Emmanuel Tumininu Obishakin

Outbreaks of bluetongue (BT) virus (BTV) serotype 3 (BTV‐3) have been reported across Europe since late 2023, causing significant levels of disease in sheep, goats and cattle. The infection dynamics and clinical disease severity in the UK cattle and the infection rate of European Culicoides vectors to this BTV‐3 strain have yet to be investigated. Four Holstein‐Friesian calves were infected with BTV‐3 UKG2023/04 using a host:virus:vector transmission model with Culicoides sonorensis biting midges. Clinical signs, gross pathology, infection kinetics, duration of infectious viraemia in the blood and host immune response were assessed. The potential for onwards BTV transmission from infected calves to colony‐reared and the UK field‐caught Culicoides biting midge vectors was quantified over the study period. All four calves were infected with BTV‐3, even when few infected Culicoides had acquired a blood meal. Infected calves experienced mild clinical signs and transient elevation in rectal temperatures, presenting lower disease severity than previously reported in European cattle in the field. BTV infection, measured through the detection of viral RNA by real‐time RT‐PCR of the blood, peaked at 6–10 days post‐infection (dpi) for all individuals. Infectious BTV‐3 was isolated from the blood of three infected calves up to 56 dpi, although the consistency with which BTV was isolated declined after 24 dpi. Protective neutralising antibodies against BTV VP2 were first detected in calves from between 10 and 16 dpi. BTV RNA was detected in colony‐reared and the UK field‐caught Culicoides that had fed on infected calves at peak viraemia (6–8 dpi) and later in infection (42 and 55 dpi). Estimates of the vector competence of the Culicoides obsoletus group for BTV‐3 were low (0.68%). Our data indicate that whilst cattle are less likely than sheep to exhibit clinical disease following infection with BTV‐3, the duration of infectious viraemia observed may permit transmission to Culicoides vectors for several weeks post‐infection.

Zika and malaria are important vector-borne febrile illnesses in humans. In this study, we determined the circulation of Zika virus and malaria infections, their hotspots, and their predominant clinical features. A cross-sectional study was carried out in six Local Government Areas (LGAs) in Kaduna State, Nigeria, from September 2018 to May 2019. Four hundred and twenty sera were screened for Zika virus (ZV) IgM and IgG, and Plasmodium falciparum antigen using ELISA and immunochromatographic test, respectively. Overall, a seroprevalence of 14.5% was found for Zika, and 9.3% for malaria. Nineteen (4.5%) and thirty-five (8.3%) patients were seropositive for ZV IgM and IgG, respectively. Co-infection rates for Zika (ZV IgM) and malaria (0.5%: 2/420), and for ZV IgG and malaria (0.7%: 3/420) were observed. Lere (10%: 7/70 for ZV IgM), Kachia (14.3%: 10/70 for ZV IgG) and Zaria (18.6%: 13/70 for malaria) LGAs were identified as hotspots for Zika and malaria. Age was significantly associated with malaria (p = 0.008) and ZV IgG (p = 0.004). Patients aged 1–10 years had the highest malaria seroprevalence (18.4%), while those aged 21–30 years had the highest ZV IgM prevalence (6.1%: 7/114). Out of the pregnant patients (56/420) tested, 5.37% (3/56) had antibodies to both recent and past ZV infection. A significant association was found between maculopapular rash (p = 0.021) and Zika, as well as between duration of the fever and recent Zika infection (p = 0.041). We highlight that malaria is endemic in Kaduna and that ZV is silently circulating, providing baseline data for further molecular epidemiological studies.

Sarcocystis are Apicomplexan protozoa with a dixenous life cycle that includes a predator and a prey as definitive and intermediate hosts, respectively. Domestic and wild pigs are intermediate hosts of S. suihominis, with formation of sarcocysts in their muscles, while humans and non-human primates act as final hosts. After ingesting raw or undercooked sarcocyst-infested pork, signs of gastroenteritis including inappetence, nausea, vomiting, and diarrhea may develop in humans. Moreover, excretion of infective forms with human feces leads to dissemination of the parasite in the environment. In this study, macroscopic sarcocysts of white color, oval shape, and a diameter of approximately 3–8 mm were found in the skeletal muscle of a slaughtered domestic pig (Sus scrofa domesticus) destined for human consumption in an abattoir of Makurdi, Benue State, Nigeria. Sarcocyst DNA was used as template to PCR amplify the near-complete length of the 18S rRNA gene and a fragment of the cytochrome c oxidase subunit 1 (cox-1) gene. Amplicons were sequenced and used to construct phylogenetic trees with selected available Sarcocystis spp. sequences. In both cases, the placement of the analyzed sequences with S. suihominis was strongly supported, confirming the species identity of this macroscopic sarcocyst-forming parasite. This constitutes the first molecular identification of S. suihominis in Nigeria and the African continent. Proximity between pigs and humans, and poor sanitary conditions frequently encountered in pig farms of Nigeria might favor the dissemination of this zoonotic parasite, posing a threat to public health.

The COVID-19 pandemic has caused the death of 7.1 million people worldwide as of 7 July 2024. In Nigeria, the first confirmed case was reported on 27 February 2020, subsequently followed by a nationwide spread of SARS-CoV-2 with morbidity and mortality reaching 267 173 and 3155, respectively, as of 7 July 2024. At the beginning of the pandemic, only a few public health laboratories in Nigeria had the capacity for SARS-CoV-2 molecular diagnosis. The National Veterinary Research Institute (NVRI), already experienced in influenza diagnosis, responded to the public health challenge for the diagnosis of COVID-19 samples from humans. The feat was possible through the collective utilisation of NVRI human and material resources, including biosafety facilities, equipment, reagents and consumables donated by international partners and collaborators. Within 6 months of the reported COVID-19 outbreak in Nigeria, over 33 000 samples were processed in NVRI facilities covering five states. Thereafter, many field and laboratory projects were jointly implemented between NVRI and collaborating sectors including the Nigerian Centre for Disease Control (NCDC) and the National Institute for Medical Research (NIMR), which brought together professionals in the health, veterinary, education and socio-sciences. In addition, One Health grants were secured to enhance surveillance for coronavirus and other zoonoses and build capacity in genomics. Bio-surveillance for coronaviruses and other emerging zoonotic pathogens at the human–animal interface was activated and continued with sample collection and analysis in the laboratory for coronaviruses, Lassa fever virus and Mpox. One Health approach has shown that inter-sectoral and multinational collaboration for diagnosis, research and development in animals, and the environment to better understand pathogen spillover events at the human–animal interface is an important global health priority and pandemic preparedness.

Orthopoxvirus Infections in Rodents, Nigeria, 2018–2019

Background: In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. Results: We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r ² > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. Conclusions: Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.

Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent’s economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.