Partial spike gene sequencing for the identification of SARS-CoV-2 variants circulating in Cameroon in 2021.

INTRODUCTION: Global monitoring of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2) genetic sequences and associated metadata is essential for coronavirus disease 2019 (COVID-19) response. Therefore, Sanger's partial genome sequencing technique was used to monitor the circulating variants of SARS-CoV-2 in Cameroon. METHODOLOGY: Nasopharyngeal specimen was collected from persons suspected of SARS-CoV-2 following the national guidelines between January and December 2021. All specimens with cycle threshold (Ct) below 30 after amplification were eligible for sequencing of the partial spike (S) gene of SARS-CoV-2 using the Sanger sequencing method. RESULTS: During the year 2021, 1481 real time reverse transcriptase polymerase chain reaction (RT-PCR) SARS-CoV-2 positive samples were selected for partial sequencing of the S gene of SARS-CoV-2. Amongst these, 878 yielded good sequencing products. A total of 231 probable variants (26.3%) were identified. The variants were mainly represented by Delta (70.6%), Alpha (15.6%), Omicron (7.4%), Beta (3.5%), Mu (1.7%) and Gamma (0.4%). Phylogenetic analysis of the probable variants from Cameroon with reference strains confirmed that all prior and current variants of concern (VOC) clustered with their respective reference sequences. CONCLUSIONS: The surveillance strategy implemented in Cameroon, based on partial sequencing of the S gene enabled identification of the major circulating variants and provided information on the distribution of these variants, which contributed to implementing public health measures to control disease spread in the country.

Detection and genetic diversity of parechoviruses in children with acute flaccid paralysis in Cameroon.

Human Parechoviruses (HPeVs) have rarely been considered in the virological investigation of Acute Flacid Paralysis (AFP) cases in Africa, where enteric infections are very common. This study investigated the prevalence and genetic diversity of HPeV in 200 children aged ≤ 15 years with AFP in Cameroon from 2018 to 2019. HPeVs were detected in their faecal RNA using 5'-untranslated real-time RT-PCR. Detected HPeVs were typed by phylogenetic comparison with homologous sequences from homotypic reference strains. Overall, HPeV RNA was detected in 11.0% (22/200) of the 200 stool samples tested. Twelve HPeVs were successfully sequenced and reliably assigned to HPeV-A1, A4, A5, A10, A14, A15, A17 and A18 genotypes. Phylogenetic analyses revealed a high genetic variability among the studied HPeVs, as well as between the studied HPeVs and their previously reported counterparts from Cameroon in 2014. These findings suggest that different HPeV genotypes co-circulate in Cameroon without documented epidemics.

First detection of Rift Valley fever virus antibodies in non-human primates in Cameroon.

We tested for Rift Valley fever virus (RVFV) from at least 15 species of non-human primates. RVFV IgG/IgM antibodies were detected in 3.7% (2 out of 53) of chimpanzees (Pan troglodytes) and in 1.4% (1 out of 72) of unidentified non-human primate species. This study was the first investigation of RVFV in monkeys in Cameroon.

Neutralization of African enterovirus A71 genogroups by antibodies to canonical genogroups.

Enterovirus 71 (EV-A71) is a major public health problem, causing a range of illnesses from hand-foot-and-mouth disease to severe neurological manifestations. EV-A71 strains have been phylogenetically classified into eight genogroups (A to H), based on their capsid-coding genomic region. Genogroups B and C have caused large outbreaks worldwide and represent the two canonical circulating EV-A71 subtypes. Little is known about the antigenic diversity of new genogroups as compared to the canonical ones. Here, we compared the antigenic features of EV-A71 strains that belong to the canonical B and C genogroups and to genogroups E and F, which circulate in Africa. Analysis of the peptide sequences of EV-A71 strains belonging to different genogroups revealed a high level of conservation of the capsid residues involved in known linear and conformational neutralization antigenic sites. Using a published crystal structure of the EV-A71 capsid as a model, we found that most of the residues that are seemingly specific to some genogroups were mapped outside known antigenic sites or external loops. These observations suggest a cross-neutralization activity of anti-genogroup B or C antibodies against strains of genogroups E and F. Neutralization assays were performed with diverse rabbit and mouse anti-EV-A71 sera, anti-EV-A71 human standards and a monoclonal neutralizing antibody. All the batches of antibodies that were tested successfully neutralized all available isolates, indicating an overall broad cross-neutralization between the canonical genogroups B and C and genogroups E and F. A panel constituted of more than 80 individual human serum samples from Cambodia with neutralizing antibodies against EV-A71 subgenogroup C4 showed quite similar cross-neutralization activities between isolates of genogroups C4, E and F. Our results thus indicate that the genetic drift underlying the separation of EV-A71 strains into genogroups A, B, C, E and F does not correlate with the emergence of antigenically distinct variants.

Contemporary epidemiological data of Rift Valley fever virus in humans, mosquitoes and other animal species in Africa: A systematic review and meta-analysis.

Rift Valley fever (RVF) is a severe zoonotic mosquito-borne disease that represents an important threat to human and animal health, with major public health and socioeconomic impacts. This disease is endemic throughout many African countries and the Arabian Peninsula. This systematic review with meta-analysis was conducted to determine the RVF prevalence in humans, mosquitoes and other animal species in Africa. The review also provides contemporary data on RVF case fatality rate (CFR) in humans. In this systematic review with meta-analysis, a comprehensive literature search was conducted on the PubMed, Embase, Web of Science and Global Index Medicus databases from January 2000 to June 2022 to identify relevant studies. Pooled CFR and prevalence estimates were calculated using the random-effects model. Subgroup analysis and sensitivity analysis were performed, and the I2 -statistic was used to investigate a potential source of heterogeneity. A total of 205 articles were included in the final analysis. The overall RVF CFR in humans was found to be 27.5% [95% CI = 8.0-52.5]. The overall pooled prevalence was 7.8% [95% CI = 6.2-9.6] in humans and 9.3% [95% CI = 8.1-10.6] in animals, respectively. The RVF prevalence in individual mosquitoes ranged from 0.0% to 25%. Subgroup analysis showed substantial heterogeneity with respect to geographical regions and human categories. The study shows that there is a correspondingly similar prevalence of RVF in human and animals; however, human CFR is much higher than the observed prevalence. The lack of a surveillance programme and the fact that this virus has subclinical circulation in animals and humans could explain these observations. The implementation of a One Health approach for RVF surveillance and control would be of great interest for human and animal health.

Update on laboratory data of animal rabies at the Centre Pasteur of Cameroon from 2014 to 2021.

Rabies is a worldwide zoonotic disease mainly transmitted to humans by an infected dog bite. Despite the endemicity of rabies in dogs and few documented cases in Cameroon, there is still not enough data on frequency of rabies cases in animals. The present study aims to update data on the circulation of rabies in animals screened at the Centre Pasteur of Cameroon (CPC) between 2014 and 2021. The detection of rabies in animals was based on passive surveillance. Animal rabies cases were confirmed on brain biopsies using fluorescent antibody test and SYBR green based real-time RT-PCR for negative results confirmation. The total nucleoprotein (N) gene of animal-derived RABV isolated were amplified by hemi nested RT-PCR and subjected to phylogenetic analyses. From 2014 to 2021, a total of 92 animals including 86 dogs (93.5%), 3 cats, 2 pigs and 1 chiropteran were screened for rabies at the CPC. From the 86 dog sampled, 62.3% (54/86) were tested positive for rabies and 1 out of 3 cat samples was also tested positive. The PEP demand was very high (59,371) during the study period. Phylogenetic analyses assigned all 15 studied isolates successfully sequenced to the Africa-1a lineage belonging to the Cosmopolitan clade. The study highlights the frequent circulation of rabies in Cameroon and the role of dogs and cat as main reservoir and vector of rabies.

Serological evidence of the circulation of the Rift Valley fever virus in sheep and goats slaughtered in Yaoundé, Cameroon.

BACKGROUND: Rift Valley fever (RVF) is an emerging mosquito-borne haemorrhagic fever disease capable of causing severe outbreaks with high mortality and morbidity in human, livestock, and wildlife species, particularly in Africa. The onset of the disease in humans is often preceded by epizootic circulation in animals. Therefore, this study was conducted to investigate the seroprevalence of Rift Valley fever virus (RVFV) infection in animals slaughtered in the "Marché huitième" slaughterhouse in Yaoundé, Cameroon. METHODS: A cross-sectional study was conducted at the "Marché huitième" slaughterhouse in Yaoundé, Centre region of Cameroon in March 2020. Blood samples of two species of small ruminants (sheep and goat) were collected and processed. Serum was analysed for detection of RVFV IgG and IgM using commercial ELISA tests. RESULTS: Of the 191 ruminants tested, RVFV IgG antibodies were positive in 10 (5.2%). Regarding categorization of the population based on the species and gender, sheep and female animal had the highest seroprevalence of 6.4% (3/47) and 7.0% (8/115), respectively. All sera from IgG antibodies-positive samples were negative to IgM antibodies. CONCLUSION: This study provides evidence of the circulation of RVFV in small ruminants sold and slaughtered at the "Marché huitième" slaughterhouse in Yaoundé and highlights the need to develop a surveillance system for this virus encompassing humans, livestock, wildlife, and vectors in Cameroon.

Global prevalence and case fatality rate of Enterovirus D68 infections, a systematic review and meta-analysis.

A substantial amount of epidemiological data has been reported on Enterovirus D68 (EV-D68) infections after the 2014 outbreak. Our goal was to map the case fatality rate (CFR) and prevalence of current and past EV-D68 infections. We conducted a systematic review (PROSPERO, CRD42021229255) with published articles on EV-68 infections in PubMed, Embase, Web of Science and Global Index Medicus up to January 2021. We determined prevalences using a model random effect. Of the 4,329 articles retrieved from the databases, 89 studies that met the inclusion criteria were from 39 different countries with apparently healthy individuals and patients with acute respiratory infections, acute flaccid myelitis and asthma-related diseases. The CFR estimate revealed occasional deaths (7/1353) related to EV-D68 infections in patients with severe acute respiratory infections. Analyses showed that the combined prevalence of current and past EV-D68 infections was 4% (95% CI = 3.1-5.0) and 66.3% (95% CI = 40.0-88.2), respectively. The highest prevalences were in hospital outbreaks, developed countries, children under 5, after 2014, and in patients with acute flaccid myelitis and asthma-related diseases. The present study shows sporadic deaths linked to severe respiratory EV-D68 infections. The study also highlights a low prevalence of current EV-D68 infections as opposed to the existence of EV-D68 antibodies in almost all participants of the included studies. These findings therefore highlight the need to implement and/or strengthen continuous surveillance of EV-D68 infections in hospitals and in the community for the anticipation of the response to future epidemics.

Incidence and seroprevalence of rabies virus in humans, dogs and other animal species in Africa, a systematic review and meta-analysis.

Rabies is transmitted to humans mainly by dogs but also by other animal species. Reliable data on the incidence of Rabies virus (RABV) in humans, dogs, and other animal species in Africa, could be essential in the implementation of a global strategic plan to eliminate the RABV by 2030 as adopted by the WHO, OIE, and FAO. We searched the Pubmed, Embase, Scopus, African Journal Online, and African Index Medicus databases for relevant studies that report data on the incidence of RABV in Africa up to February 17, 2020. Information on active and past RABV exposures in various categories of dogs, humans and other animal species were extracted. Incidence and seroprevalence estimates were pooled using a random-effect meta-analysis. We included 73 articles which provided 142 RABV incidence and seroprevalence records in 21 African countries. The estimated incidence of RABV in 222 humans, 15,600 dogs, and 12,865 other animal species was 83.4% (95% CI = 64.6-96.5), 44.1% (95% CI = 35.1-53.4), and 41.4% (95% CI = 29.6-53.8), respectively. The estimated seroprevalence of RABV in 420 humans, 3577 dogs, and 8,55 other animal species was 33.8% (95% CI = 21.9-46.8), 19.8% (95% CI = 13.3-27.3), and 3.6% (95% CI = 0.3-9.2), respectively. The incidence of RABV in general was higher in suspected rabid dogs, other animal species of the Orders Perissodactyla, Artiodactyla and Carnivora. The incidence of RABV was higher for humans in regions of West and East Africa, for dogs in urban areas and in regions of Central and South Africa, and for animals of the order Perissodactyla in urban areas. This meta-analysis demonstrated a high incidence of RABV in Africa. Itis necessary to improve surveillance system to provide reliable data on RABV in Africa, essential for the implementation of an effective control strategy.

Coding-Complete Genome Sequence and Phylogenetic Relatedness of a SARS-CoV-2 Strain Detected in March 2020 in Cameroon.

We describe the coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain obtained in Cameroon from a 58-year-old French patient who arrived from France on 24 February 2020. Phylogenetic analysis showed that this virus, named hCoV-19/Cameroon/1958-CMR-YAO/2020, belongs to lineage B.1.5 and is closely related to an isolate from France.

Molecular epidemiology of Enteroviruses and Rhinoviruses in patients with acute respiratory infections in Yaounde, Cameroon.

BACKGROUND: Acute respiratory infections (ARI) are associated with a huge morbidity and mortality worldwide. Rhinoviruses (RVs) and Enteroviruses (EVs) are recognized as leading causes of ARI. OBJECTIVES: The present study describes the molecular epidemiology of RVs and EVs in Cameroon over a 3-year surveillance period. METHODS: From September 2011 to October 2014, nasopharyngeal swabs were collected from patients with influenza-like illness (ILI) and severe acute respiratory infections (SARI). Two sub-genomic regions of the EVs and RVs were targeted for molecular characterization. These included the most conserved 5'-untranslated region (5'UTR) and the viral protein 4/viral protein 2 transition region (VP4/VP2). RESULTS: A total of 974 samples were collected. Children ≤5 years accounted for 85.7% (835/974) of all participants. Among them, 160 (16.4%) were positive for RVs and/or EVs. RVs and/or EVs were significantly more identified in ILI compared to SARI patients (P = .015). Both viruses co-circulated all year long with a marked increase of occurrence during rainy and cold season. All RV species were found to circulate in Cameroon, with 6, 10 and 6 virus types belonging to the RV-A, RV-B and RV-C, respectively. EV species identified comprised EV-A (1 Coxsackie virus A5), EV-B (1 Coxsackie virus A9 and 2 Coxsackie virus B1) and EV-C (1 EV-C117). CONCLUSIONS: This study indicates a strong year-round occurrence of EV and RV associated respiratory infections in Cameroon. Molecular characterization identified a wide variety of RVs and EVs in patients with ARI in Cameroon.

Dog rabies control in West and Central Africa: A review.

Rabies is a neglected but preventable zoonotic disease that predominantly affects the most vulnerable populations living in remote rural areas of resource-limited countries. To date, every country on the African mainland is considered endemic for dog-mediated rabies with an estimated 21'500 human rabies deaths occurring each year. In 2018, the United Against Rabies collaboration launched the Global Strategic Plan to end human deaths from dog-mediated rabies by 2030. The epidemiology of rabies from most Western and Central African countries remains poorly defined, making it difficult to assess the overall rabies situation and progress towards the 2030 goal. In this review, we attempt to provide an overview of the current rabies situation in 22 West and Central African countries based on published scientific literature and information obtained from rabies focal points. To this end, information was collected on i) established surveillance, ii) diagnostic capacity, iii) post-exposure prophylaxis (PEP) availability and coverage, iv) dog population estimates, v) dog vaccination campaigns, vi) animal and human health communication (One Health), vii) molecular studies, viii) Knowledge, Attitude and Practices (KAP), ix) cost estimates and x) national control strategies. Although rabies is a notifiable disease in the majority of the studied countries, national surveillance systems do not adequately capture the disease. A general lack of rabies diagnostic capacity has an additional negative impact on rabies surveillance and attempts to estimate rabies burden. Recurrent shortages of human rabies vaccine are reported by all of the countries, with vaccine availability usually limited to major urban centers but no country has yet adopted the new WHO-recommended 1-week intradermal vaccination regimen. Most countries carry out subsidized mass dog vaccination campaigns on World Rabies Day. Such activities are indispensable to keep rabies in the public consciousness but are not of the scale and intensity that is required to eliminate rabies from the dog population. Countries will need to scale up the intensity of their campaigns, if they are to progress towards the 2030 goal. But more than half of the countries do not yet have reliable figures on their dog populations. Only two countries reached stage 2 on the Stepwise Approach towards Rabies Elimination ladder - indicating that their national governments have truly prioritized rabies elimination and are thus providing the necessary support and political buy-in required to achieve success. In summary, the sub-region of West and Central Africa seems to be divided into countries which have accepted the challenge to eliminate rabies with governments committed to pushing forward rabies elimination, while other countries have achieved some progress, but elimination efforts remain stuck due to lacking government commitment and financial constraints. The possibility to meet the 2030 goal without international solidarity is low, because more than two-thirds of the countries rank in the low human development group (HDI ≤ 152). Leading countries should act as role models, sharing their experiences and capacities so that no country is left behind. Unified and with international support it is possible to reach the common goal of zero human rabies deaths by 2030.

Development of a New Internally Controlled One-Step Real-Time RT-PCR for the Molecular Detection of Enterovirus A71 in Africa and Madagascar.

Enterovirus A71 (EV-A71) is a leading cause of hand-foot-and-mouth disease (HFMD) and can be associated with severe neurological complications. EV-A71 strains can be classified into seven genogroups, A-H, on the basis of the VP1 capsid protein gene sequence. Genogroup A includes the prototype strain; genogroups B and C are responsible of major outbreaks worldwide, but little is known about the others, particularly genogroups E and F, which have been recently identified in Africa and Madagascar, respectively. The circulation of EV-A71 in the African region is poorly known and probably underestimated. A rapid and specific assay for detecting all genogroups of EV-A71 is required. In this study, we developed a real-time RT-PCR assay with a competitive internal control (IC). The primers and TaqMan probe specifically target the genomic region encoding the VP1 capsid protein. Diverse EV-A71 RNAs were successfully amplified from the genogroups A, B, C, D, E, and F, with similar sensitivity and robust reproducibility. Neither cross reaction with other EVs nor major interference with the competitive IC was detected. Experimentally spiked stool and plasma specimens provided consistent and reproducible results, and validated the usefulness of the IC for demonstrating the presence of PCR inhibitors in samples. The analysis in an African laboratories network of 1889 untyped enterovirus isolates detected 15 EV-A71 of different genogroups. This specific real-time RT-PCR assay provides a robust and sensitive method for the detection of EV-A71 in biological specimens and for the epidemiological monitoring of EV-A71 including its recently discovered genogroups.

Systematic review and meta-analysis of the epidemiology of Lassa virus in humans, rodents and other mammals in sub-Saharan Africa.

Accurate data on the Lassa virus (LASV) human case fatality rate (CFR) and the prevalence of LASV in humans, rodents and other mammals are needed for better planning of actions that will ultimately reduce the burden of LASV infection in sub-Saharan Africa. In this systematic review with meta-analysis, we searched PubMed, Scopus, Africa Journal Online, and African Index Medicus from 1969 to 2020 to obtain studies that reported enough data to calculate LASV infection CFR or prevalence. Study selection, data extraction, and risk of bias assessment were conducted independently. We extracted all measures of current, recent, and past infections with LASV. Prevalence and CFR estimates were pooled using a random-effect meta-analysis. Factors associated with CFR, prevalence, and sources of between-study heterogeneity were determined using subgroup and metaregression analyses. This review was registered with PROSPERO, CRD42020166465. We initially identified 1,399 records and finally retained 109 reports that contributed to 291 prevalence records from 25 countries. The overall CFR was 29.7% (22.3-37.5) in humans. Pooled prevalence of LASV infection was 8.7% (95% confidence interval: 6.8-10.8) in humans, 3.2% (1.9-4.6) in rodents, and 0.7% (0.0-2.3) in other mammals. Subgroup and metaregression analyses revealed a substantial statistical heterogeneity explained by higher prevalence in tissue organs, in case-control, in hospital outbreak, and surveys, in retrospective studies, in urban and hospital setting, in hospitalized patients, and in West African countries. This study suggests that LASV infections is an important cause of death in humans and that LASV are common in humans, rodents and other mammals in sub-Saharan Africa. These estimates highlight disparities between sub-regions, and population risk profiles. Western Africa, and specific key populations were identified as having higher LASV CFR and prevalence, hence, deserving more attention for cost-effective preventive interventions.

Detection of herpesviruses and enteroviruses in patients with suspected infectious meningoencephalitis in three referral hospitals in Yaounde, Cameroon.

In Cameroon, routine diagnosis of central nervous system (CNS) infections is based on the detection of bacteria, fungi, parasites, and mycobacteria in cerebrospinal fluids. Therefore, there is no data on viral etiologies of meningoencephalitis (ME) in the country. We aim to identify viral etiologies (herpesviruses and enteroviruses) of ME in Cameroon, to provide useful information to physicians that will help improving management of ME. From February to May 2018, adult patients with clinical signs of ME in three referral hospitals in Yaounde were included. Detection of herpesviruses and enteroviruses was performed using reverse transcriptase polymerase chain reaction. P value of 5% was chosen as the threshold for statistical significance in statistical analyses. Eighty-one patients were included and 15 (18.51%) were positive for herpesviruses. No enterovirus was detected. The most prevalent virus was Epstein-Barr virus (8.6%) and most of herpesviruses were detected from human immunodefeciency virus (HIV)-positive patients (86.7%). The overall mortality rate was high, 60.5% (49/81) and analysis of risk factors showed that HIV-positive status and altered state of consciousness were associated with higher risk of death (odds ratio [OR], 5.41; confidence interval [CI]: 1.91-16.88; P = .002 and OR, 3.24; CI: 1.11-0.13; P = .036 respectively). We showed that herpesviruses are present in patients with ME symptoms in Yaounde and can be sometimes in coinfection with others common pathogens of CNS infections. There is therefore a need for increased clinician awareness and education regarding the diagnostic and management of CNS infections in Cameroon to limit unnecessary use of antibiotics.

Genetic and phenotypic characterization of recently discovered enterovirus D type 111.

Members of the species Enterovirus D (EV-D) remain poorly studied. The two first EV-D types (EV-D68 and EV-D70) have regularly caused outbreaks in humans since their discovery five decades ago but have been neglected until the recent occurrence of severe respiratory diseases due to EV-D68. The three other known EV-D types (EV-D94, EV-D111 and EV-D120) were discovered in the 2000s-2010s in Africa and have never been observed elsewhere. One strain of EV-D111 and all known EV-D120s were detected in stool samples of wild non-human primates, suggesting that these viruses could be zoonotic viruses. To date, EV-D111s are only known through partial genetic sequences of the few strains that have been identified so far. In an attempt to bring new pieces to the puzzle, we genetically characterized four EV-D111 strains (among the seven that have been reported until now). We observed that the EV-D111 strains from human samples and the unique simian EV-D111 strain were not phylogenetically distinct, thus suggesting a recent zoonotic transmission. We also discovered evidences of probable intertypic genetic recombination events between EV-D111s and EV-D94s. As recombination can only happen in co-infected cells, this suggests that EV-D94s and EV-D111s share common replication sites in the infected hosts. These sites could be located in the gut since the phenotypic analysis we performed showed that, contrary to EV-D68s and like EV-D94s, EV-D111s are resistant to acid pHs. We also found that EV-D111s induce strong cytopathic effects on L20B cells, a cell line routinely used to specifically detect polioviruses. An active circulation of EV-D111s among humans could then induce a high number of false-positive detection of polioviruses, which could be particularly problematic in Central Africa, where EV-D111 circulates and which is a key region for poliovirus eradication.

Detection and characterization of polioviruses originating from urban sewage in Yaounde and Douala, Cameroon 2016-2017.

OBJECTIVE: Transmission of wild polioviruses (WPVs) and vaccine-derived polioviruses (VDPVs) have been interrupted in Cameroon since July 2014. Subsequently, Cameroon withdrew Sabin type 2 from routine immunization in April 2016. This study aimed to investigate the detection rates and overtime distribution of the types of PVs recovered from urban sewage in Cameroon. RESULTS: From January 2016 to December 2017, 517 sewage specimens originating from Yaounde (325 specimens) and Douala (192 specimens) were analyzed. No WPVs and VDPVs were isolated in this study. In contrast, vaccine strains of poliovirus were detected throughout the study period. Isolates Sabin types 1 and 3 were sporadically detected whereas Sabin 2 was found only from January to May 2016 both in Yaounde and Douala. The absence of Sabin 2 in sewage specimens since June 2016 indicates its rapid disappearance after withdrawal from routine immunization in April 2016. This study provides substantial support to the observation that WPV and VDPVs have been successfully eliminated in Cameroon. However, it remains essential to maintain and extend high quality environmental surveillance as long as WPV reservoirs and VDPV outbreaks are detected in Africa.

Case fatality rate and risk factors for Nipah virus encephalitis: A systematic review and meta-analysis.

BACKGROUND: A wide range of Nipah virus (NiV) encephalitis case fatality rates (CFR) have been reported. Data on the involvement of several potential risk factors in Nipah virus transmission remain controversial. We performed a systematic review and meta-analysis to estimate the pooled CFR of NiV encephalitis and to assess the risk factors for NiV infection. METHODS: Articles published up to the 27thof November 2018 in MedLine, Embase and Web of knowledge databases were considered for this study. We included cross-sectional, cohort, and case-control studies that have reported NiV CFR and/or risk factors. Data were pooled with random-effects model. This review was registered in the PROSPERO, CRD42018116242. FINDINGS: This global review included 22 citations (25 studies) including 2156, 1682, and 474 suspected, probable, and confirmed cases of NiV encephalitis, respectively. We determined a pooled CFR for NiV encephalitis at 61.0% (95% CI, 45.7-75.4; I² = 96.8%). Climbing trees (OR = 1.4; 95% CI; 1.0-1.9), male gender (OR = 1.5; 95% CI; 1.1-2.0), travel outside their own sub-district (OR = 2.0; 95% CI; 1.4-2.9), and exposure to date palm sap (DPS) (OR = 5.7; 95% CI; 3.8-8.6) or pigs (OR = 7.6; 95% CI; 1.2-45.4) were significantly associated with NiV infection. CONCLUSION: Findings from this study suggest that NiV Encephalitis is associated with a high CFR and that male gender, travel outside their sub-district, climbing trees, and exposure to pigs and DPS are associated with an increased risk of NiV encephalitis.

Genetic landscape and macro-evolution of co-circulating Coxsackieviruses A and Vaccine-derived Polioviruses in the Democratic Republic of Congo, 2008-2013.

Enteroviruses (EVs) are among the most common viruses infecting humans worldwide but only a few Non-Polio Enterovirus (NPEV) isolates have been characterized in the Democratic Republic of Congo (DR Congo). Moreover, circulating vaccine-derived polioviruses (PVs) [cVDPVs] isolated during multiple outbreaks in DR Congo from 2004 to 2018 have been characterized so far only by the sequences of their VP1 capsid coding gene. This study was carried to i) investigate the circulation and genetic diversity of NPEV and polio vaccine isolates recovered from healthy children and Acute Flaccid Paralysis (AFP) patients, ii) evaluate the occurrence of genetic recombination among EVs belonging to the Enterovirus C species (including PVs) and iii) identify the virological factors favoring multiple emergences of cVDPVs in DR Congo. The biological material considered in this study included i) a collection of 91 Sabin-like PVs, 54 cVDPVs and 150 NPEVs isolated from AFP patients between 2008 and 2012 in DR Congo and iii) a collection of 330 stool specimens collected from healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. Studied virus isolates were sequenced in four distinct sub-genomic regions 5'-UTR, VP1, 2CATPase and 3Dpol. Resulting sequences were compared through comparative phylogenetic analyses. Virus isolation showed that 19.1% (63/330) healthy children were infected by EVs including 17.9% (59/330) of NPEVs and 1.2% (4/330) of type 3 Sabin-like PVs. Only one EV-C type, EV-C99 was identified among the NPEV collection from AFP patients whereas 27.5% of the 69 NPEV isolates typed in healthy children belonged to the EV-C species: CV-A13 (13/69), A20 (5/69) and A17 (1/69). Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences in at least one of the targeted non-structural regions of their genomes: 5'UTR, 2CATPase and 3Dpol. Some of these non-vaccine sequences of the recombinant cVDPVs were strikingly related to homologous sequences from co-circulating CV-A17 and A20 in the 2CATPase region as well as to those from co-circulating CV-A13, A17 and A20 in the 3Dpol region. This study provided the first evidence uncovering CV-A20 strains as major recombination partners of PVs. High quality AFP surveillance, sensitive environmental surveillance and efficient vaccination activities remain essential to ensure timely detection and efficient response to recombinant cVDPVs outbreaks in DR Congo. Such needs are valid for any epidemiological setting where high frequency and genetic diversity of Coxsackieviruses A13, A17 and A20 provide a conducive viral ecosystem for the emergence of virulent recombinant cVDPVs.

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

A 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.