Hepatitis E, Central African Republic

Hepatitis E, Central African Republi

Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

Free PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9451062/We propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause of the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomic surveillance.info:eu-repo/semantics/publishedVersio

Influenza surveillance capacity improvements in Africa during 2011-2017.

BACKGROUND: Influenza surveillance helps time prevention and control interventions especially where complex seasonal patterns exist. We assessed influenza surveillance sustainability in Africa where influenza activity varies and external funds for surveillance have decreased. METHODS: We surveyed African Network for Influenza Surveillance and Epidemiology (ANISE) countries about 2011-2017 surveillance system characteristics. Data were summarized with descriptive statistics and analyzed with univariate and multivariable analyses to quantify sustained or expanded influenza surveillance capacity in Africa. RESULTS: Eighteen (75%) of 24 ANISE members participated in the survey; their cumulative population of 710 751 471 represent 56% of Africa's total population. All 18 countries scored a mean 95% on WHO laboratory quality assurance panels. The number of samples collected from severe acute respiratory infection case-patients remained consistent between 2011 and 2017 (13 823 vs 13 674 respectively) but decreased by 12% for influenza-like illness case-patients (16 210 vs 14 477). Nine (50%) gained capacity to lineage-type influenza B. The number of countries reporting each week to WHO FluNet increased from 15 (83%) in 2011 to 17 (94%) in 2017. CONCLUSIONS: Despite declines in external surveillance funding, ANISE countries gained additional laboratory testing capacity and continued influenza testing and reporting to WHO. These gains represent important achievements toward sustainable surveillance and epidemic/pandemic preparedness

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

Monkeypox

International audienceNo abstract availabl

Orthobunyavirus de la République Centrafricaine (détection, séquençage et analyse phylogénétique)

La famille des Bunyaviridae regroupe plus de 350 virus transmis par des arthropodes, classés en cinq genres. La prévalence de ces virus en République Centrafricaine est mal connue et mérite des études moléculaires afin mettre en place un diagnostic fiable, de mieux caractériser les vecteurs et d'identifier les réservoirs qui sont le plus souvent inconnus. Etant donnée la diversité de ces virus, seuls les virus du genre Orthobunyavirus ont été caractérisés dans cette étude. La caractérisation génomique de Bunyaviridae a été réalisée par le séquençage de segments encadrés par des amorces consensus pour un diagnostic d'espèce. Parmi les orthobunyavirus isolés à l'Institut Pasteur de Bangui (RCA), 12 souches classées dans six sérogroupes ont été incluses dans cette étude. Des couples d'amorces définies dans notre laboratoire ont permis d'amplifier et d'obtenir une séquence complète du segment S de dix souches virales. Une séquence partielle de la glycoprotéine G2 (segment M) de ces souches a également été obtenue. L'organisation génétique du segment S de ces souches de RCA recoupe celle des sérogroupes Bunyamwera, California et Simbu. Leur génome est constitué de deux cadres ouverts et chevauchants de lecture qui codent une protéine de la nucléocapside et une protéine non structurale. La comparaison des séquences nucléiques du segment S et de la protéine G2 des souches de RCA à celle de la souche de référence Bunyamwera NC_001927 montre une différence de 5 % à 15 % et 3,3 % à 42,2 % respectivement. Les séquences des protéines N et G2 de la souche M'Poko ArB365 ont été les plus divergentes (15 % et 42,2 % de différence respectivement). L'arbre phylogénétique construit avec les séquences de la protéine N est monophylétique tandis que celui obtenu avec les séquences de la protéine G2 ne l'est pas.The Orthobunyavirus genus is composed of segmented negative sense RNA viruses that are responsible for mild to severe human diseases. To date, no molecular studies of Bunyaviridae of the genus Orthobunyavirus from Central Africa have been reported, and their classification relies on serological testing. We have designed and evaluated four new primer pairs for amplification by RT -PCR and sequencing of the complete genomic small (S) RNA segments often Orthobunyavirus viruses isolated from Central African Republic (CAR) and pertaining to 5 different serogroups. Phylogenetic analysis showed that these 10 viroses belong to the Bunyamwera serogroup. The S segment sequences differ from those of the Bunyamwera virus reference strain by 5-15 % at the nucleotide level, and both overlapping reading frames encoding nucleocapsid (N) and non-structural (NS) protein were evident in sequenced genomes. Partial sequencing of M segment was also performed and inversely to the S fragment, the obtained phylogenetic p-ee was not monophyletic as M'Poko strain was highly divergent. This study should improve diagnosis and surveillance of African bunyaviruses.NANCY1-SCD Medecine (545472101) / SudocSudocFranceF

Hotspot or blind spot? Historical perspectives on surveillance and response to epidemics in the Central African Republic

Objectives The Central African Republic (CAR), a site of recurrent disease emergence, developed a noteworthy epidemiological surveillance system from the colonial period, but its health measures have remained among the world’s lowest. To understand this disparity between surveillance and public health, we examined selected moments in its history of surveillance and changing relations with public health structures. Methods We conducted archival research in CAR and French archives and 18 semi-structured interviews with key researchers working in CAR. Results We find long-term continuities in privileging surveillance over the health system and population health, making the CAR a ‘‘hotspot’’ for emerging diseases and a ‘‘blind spot’’ of primary health care. From the colonial period, the country attracted considerable support for surveillance, without concomitant investment in public health system. Political disputes and financial constraints have obscured real primary care needs on the ground. Conclusions As both a hotspot and a blind spot for global health, the CAR signals the need to reorient health interventions to address the long-term health of Central African people

Complete Genome Sequence of the Tataguine Virus, Isolated in the Central African Republic in 1972 from a Human with an Acute Febrile Syndrome

International audienceTataguine virus (TATV) is an orthobunyavirus that causes febrile illnesses in Africa. Here, we report the complete genome sequences of TATV strain HB72P583, isolated in the Central African Republic in 1972. Several genetic variations were detected in the small (S), medium (M), and large (L) segments relative to a TATV strain isolated in Nigeria in 1966

Identification of pathogens for differential diagnosis of fever with jaundice in the Central African Republic: a retrospective assessment, 2008–2010

Abstract Background Febrile jaundice results clinically in generalized yellow coloration of the teguments and mucous membranes due to excess plasma bilirubin, accompanied by fever. Two types are found: conjugated and unconjugated bilirubin jaundice. Jaundice is a sign in several diseases due to viruses (viral hepatitis and arbovirus), parasites (malaria) and bacteria (leptospirosis). In the Central African Republic (CAR), only yellow fever is included on the list of diseases for surveillance. The aim of this study was to identify the other pathogens that can cause febrile jaundice, for better management of patients. Methods Between 2008 and 2010, 198 sera negative for yellow fever IgM were randomly selected from 2177 samples collected during yellow fever surveillance. Laboratory analyses targeted four groups of pathogens: hepatitis B, C, delta and E viruses; dengue, chikungunya, Zika, Crimean–Congo haemorrhagic fever, West Nile and Rift Valley arboviruses; malaria parasites; and bacteria (leptospirosis). Results Overall, 30.9% sera were positive for hepatitis B, 20.2% for hepatitis E, 12.3% for hepatitis C and 8.2% for malaria. The majority of positive sera (40.4%) were from people aged 16–30 years. Co-infection with at least two of these pathogens was also found. Conclusion These findings suggest that a systematic investigation should be undertaken of infectious agents that cause febrile jaundice in the CAR

Entomological profile of yellow fever epidemics in the Central African Republic, 2006–2010

Abstract Background The causative agent of yellow fever is an arbovirus of the Flaviviridae family transmitted by infected Aedes mosquitoes, particularly in Africa. In the Central African Republic since 2006, cases have been notified in the provinces of Ombella-Mpoko, Ouham-Pende, Basse-Kotto, Haute-Kotto and in Bangui the capital. As the presence of a vector of yellow fever virus (YFV) represents a risk for spread of the disease, we undertook entomological investigations at these sites to identify potential vectors of YFV and their abundance. Findings Between 2006 and 2010, 5066 mosquitoes belonging to six genera and 43 species were identified. The 20 species of the Aedes genus identified included Ae. aegypti, the main vector of YFV in urban settings, and species found in tropical forests, such as Ae. africanus, Ae. simpsoni, Ae. luteocephalus, Ae. vittatus and Ae. opok. These species were not distributed uniformly in the various sites studied. Thus, the predominant Aedes species was Ae. aegypti in Bangui (90.7 %) and Basse-Kotto (42.2 %), Ae. africanus in Ombella-Mpoko (67.4 %) and Haute-Kotto (77.8 %) and Ae. vittatus in Ouham-Pende (62.2 %). Ae. albopictus was also found in Bangui. The distribution of these dominant species differed significantly according to study site (P Aedes mosquitoes analysed by polymerase chain reaction contained the YFV genome. Conclusion The results indicate a wide diversity of vector species for YFV in the Central African Republic. The establishment of surveillance and vector control programs should take into account the ecological specificity of each species.</p