Infections/virology , Zambia/epidemiologyABSTRACT
Whilst bovine leukemia virus (BLV) causes considerable economic losses to the dairy industry worldwide, information on its molecular epidemiology and economic impact in beef cattle is limited. Here, blood from 880 animals from Zambia's major cattle-rearing provinces was screened for BLV by nested PCR. Positive pools were sequenced and phylogenetically analyzed. The estimated pooled prevalence was 2.1%. All strains belonged to genotype 1 and formed a distinct phylogenetic cluster. The study suggests circulation of genotype 1 BLV in beef cattle in these regions. This is the first report on molecular detection and characterization of BLV from beef cattle in Africa.
Subject(s)
Enzootic Bovine Leukosis/epidemiology , Enzootic Bovine Leukosis/virology , Genotype , Leukemia Virus, Bovine/genetics , Leukemia Virus, Bovine/isolation & purification , Animals , Cattle , Leukemia Virus, Bovine/classification , Molecular Epidemiology , Phylogeny , Polymerase Chain Reaction , Prevalence , Sequence Analysis, DNA , Zambia/epidemiologyABSTRACT
Rickettsial pathogens are among the emerging and re-emerging vector-borne zoonoses of public health importance. Reports indicate human exposure to Rickettsial pathogens in Namibia through serological surveys, but there is a lack of data on infection rates in tick vectors, hindering the assessment of the relative risk to humans. Our study sought to screen Ixodid ticks collected from livestock for the presence of Rickettsia species in order to determine infection rates in ticks and to determine the Rickettsia species circulating in the country. We collected and pooled Hyalomma and Rhipicephalus ticks from two adjacent regions of Namibia (Khomas and Otjozondjupa) and observed an overall minimum Rickettsia infection rate of 8.6% (26/304), with an estimated overall pooled prevalence of 9.94% (95% CI: 6.5-14.3). There were no statistically significant differences in the estimated pooled prevalence between the two regions or tick genera. Based on the nucleotide sequence similarity and phylogenetic analysis of the outer membrane protein A (n = 9) and citrate synthase (n = 12) genes, BLAST analysis revealed similarity between Rickettsia africae (n = 2) and Rickettsia aeschlimannii (n = 11), with sequence identities ranging from 98.46 to 100%. Our initial study in Namibia indicates that both zoonotic R. africae and R. aeschlimannii are in circulation in the country, with R. aeschlimannii being the predominant species.
ABSTRACT
This research examined the positivity ratio of Crimean-Congo haemorrhagic fever (CCHF) antibodies in cattle and sheep within Namibia's Omaheke region after a human disease outbreak in the same geographical area. A total of 200 samples (100 cattle and 100 sheep) were randomly collected from animals brought to two regional auction sites, and then tested using the ID Screen® CCHF Double Antigen Multi-Species Enzyme-Linked Immunosorbent Assay kit. Of the cattle samples, 36% tested positive, while 22% of the sheep samples were seropositive. The cattle had a significantly higher positivity ratio than sheep at the individual animal level (p = 0.0291). At the herd level, 62.5% of cattle herds and 45.5% of sheep flocks had at least one positive animal, but this difference was statistically insignificant (p = 0.2475). The fourteen cattle farms with at least one seropositive animal were dispersed across the Omaheke region. In contrast, the ten sheep farms with seropositive cases were predominantly situated in the southern half of the region. The study concluded that the CCHF is endemic in the Omaheke region and likely in most of Namibia, underscoring the importance of continued surveillance and preventive measures to mitigate the impact of CCHFV on animal health and potential spillover into human populations.
ABSTRACT
BACKGROUND: The study aimed to estimate the burden of ticks and tick-borne diseases (TBDs) among rural cattle-keeping households of the Eastern Cape province of South Africa using Productivity Adjusted Life Years (PALYs). We modified Disability Adjusted Life Year (DALY) equations for humans to PALYs to estimate the societal burden of tick-borne animal diseases. Whilst the World Health Organization has indicated the adaptability of DALYs to assess burden of animal diseases, nothing has been done in this regard. This could be due to several reasons including that the assessment of animal disease burden is often less of a priority compared to human diseases, particularly in low- and middle-income countries where resources may be limited. As a result, less funding and attention may be given to developing and implementing PALYs for animal diseases. Furthermore, technical and conceptual challenges may be associated with applying DALYs equations to animal diseases, such as determining appropriate measures of productivity loss for different types and categories of animals and diseases. This motivated our study, which is focused on modelling the burden of ticks and TBDs in cattle (cows, oxen and bulls) reared in resource-poor settings. METHOD: We formulated a PALYs approach for cattle populations by adapting the DALYs approach to assess the burden of ticks and TBDs for cattle populations in 20 villages in the Eastern Cape province of South Africa. PALYs is a measurement used to assess the burden of disease in cattle populations, quantifying the years of life lost due to premature mortality and disability. It encompasses years of life lost due to premature mortality (YLL) and years lost due to disability (YLD) caused by health conditions. PALYs provide a comprehensive perspective on the effective number of years lost due to disability and premature death in cattle populations. The PALYs model involves several parameters that are examined to understand their impact on the model's behavior. To illustrate this, we used a structured questionnaire to collect data on parameters that feed into PALY equations. We coded and entered data from questionnaires directly into Statistical Package of Social Sciences (IBM SPSS Version 20) and entered the estimated values of PALY parameters to calculate PALYs equations, which were to estimate the societal disease burden of ticks and TBDs in cattle. PALYs calculations were done in three categories; PALYs without discounting and age weighting, PALYs with only discounting, and PALYs with discounting and age weighting in a practical example to study how these parameters influence the outcomes of the PALYs model. RESULTS: Our results revealed that the years of productivity lost by a cow, bull, and ox that suffered from ticks and TBDs could be estimated at various disability weights. Approximately 26%, 23% and 35% of the productivity years of a cow, ox and bull, respectively, reared by resource-poor livestock owners are lost due to the burden of ticks and TBDs in the Eastern Cape province of South Africa. However, introducing tick control measures reduces the loss to approximately 3%, 2% and 3% of their lifespan productivity, an indication that tick control will save approximately 23%, 21% and 32% of years of the productive life of cows, oxen and bulls, respectively. Therefore, it is evident that using ticks and TBD prevention measures at an early age of cattle will improve cattle productivity and hence the socioeconomic welfare of resource-poor rural farming communities in the Eastern Cape province of South Africa. CONCLUSION: The findings generated from the PALYs approach are helpful in projections for the future burden of any livestock disease. They may be used as a basis in policy formulation and decision-making by various stakeholders, and hence a priority in animal health economics. We recommend that a classification of livestock diseases of national economic importance should consider both the societal burden (non-monetary) and economic impact instead of the common practice of only considering the economic (monetary) impact. Adding a societal burden measure to existing economic measures provides a holistic understanding of the impact of a disease on society especially in resource-limited settings where the livestock value goes beyond monetary value.
Subject(s)
Cattle Diseases , Tick-Borne Diseases , Ticks , Female , Cattle , Male , Humans , Animals , South Africa/epidemiology , Tick-Borne Diseases/epidemiology , Tick-Borne Diseases/veterinary , Tick-Borne Diseases/prevention & control , Cost of Illness , Cattle Diseases/epidemiology , Cattle Diseases/prevention & controlABSTRACT
Neospora caninum is a coccidian parasite that occurs worldwide and is one of the most important causes of abortion, especially in cattle. However, no studies have been performed in Namibia to determine the N. caninum status in livestock. Therefore, this study aimed to determine the seroprevalence of N. caninum in cattle and the associated risk factors in the Khomas region of Namibia. A total of 736 sera were collected from cows in 32 farming establishments. These comprised 698 beef and 38 dairy cattle sera and were tested using a commercial enzyme-linked immunosorbent assay (ELISA) kit. Questionnaires were concurrently administered to determine possible risk factors associated with N. caninum seropositivity. A total of 42 sera were positive (all beef), giving an animal-level seroprevalence rate of 5.7%. Eight of the 32 establishments had at least one positive animal, giving a herd-level seroprevalence of 25%. There was no significant association between seropositivity and the presence of dogs, jackals, history of abortions, farm size, number of cattle or average annual rainfall. The establishments with moderate to high numbers of Feliformia were 9.8 times more likely to be seropositive to N. caninum than those with none to low levels of the former (p = 0.0245). The authors concluded that the seroprevalence level of N. caninum in the Khomas region was relatively low compared with other parts of the world and that the role of Feliformia in the epidemiology of bovine neosporosis needed to be further investigated.Contribution: Serological evidence of bovine neosporosis and the associated risk factors are reported in Namibia for the first time. This study contributes to the scientific body of knowledge on N. caninum in Africa, which is currently limited.
Subject(s)
Cattle Diseases , Coccidiosis , Neospora , Animals , Cattle , Antibodies, Protozoan/blood , Cattle Diseases/blood , Cattle Diseases/diagnosis , Cattle Diseases/epidemiology , Cattle Diseases/parasitology , Coccidiosis/blood , Coccidiosis/epidemiology , Coccidiosis/parasitology , Coccidiosis/veterinary , Namibia/epidemiology , Risk Factors , Seroepidemiologic Studies , FeliformiaABSTRACT
Rickettsiales of the genus Anaplasma are globally distributed tick-borne pathogens of animals and humans with complex epidemiological cycles. Anaplasmosis is an important livestock disease in Zambia but its epidemiological information is inadequate. This study aimed to detect and characterize the species of Anaplasma present in domestic and wild ruminants in Zambia with a focus on the infection risk posed by the translocation of sable antelope (Hippotragus niger) from North-Western Province to Lusaka Province. Archived DNA samples (n = 100) extracted from whole blood (sable n = 47, cattle n = 53) were screened for Anaplasmataceae using 16S rRNA partial gene amplification followed by species confirmation using phylogenetic analysis. Out of the 100 samples, Anaplasma species were detected in 7% (4/57) of the cattle and 24% (10/43) of the sable antelope samples. Of the 14 positive samples, five were determined to be A. marginale (four from cattle and one from sable), seven were A. ovis (sable) and two were A. platys (sable). Phylogenetic analysis of the 16S rRNA partial gene sequences revealed genetic proximity between A. ovis and A. marginale, regardless of host. The detection of Anaplasma in wildlife in Zambia shows the risk of transmission of Anaplasma species associated with wildlife translocation.
Subject(s)
Antelopes , Mustelidae , Humans , Animals , Cattle , Sheep , Anaplasma/genetics , RNA, Ribosomal, 16S/genetics , Zambia/epidemiology , PhylogenyABSTRACT
BACKGROUND: Cryptosporidium species are leading causes of diarrhoea in children and immunocompromised individuals. This study aimed to characterise Cryptosporidium species from children in rural and urban settings of Zambia. METHODS: Stool samples collected from 490 children aged <5 y with diarrhoea were assessed for Cryptosporidium oocysts microscopically. A structured questionnaire was used to collect demographic and socioeconomic characteristics. Positive samples were subjected to PCR and gp60 sequence analysis. RESULTS: The overall prevalence was 10% (50/490, 95% CI 7.8 to 13.2) with a peak in March, the late rainy season. Children who came from households where boiling water was not practised (OR=2.5, 95% CI 1.29 to 5.17; p=0.007) or who had experienced recurrent episodes of diarrhoea (OR=9.31, 95% CI 3.02 to 28.73; p=0.001) were more likely to have Cryptosporidium infection. Genotyping of 16 positive samples (14 from urban and 2 from rural sources) revealed Cryptosporidium hominis (14/16) and Cryptosporidium parvum (2/16). The Cryptosporidium hominis subtypes identified were Ia, Ib and Ie with subtype families IeAIIG3 (1), IbA9G3R2 (2), IaA31R3 (3), IbA9G3 (5), IaA27R3 (1), IaA30R3 (1) and Ia (1). Subtypes IbA9G3 and Ia were identified in children from a rural area. Cryptosporidium parvum subtypes were IIcA5G3R2 (1) and IIcA5G3a (1). CONCLUSIONS: All isolates successfully genotyped were C. hominis or anthroponotic C. parvum, suggesting that anthroponotic transmission dominates in Lusaka and the surrounding countryside.
Subject(s)
Communicable Diseases , Cryptosporidiosis , Cryptosporidium , Child , Cryptosporidiosis/epidemiology , Cryptosporidium/genetics , DNA, Protozoan , Diarrhea/epidemiology , Feces , Genotype , Humans , Zambia/epidemiologyABSTRACT
Transmission dynamics and the maintenance of mammarenaviruses in nature are poorly understood. Using metagenomic next-generation sequencing (mNGS) and RT-PCR, we investigated the presence of mammarenaviruses and co-infecting helminths in various tissues of 182 Mastomys natalensis rodents and 68 other small mammals in riverine and non-riverine habitats in Zambia. The Luna virus (LUAV) genome was the only mammarenavirus detected (7.7%; 14/182) from M. natalensis. Only one rodent from the non-riverine habitat was positive, while all six foetuses from one pregnant rodent carried LUAV. LUAV-specific mNGS reads were 24-fold higher in semen than in other tissues from males. Phylogenetically, the viruses were closely related to each other within the LUAV clade. Helminth infections were found in 11.5% (21/182) of M. natalensis. LUAV-helminth co-infections were observed in 50% (7/14) of virus-positive rodents. Juvenility (OR = 9.4; p = 0.018; 95% CI: 1.47-59.84), nematodes (OR = 15.5; p = 0.001; 95% CI: 3.11-76.70), cestodes (OR = 10.8; p = 0.025; 95% CI: 1.35-86.77), and being male (OR = 4.6; p = 0.036; 95% CI: 1.10-18.90) were associated with increased odds of LUAV RNA detection. The role of possible sexual and/or congenital transmission in the epidemiology of LUAV infections in rodents requires further study, along with the implications of possible helminth co-infection.
ABSTRACT
BACKGROUND: Although vector-borne zoonotic diseases are a major public health threat globally, they are usually neglected, especially among resource-constrained countries, including those in sub-Saharan Africa. This scoping review examined the current knowledge and identified research gaps of vector-borne zoonotic pathogens in Zambia. METHODS AND FINDINGS: Major scientific databases (Web of Science, PubMed, Scopus, Google Scholar, CABI, Scientific Information Database (SID)) were searched for articles describing vector-borne (mosquitoes, ticks, fleas and tsetse flies) zoonotic pathogens in Zambia. Several mosquito-borne arboviruses have been reported including Yellow fever, Ntaya, Mayaro, Dengue, Zika, West Nile, Chikungunya, Sindbis, and Rift Valley fever viruses. Flea-borne zoonotic pathogens reported include Yersinia pestis and Rickettsia felis. Trypanosoma sp. was the only tsetse fly-borne pathogen identified. Further, tick-borne zoonotic pathogens reported included Crimean-Congo Haemorrhagic fever virus, Rickettsia sp., Anaplasma sp., Ehrlichia sp., Borrelia sp., and Coxiella burnetii. CONCLUSIONS: This study revealed the presence of many vector-borne zoonotic pathogens circulating in vectors and animals in Zambia. Though reports of human clinical cases were limited, several serological studies provided considerable evidence of zoonotic transmission of vector-borne pathogens in humans. However, the disease burden in humans attributable to vector-borne zoonotic infections could not be ascertained from the available reports and this precludes the formulation of national policies that could help in the control and mitigation of the impact of these diseases in Zambia. Therefore, there is an urgent need to scale-up "One Health" research in emerging and re-emerging infectious diseases to enable the country to prepare for future epidemics, including pandemics.
Subject(s)
Communicable Diseases, Emerging , Vector Borne Diseases/epidemiology , Zoonoses/epidemiology , Animals , Arthropod Vectors , Bacteria , Humans , One Health , Trypanosoma , Viruses , Zambia/epidemiologyABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.
Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Codon, Terminator , Genomics , Humans , Mutation , Phylogeny , SARS-CoV-2/genetics , Zambia/epidemiologyABSTRACT
Tick-borne zoonotic pathogens are increasingly becoming important across the world. In sub-Saharan Africa, tick-borne pathogens identified include viruses, bacteria and protozoa, with Rickettsia being the most frequently reported. This study was conducted to screen and identify Rickettsia species in ticks (Family Ixodidae) infesting livestock in selected districts of southern Zambia. A total of 236 ticks from three different genera (Amblyomma, Hyalomma, and Rhipicephalus) were collected over 14 months (May 2018-July 2019) and were subsequently screened for the presence of Rickettsia pathogens based on PCR amplification targeting the outer membrane protein B (ompB). An overall Rickettsia prevalence of 18.6% (44/236) was recorded. Multi-locus sequencing and phylogenetic characterization based on the ompB, ompA, 16S rRNA and citrate synthase (gltA) genes revealed the presence of Rickettsia africae (R. africae), R. aeschlimannii-like species and unidentified Rickettsia species. While R. aeschlimannii-like species are being reported for the first time in Zambia, R. africae has been reported previously, with our results showing a wider distribution of the bacteria in the country. Our study reveals the potential risk of human infection by zoonotic Rickettsia species and highlights the need for increased awareness of these infections in Zambia's public health systems.
ABSTRACT
Crimean-Congo hemorrhagic fever virus (CCHFV) is endemic in Africa, Asia, and Eastern Europe where it circulates among animals and ticks causing sporadic outbreaks in humans. Although CCHF is endemic in sub-Saharan Africa, epidemiological information is lacking in many countries, including Malawi. To assess the risk of CCHF in Malawi, we conducted an epidemiological study in cattle reared by smallholder livestock farmers in central Malawi. A cross-sectional study was conducted in April 2020 involving seven districts, four from Kasungu and three from Lilongwe Agriculture Development Divisions. A structured questionnaire was administered to farmers to obtain demographic, animal management, and ecological risk factors data. Sera were collected from randomly selected cattle and screened for CCHF virus (CCHFV) specific antibodies using a commercial ELISA kit. Ticks were collected from cattle and classified morphologically to species level. An overall CCHFV seropositivity rate of 46.9% (n = 416; 95% CI: 42.0-51.8%) was observed. The seropositivity was significantly associated with the age of cattle (p < 0.001), sex (p < 0.001), presence of ticks in herds (p = 0.01), district (p = 0.025), and type of grazing lands (p = 0.013). Five species of ticks were identified, including Hyalomma truncatum, a known vector of CCHFV. Ticks of the species Hyalomma truncatum were not detected in two districts with the highest seroprevalence for CCHF and vector competency must be further explored in the study area. To our knowledge, this is the first report of serologic evidence of the presence of CCHV among smallholder cattle in central Malawi. This study emphasizes the need for continued monitoring of CCHFV infection among livestock, ticks, and humans for the development of data-based risk mitigation strategies.
ABSTRACT
Rickettsial pathogens are amongst the emerging and re-emerging vector-borne zoonoses of public health importance. Though traditionally considered to be transmitted by ixodid ticks, the role of argasid ticks as vectors of these pathogens is increasingly being recognized. While bat-feeding (Ornithodoros faini) and chicken-feeding (Argas walkerae) argasid ticks have been shown to harbor Rickettsia pathogens in Zambia, there are currently no reports of Rickettsia infection in southern Africa from warthog-feeding (Phacochoerus africanus) soft ticks, particularly Ornithodoros moubata and Ornithodoros porcinus. Our study sought to expand on the existing knowledge on the role of soft ticks in the epidemiology of Rickettsia species through screening for Rickettsia pathogens in warthog burrow-dwelling soft ticks from two national parks in Zambia. The tick species from which Rickettsia were detected in this study were identified as Ornithodoros porcinus, and an overall minimal Rickettsia infection rate of 19.8% (32/162) was observed. All of the sequenced Rickettsia were identified as Rickettsia lusitaniae based on nucleotide sequence similarity and phylogenetic analysis of the citrate synthase (gltA) and 17kDa common antigen (htrA) genes. Utilizing all of the gltA (n = 10) and htrA (n = 12) nucleotide sequences obtained in this study, BLAST analysis showed 100% nucleotide similarity to Rickettsia lusitaniae. Phylogenetic analysis revealed that all of the Zambian gltA and htrA gene sequences could be grouped with those of Rickettsia lusitaniae obtained in various parts of the world. Our data suggest that Rickettsia lusitaniae has a wider geographic and vector range, enhancing to our understanding of Rickettsia lusitaniae epidemiology in sub-Saharan Africa.
ABSTRACT
Emerging and re-emerging mosquito-borne viral diseases are a threat to global health. This systematic review aimed to investigate the available evidence of mosquito-borne viral pathogens reported in Zambia. A search of literature was conducted in PubMed and Google Scholar for articles published from 1 January 1930 to 30 June 2020 using a combination of keywords. Eight mosquito-borne viruses belonging to three families, Togaviridae, Flaviviridae and Phenuiviridae were reported. Three viruses (Chikungunya virus, Mayaro virus, Mwinilunga virus) were reported among the togaviruses whilst four (dengue virus, West Nile virus, yellow fever virus, Zika virus) were among the flavivirus and only one virus, Rift Valley fever virus, was reported in the Phenuiviridae family. The majority of these mosquito-borne viruses were reported in Western and North-Western provinces. Aedes and Culex species were the main mosquito-borne viral vectors reported. Farming, fishing, movement of people and rain patterns were among factors associated with mosquito-borne viral infection in Zambia. Better diagnostic methods, such as the use of molecular tools, to detect the viruses in potential vectors, humans, and animals, including the recognition of arboviral risk zones and how the viruses circulate, are important for improved surveillance and design of effective prevention and control measures.