Chimpanzee Malaria Parasites Related to Plasmodium ovale in Africa

Since the 1970's, the diversity of Plasmodium parasites in African great apes has been neglected. Surprisingly, P. reichenowi, a chimpanzee parasite, is the only such parasite to have been molecularly characterized. This parasite is closely phylogenetically related to P. falciparum, the principal cause of the greatest malaria burden in humans. Studies of malaria parasites from anthropoid primates may provide relevant phylogenetic information, improving our understanding of the origin and evolutionary history of human malaria species. In this study, we screened 130 DNA samples from chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla) from Cameroon for Plasmodium infection, using cytochrome b molecular tools. Two chimpanzees from the subspecies Pan t. troglodytes presented single infections with Plasmodium strains molecularly related to the human malaria parasite P. ovale. These chimpanzee parasites and 13 human strains of P. ovale originated from a various sites in Africa and Asia were characterized using cytochrome b and cytochrome c oxidase 1 mitochondrial partial genes and nuclear ldh partial gene. Consistent with previous findings, two genetically distinct types of P. ovale, classical and variant, were observed in the human population from a variety of geographical locations. One chimpanzee Plasmodium strain was genetically identical, on all three markers tested, to variant P. ovale type. The other chimpanzee Plasmodium strain was different from P. ovale strains isolated from humans. This study provides the first evidence of possibility of natural cross-species exchange of P. ovale between humans and chimpanzees of the subspecies Pan t. troglodytes

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

Circulation, genetic diversity and evolution of human enteroviruses in Cameroon - interactions with vaccine polioviruses and simian enteroviruses

La diversité génétique des entérovirus (EVs) humains, y compris les poliovirus (PVs), circulant au Cameroun a été évaluée d'une part sur tout le territoire chez des patients atteints de paralysie flasque aiguë, et d'autre part, chez des enfants sains dans la région de l'extrême Nord du pays. Les résultats obtenus indiquent une fréquence élevée couplée à une importante diversité génétique des EVs au Cameroun. Les EVs de l'espèce Human Enterovirus C (HEV-C) représentaient jusqu'à 56,5% des isolats identifiés. En dehors des types viraux mondialement distribués, des types et variants d'EV spécifiquement Africains ont été identifiés. L'étude des échanges génétiques entre HEV-C, incluant les PVs vaccinaux, a confirmé que des recombinaisons fréquentes dans les régions non structurales du génome participent à leur diversité génétique. En particulier les PVs co-circulent et échangent les séquences de leurs régions non structurales avec les autres HEV-C notamment avec les CVA-13, -17 et -20. La co-circulation des PVs et de divers HEV-C pourrait constituer un facteur viral majeur pour l'émergence des PVs recombinants pathogènes dérivés du vaccin (VDPVs). Par ailleurs, des EVs typiquement simiens, mais aussi des EVs précédemment connus comme étant des pathogènes humains ont été identifiés dans les selles de primates non humains (PNH) vivant en captivité et en faune sauvage. En particulier, quatre nouveaux types d'EVs simiens ont été identifiés. Les résultats confirment que la transmission inter-espèces d'au moins certains types d'EV est naturellement possible et pourrait jouer un rôle dans l'émergence de nouveaux EVs de l'homme chez les PNH et vice-versa.The genetic diversity of human enteroviruses (EVs), including polioviruses (PVs), circulating in Cameroon was investigated in acute flaccid paralysis patients throughout the entire territory as well as in healthy children from the far northern region of the country. The results showed a high frequency combined with a high genetic diversity of human EVs in Cameroon. The frequency of EVs belonging to the Human Enterovirus C species (HEV-C) was as high as 56.5% of the identified isolates. Apart from worldwide distributed types, several African specific types and variants were identified. The investigation of genetic exchanges between HEV-C, including vaccine polioviruses, confirmed the fact that frequent recombination in the non structural regions of the genome contribute to their genetic diversity. PVs in particular co-circulate and exchange the sequences of their non structural regions with CVA-13, -17 and -20. The co-circulation of PVs and diverse HEV-C may be a major viral factor for the emergence of pathogenic recombinant vaccine derived PVs (VDPVs). In the other hand, simian specific EVs as well as EVs previously known human EVs were identified in the stools of captive and wild non human primates (NHP). Four novel types of simian EVs in particular were identified. The results confirm that cross-species transmission of at least some EV types can happen naturally and could play a role in the emergence of new EV types from humans to NHP and vice-versa.PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

Serological evidence of rift valley fever Phlebovirus and Crimean-Congo hemorrhagic fever orthonairovirus infections among pygmies in the east region of Cameroon

Abstract Background Rift Valley Fever Phlebovirus (RVFV) and Crimean-Congo Hemorrhagic Fever Orthonairovirus (CCHFV) specific antibodies had been documented among humans in urban settings of the southwestern and northern Cameroon in the late 1980s. Recently, evidence for enzootic circulation of RVFV was reported among livestock in both rural and urban settings in Cameroon. However, current estimates of human exposure to RVFV and CCHFV are still to be documented in Cameroon, especially in rural areas. The aim of this study was to assess the seroprevalence of RVFV and CCHFV in rural settings in the Southeastern rain forest of Cameroon. Results Using Enzyme-linked Immunosorbent Assays, the presence of RVFV and CCHFV Immunoglobulin G antibodies was investigated in plasma samples originating from 137 Pygmies from four villages of the East region of Cameroon. The studied population was found to be 12.4% (17/137) and 4.4% (6/137) seropositive for RVFV and CCHFV, respectively. The rates of RVFV IgG were comparable between the age groups and sex. Conversely, the rate of CCHFV IgG was significantly higher among the 41–60 years old participants (p = 0.02). Conclusions This study provides a substantial evidence of the circulation of RVFV and CCHFV among rural inhabitants of the East region of Cameroon

Monkeypox virus phylogenetic similarities between a human case detected in Cameroon in 2018 and the 2017-2018 outbreak in Nigeria

International audienceA monkeypox virus was detected from a human clinical case in 2018 in Cameroon; a country where no human cases were reported since 1989. The virus exhibited close genetic relatedness with another monkeypox virus isolated in Nigeria during the 2017-2018 outbreak. Although our molecular findings argue in favor of an extension of the monkeypox outbreak from Nigeria into Cameroon, the possibility that the monkeypox virus detected could be indigenous to Cameroon cannot be ruled out

Molecular characterization and phylogenetic relatedness of dog-derived Rabies Viruses circulating in Cameroon between 2010 and 2016

<div><p>Rabies is enzootic among dog populations in some parts of Cameroon and the risk of human rabies is thought to be steadily high in these regions. However, the molecular epidemiology of circulating Rabies Virus (RABV) has been hardly considered in Cameroon as well as in most neighboring central African countries. To address this fundamental gap, 76 nucleoprotein (N) gene sequences of dog-derived RABV were obtained from 100 brain specimens sampled in Cameroon from 2010 to 2016. Studied sequences were subjected to molecular and phylogenetic analyses with reference strains retrieved from databases. The 71 studied Africa-1 isolates displayed 93.5–100% nucleotide (nt) and 98.3–100% amino-acid (aa) identities to each other while, the 5 studied Africa-2 isolates shared 99.4–99.7% sequence similarities at nt and aa levels. Maximum Likelihood based phylogenies inferred from nucleotide sequences confirmed all studied RABV isolates as members of the dog-related species 1 of the <i>Lyssavirus</i> genus. Individual isolates could be unambiguously assigned as either the Africa-1 subclade of the Cosmopolitan clade or the Africa 2 clade. The Africa-1 subclade appeared to be more prevalent and diversified. Indeed, 70 studied isolates segregated into 3 distinct circulating variants within Africa-1a lineage while a unique isolate was strikingly related to the Africa-1b lineage known to be prevalent in the neighboring Central African Republic and eastern Africa. Interestingly, all five Africa-2 isolates fell into the group-E lineage even though they appeared to be loosely related to databases available reference RABV; including those previously documented in Cameroon. This study uncovered the co-circulation of several Africa-1 and Africa-2 lineages in the southern regions of Cameroon. Striking phylogenetic outcasts to the geographic differentiation of RABV variants indicated that importation from close regions or neighboring countries apparently contributes to the sustainment of the enzootic cycle of domestic rabies in Cameroon.</p></div

Summary of the characteristics and genotyping results of the Rabies Virus isolates derived from brain specimens of rabid dogs enrolled in this study.

<p>Summary of the characteristics and genotyping results of the Rabies Virus isolates derived from brain specimens of rabid dogs enrolled in this study.</p

Annual distribution of laboratory confirmed rabies cases among dogs originating from the southern regions of Cameroon, 2010–2016.

<p>Annual distribution of laboratory confirmed rabies cases among dogs originating from the southern regions of Cameroon, 2010–2016.</p

Maximum-likelihood phylogenetic tree of nucleocapsid gene sequences depicting the phylogenetic relationships of Africa-1 Rabies Viruses originating from Cameroon with other Africa-1 from Africa.

<p>The phylogenetic tree was estimated from the alignment of 1040 nucleotides (nt) long sequence alignment (positions 41–1080 nucleotides according to the genome of the Rabies Virus strain RRV_ON-99-2) using a maximum-likelihood (ML) method under the general time-reversible (GTR) model of nucleotide substitution, with the rate of each substitution type estimated from the dataset using PHYML 3.0 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006041#pntd.0006041.ref055" target="_blank">55</a>]. The ML base frequencies, the proportion of invariable sites (I) and a gamma distribution of rate variation among sites (Γ with four rate categories) were estimated from the dataset. Newly sequenced Rabies Viruses are indicated with circles color-coded according to their respective regions of origin: CEN, Centre; EAS, East; NOW, North West; SOW, South West and WES, West. Their districts of origin are coded as specified by district codes provided in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006041#pntd.0006041.t001" target="_blank">Table 1</a>. The districts of the Centre region, other than Yaounde, are specified in bold black. The years of origin of the studied viruses are provided by two digit numbers preceding the letter “V” in the virus name (10V-, 2010; 11V-, 2011; 12V-, 2012; 13V-, 2013; 14V-, 2014; 15V-, 2015, 16V-; 2016). Database available reference viruses are named with corresponding GenBank accession numbers followed by the country (CAR, Central African Republic) and year of origin, if known. Viruses from Central Africa are specifically highlighted with red-filed triangles; except those from Cameroon that are further distinguished by the indication of the regions (CEN, Centre) and district (OBA, Obala; MON, Monatélé; SAA, Sa’a; YAO, Yaounde) codes. Clades, subclades and lineages are designated as reported in a reference study based on the ML phylogeny of 321 RABV sequences from five concatenated genes [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006041#pntd.0006041.ref021" target="_blank">21</a>]. The major clades, lineages and variants of the Rabies Virus commented in the main text are gathered in color-shaded boxes. Viruses displaying peculiar features, commented in the main text, are further highlighted by black arrows. ML bootstrap values (generated from 100 replicates) >60% are shown next to the nodes. Scale is shown at the left as substitutions per site.</p

Short Communication: Characterization of a New HIV-1 Group N Isolate Originating from a Cameroonian Patient

International audienceHIV-1 group N (HIV-1/N) remains rare and mainly restricted to Cameroon. In this study, we report a new HIV-1/N infected case identified during routine HIV screening activities in Yaounde. The genetic characterization of the near full-length genome of this virus strain revealed that it is genetically distinct to all HIV-1/N described to date. However, the Vpu protein responsible for tetherin antagonism displayed the same amino acid substitutions (E15A, V19A, I25L, and V26L) as other HIV-1/N from Cameroon