Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa.

Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa

Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever

Infection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human genetic variation underlies the heterogeneity of LASV infection, we carried out genome-wide association studies (GWAS) as well as seroprevalence surveys, human leukocyte antigen typing and high-throughput variant functional characterization assays. We analysed Lassa fever susceptibility and fatal outcomes in 533 cases of Lassa fever and 1,986 population controls recruited over a 7 year period in Nigeria and Sierra Leone. We detected genome-wide significant variant associations with Lassa fever fatal outcomes near GRM7 and LIF in the Nigerian cohort. We also show that a haplotype bearing signatures of positive selection and overlapping LARGE1, a required LASV entry factor, is associated with decreased risk of Lassa fever in the Nigerian cohort but not in the Sierra Leone cohort. Overall, we identified variants and genes that may impact the risk of severe Lassa fever, demonstrating how GWAS can provide insight into viral pathogenesis

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Detection and identification of blood-borne infections in goats in Nigeria using light microscopy and polymerase chain reaction

Haemoparasitisms in animals are known to impose substantial economic burdens on owners. In Nigeria, most laboratories utilize only Light Microscopy (LM) for their diagnosis. Hence there is a need to have an update assessment of haemoparasitism of goat in Nigeria using molecular investigation.&nbsp;Using LM, blood samples from a total of 173 goats in Ibadan were screened for haemoparasites and haemocytopathological evaluation. Among them, 126 blood samples were randomly selected and PCR tested for the 18S rRNA gene of Babesia/Theileria spp (B/T) and the 16S rRNA gene of Anaplasma/Ehrlichia spp (A/E), while 91 samples were evaluated for the 16S RNA of hemotropic mycoplasma (hemoplasma). Relationship between the haematological changes and PCR results was evaluated.&nbsp;The PCR detection rate was significantly and more than 4-fold higher compared to LM (61.5% and 14.5%, respectively; P &lt; 0.0001) alone. A total of 150 animals were tested by both methods with 62.7% overall infection proportion. Comparison of LM and PCR analyses showed approximately 50% misdiagnosis of Hemoplasma spp by LM with 82.7% and 100% false negative for A/E and B/T recorded by LM, respectively. The haemoparasites detected by LM were Borrelia spp, Hemoplasma spp, Babesia spp, Anaplasma spp and, Trypanosoma brucei. A total of 34.1%, 23% and, 51.6% samples were positive for B/T, A/E and, hemoplasma, respectively. Sequencing and phylogenetic analyses of some PCR products identified samples with high homology with Anaplasma ovis in the A/E group while the B/T were highly related to Theileria velifera. Sequencing of hemoplasma positive samples identified Mycoplasma ovis, Mycoplasma wenyonii and Pseudomonas fluorescens. The haematological changes were unspecific to infection types and, showed no significant deviation between haemoparasite positive and negative animals.The striking disparity between LM and PCR methods for haemoparasite detection and a larger repertoire of haemoparasites are presented. Borrelia spp, Mycoplasma wenyonii, Pseudomonas fluorescens and Theileria velifera are newly reported in goat with hemotropic mycoplasma being the most prevalent in Ibadan. Studies geared towards pathogenicity investigation in the unusual host, their diversity and factors of transmission are envisaged for effective prevention and control.&nbsp;</p

Detection and identification of blood-borne infections in dogs in Nigeria using light microscopy and the polymerase chain reaction

Many sick dogs brought to the University of Ibadan Veterinary Teaching Hospital (UIVTH) are infested with ticks and are anemic. Up until recently, light microscopy (LM) has been the only available means used for detection of blood-borne infections. In other parts of the world, PCR-based assays been used as a gold standard for accurate diagnosis of blood-borne infections. In this study, we used LM and broad-spectrum rRNA gene PCR-based assays on 116 blood samples from dogs brought to the UIVTH for detection of the 18S rRNA gene of Babesia and the 16S rRNA genes of Ehrlichia and hemotropic mycoplasmas. The relationship between clinicopathological findings and PCR results was evaluated. Age, sex, presence of ticks, anemia, co-infection status, and fever were also assessed in relation to PCR positivity to determine the risk factors using stepwise logistic regression analyses. Light microscopic examination revealed an overall prevalence of infection of 14.7% (17/116). Organisms detected were Babesia canis (3.5%), Ehrlichia canis (10.3%) and Trypanosoma congolense (0.9%) and a single co-infection with Babesia canis and Ehrlichia canis (0.9%). PCR analysis revealed 89/116 (76.7%) positive samples. Infections with 1, 2 and 3 infectious agents occurred in 49 (55.1%), 36 (40.4%) and 4 (4.5%) samples, respectively. Specifically, among the 89 PCR positive samples, Babesia spp. (85.4%) was the most abundant infection followed by Ehrlichia spp. (46.1%) and hemoplasmas (13.5%). Sequencing of PCR products identified two samples (1.7%) that contained Hepatozoon canis DNA. Sequencing of hemoplasma positive samples identified 'Candidatus Mycoplasma haemobos' in 0.8% of dogs. Using PCR, a 5-fold higher prevalence of blood-borne infections was found in the dogs (76.7%, 89/116) than with LM (14.7%, 17/116) alone" Dogs between 1 and 12months were the most frequently infected with multiple agents (47.2% double and 50.0% triple infections). Male dogs had the highest prevalence of infection (80.4%) and more triple infections (75.0%). A total of 57.3% of infected dogs were anemic. Anemic dogs were 2.77 times more likely to test positive for Ehrlichia spp. (OR: 2.77 95% CI: 1.25-6.16) and dogs with ticks were 3.6 times more likely to test positive for hemoplasmas (OR=3.60 95% CI: 1.05-12.38). This study underscores the abundance of blood-borne infections in dogs in Ibadan, Nigeria, which is underestimated using light microscopy. This is also the first evidence of existence of 'Candidatus Mycoplasma haemobos' in a dog in Nigeria and in Africa. Consequently there is a need for molecular diagnostic facilities for routine screening of sick animals, as multiple infections were not found by light microscopy