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

Molecular screening of tsetse flies and cattle reveal different Trypanosoma species including T. grayi and T. theileri in northern Cameroon

Abstract Background African trypanosomes are mainly transmitted through the bite of tsetse flies (Glossina spp.). The present study investigated the occurrence of pathogenic trypanosomes in tsetse flies and cattle in tsetse fly-infested areas of Northern Cameroon. Results Trypanosomes were identified using nested polymerase chain reaction (PCR) analysis of internal transcribed spacer 1 (ITS1) region, both by size estimation and sequencing of PCR products. Apparent density indices recorded in Gamba and Dodeo were 3.1 and 3.6 tsetse flies per trap and day, respectively. Trypanosoma prevalence infection rate for the tsetse fly gut (40%) and proboscis (19%) were recorded. Among the flies where trypanosomes were detected in the gut, 41.7% were positive for T. congolense and 14.6% for T. brucei ssp., whereas in the proboscis 36% harboured T. congolense and 62% contained T. vivax. T. grayi was highly prevalent in tsetse fly gut (58%). The most common mixed infections were the combination of T. congolense and T. grayi. Trypanosome prevalence rate in cattle blood was 6%. Among these, T. vivax represented 26%, T. congolense 35%, T. brucei ssp. 17% and T. theileri 17% of the infections. Surprisingly, in one case T. grayi was found in cattle. The mean packed cell volume (PCV) of cattle positive for trypanosomes was significantly lower (24.1 ± 5.6%; P < 0.05) than that of cattle in which trypanosomes were not detected (27.1 ± 4.9%). Interestingly, the occurrence of T. theileri or T. grayi DNA in cattle also correlated with low PCV at pathological levels. Conclusion This molecular epidemiological study of Trypanosoma species in Northern Cameroon revealed active foci of trypanosomes in Dodeo and Gamba. These findings are relevant in assessing the status of trypanosomosis in these regions and will serve as a guide for setting the priorities of the government in the control of the disease

Environmental data and tsetse numbers per trap in protected and tsetse invested areas in Nigeria

This data set includes data from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks, one Game Reserve and two tsetse invested areas. The dataset includes temperature and relative humidity at the set traps, and the number of total trapped and dissected Glossina sp

Tryapanosoma prevalence in tsetse proboscis (Glossina sp.) collected in protected and tsetse invested areas in Nigeria

This data set includes the results of nested PCR-analysis of tsetse (Glossina sp.) proboscis samples with primers described by Adams et.al. (2006) and Hamilton et al (2004) from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks, one Game Reserve and two tsetse invested areas. Each tsetse was identified morphologically and dissected in the field. DNA was crudely extracted from the proboscis by Proteinase K digest. Presence of trypanosomes was investigated by amplification of Internal Transcribed Spacer-1 (ITS1). Identification of the respective trypanosome species was done based on lengths polymorphism of the ITS1 region by estimating the approximate size of the DNA amplicon based on electrophoretic separation in agarose gels, as well as sequencing of selected ITS1 amplicons and additional glycosomal Glyceraldehyde-3-phosohate dehydrogenase

Tryapanosoma prevalence in tsetse (Glossina sp.) gut collected in protected and tsetse invested areas in Nigeria

This data set includes the results of nested PCR-analysis of tsetse (Glossina sp.) gut samples with primers described by Adams et.al. (2006) and Hamilton et al (2004) from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks, one Game Reserve and two tsetse invested areas. Each tsetse was identified morphologically and dissected in the field. The gut samples were homogenized in the field. DNA was purified from preserved homogenized gut using the Qiagen Blood and Tissue Kit. Presence of trypanosomes was investigated by amplification of Internal Transcribed Spacer-1 (ITS1). Identification of the respective trypanosome species was done based on lengths polymorphism of the ITS1 region by estimating the approximate size of the DNA amplicon based on electrophoretic separation in agarose gels, as well as sequencing of selected ITS1 amplicons and additional glycosomal Glyceraldehyde-3-phosohate dehydrogenase

Molecular and morphological characterization of Glossina sp. and identification of associated Trypanosoma sp. in Nigeria including analysis for sialidase activity

These data sets include morphological and molecular data generated from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks (Kainji Lake National Park, Old Oyo National Park, Cross River National Park, Gashaka Gumti National Park), one Game Reserve (Yankari Game Reserve) and two tsetse invested areas (Ijah Gwari, Tuongo). Each tsetse was identified morphologically and dissected in the field, all tissues preserved and used for further analysis. Selected tsetse wings were mounted and photographed to be used for morphometric analysis. The whole gut of each tsetse was homogenized in the field and partially preserved for DNA analysis and used to investigate for sialidase activity with a fluorescent substrate and a natural substrate. Analysis for sialidase activity was done by fluorescent measurement and reverse phase HPLC of processed gut samples. DNA was purified from preserved homogenized gut and used for phylogenetic analysis of tsetse by amplification of Cytochrome Oxidase C SU1 and Internal Transcribed Spacer-1 (ITS1). Presence of trypanosomes was investigated in gut and crudely extracted DNA from proboscis by amplification of ITS1. Identification of the respective trypanosome species was done based on lengths polymorphism of the ITS1 region as well as sequencing of selected ITS1 amplicons and additional glycosomal Glyceraldehyde-3-phosohate dehydrogenase

Tsetse wing pictures (Glossina sp.) from tsetse collected in protected and tsetse invested areas in Nigeria

This data set includes images of tsetse wings generated from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks, one Game Reserve and two tsetse invested areas. Each tsetse was identified morphologically and dissected in the field. Selected tsetse wings were mounted in Faures' Solution and photographed to be used for morphometric analysis of wing size and relative vain distances. Species included are G. morsitans submorsitans, G. tachinoides, G. palpalis palpalis and some unidentified Glossina species

Sialidase assay and analysis of free sialic acid in tsetse (Glossina sp.) collected in protected and tsetse invested areas in Nigeria

This data set includes results of a sialidase assay applied in tsetse gut tissue from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks, one Game Reserve and two tsetse invested areas. Each tsetse was identified morphologically and dissected in the field, all tissues preserved and used for further analysis. The whole gut of each tsetse was homogenized in the field and partially preserved for DNA analysis and used to investigate for sialidase activity with a fluorescent substrate and a natural substrate. Analysis for sialidase activity was done by fluorescent measurement and reverse phase HPLC of processed gut samples

Collected tsetse tissue and tsetse species (Glossina sp.) collected in protected and tsetse invested areas in Nigeria

This data set includes data from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks, one Game Reserve and two tsetse invested areas. Each tsetse was identified morphologically and dissected in the field. Wings were removed and stored dry. Legs were immersed in a DNA-preservation agent. Salivary glands and ovaries were dissected and stored in a DNA-preservation agent. The whole gut was dissected, homogenized in the field and partially preserved for DNA analysis and used to investigate for sialidase activity. The data table summarizes the available tissue, sex and species information for each dissected specimen. Species collected were G. morsitans submorsitans, G. tachinoides, G. palpalis palpalis and several unidentified Glossina species

SARS-CoV-2 active infection and antibodies amongst health personnel during the outbreak in Cameroon: Strengthening the health system for response to future public health emergencies.

BackgroundHealth personnel (HP) are on the frontlines during response to public health emergencies like COVID-19. This risk of exposure suggests the need for safety in responding to any pandemic. Therefore, to ascertain the rate of SARS-CoV-2 infection and immunity, and their determinants amongst HP become relevant.MethodsA cross sectional health facility-based study was carried-out amongst HP in the Centre Region of Cameroon from 1st February to 30th June 2021. Characteristics and access to preventive tools were collected using face-to-face administered questionnaire. Nasopharyngeal swabs and whole blood were collected for PCR, IgG and IgM testing respectively. STATA version 17 software was used for data analysis. Determinants of COVID-19 infection were explored by estimating crude and adjusted Odd Ratio.ResultsOut of 510 HP reached, 458 were enrolled with mean age of 35 (±10) years. Thirty-four (7.4%) were PCR-positive to SARS-CoV-2 with 73.5% being clinicians versus 9 (26.4%) non-clinicians (p = 0.05). Sero-positivity to SARS-CoV-2 IgG/IgM was 40.2% (184/458), with 84.2% being clinicians versus 29 (15.8%) non-clinicians (p = 0.733). Amongst the 34 HP with PCR-positivity, 16 (47%) had no antibodies, while, 15 (44%) were IgG only. An estimate of HP (43.7%) had at least an evidence of PCR, IgG or IgM contact to COVID-19. Determinants of PCR-positivity was being clinical staff (AOR = 0.29, P = 0.039); and that of IgG/IgM were being non clinical staff (AOR = 0.41, p = 0.018) and regular use of face masks (AOR = 0.44, p = 0.001). HP trained on IPC (24%) were mainly from peripheral level (74.7%, p = 0.002).ConclusionActive infections were within the range of pandemic control (<10%). However, around two-fifths of participants have had contact with the virus, indicating that HP remains a population at risk of COVID-19 and other similarly-transmitted epidemic prone diseases, and also an important source of transmission. There is need of vaccine to achieve protectiveness, and optimal response also requires capacity building to improve the health system when challenged by a future pandemic