Laboratory capacity assessments in 25 African countries at high risk of yellow fever, August-December 2018.

INTRODUCTION: accurate and timely laboratory diagnosis of yellow fever (YF) is critical to the Eliminate Yellow Fever Epidemics (EYE) strategy. Gavi, the Vaccine Alliance recognized the need to support and build capacity in the national and regional laboratories in the Global YF Laboratory Network (GYFLN) as part of this strategy. METHODS: to better understand current capacity, gaps and needs of the GYFLN laboratories in Africa, assessments were carried out in national and regional reference laboratories in the 25 African countries at high risk for YF outbreaks that were eligible for new financial support from Gavi. RESULTS: the assessments found that the GYFLN in Africa has high capacity but 21% of specimens were not tested due to lack of testing kits or reagents and approximately 50% of presumptive YF cases were not confirmed at the regional reference laboratory due to problems with shipping. CONCLUSION: the laboratory assessments helped to document the baseline capacities of these laboratories prior to Gavi funding to support strengthening YF laboratories.

Geographical Distribution of Ticks Ixodidae in Côte d'Ivoire: Potential Reservoir of the Crimean-Congo Hemorrhagic Fever Virus.

Background: Ticks and tick-borne diseases are a major issue. These recent years, tick-borne diseases have attracted much attention because of their increasing incidence and the significant damage that they cause to livestock and human health. The objective was to identify the different species of ticks found in cattle and to determine the prevalence of Crimean-Congo hemorrhagic fever virus (CCHFV) in these different areas. Methods: The study was conducted in five regions of Côte d'Ivoire belonging to different geographic areas. The ticks were collected from cattle. The identification of ticks was done with a binocular microscope using the identification keys. The detection of CCHFV was done by RT-PCR using specific primers and probes. Findings: Of the ticks sampled, 4088 (96.9%) were adults. Of the genera Amblyomma, Hyalomma, and Rhipicephalus. The genus Rhipicephalus had the highest number with 54.3% of the collected ticks embodied in five species. It is followed by the genus Amblyomma with 43.7% and represented by only one species. The genus Hyalomma represented by seven species was obtained in a low proportion of 2.1%. The predominant species identified was Rhipicephalus (Boophilus) microplus with (48.7%), followed by the species Amblyomma variegatum (43.7%), and the other species <2%. In this study, CCHFV was detected in ticks belonging to the three genera identified. All-inclusive, 16 ticks (0.37%) out of 4219 collected from cattle tested positive for CCHFV. The species tested positive for CCHFV are A. variegatum, Hyalomma impressum, Rhipicephalus (Boophilus) geigyi, R. (B.) microplus, and Rhipicephalus sanguineus. All 16 ticks positive for CCHFV are adults and were obtained from the Korogho (11 ticks) and Bouaflé (5 ticks) regions. Conclusion: Three genera of ticks, Amblyomma, Hyalomma, and Rhipicephalus and 13 species infesting cattle were identified during this study. Eleven ticks were positive for CCHFV in Korhogo and five in Bouaflé. The genus mainly infested was A. Variegatum.

Fatal Case of Lassa Fever, Bangolo District, Côte d'Ivoire, 2015.

Lassa fever has not been reported in Côte d'Ivoire. We performed a retrospective analysis of human serum samples collected in Côte d'Ivoire in the dry seasons (January-April) during 2015-2018. We identified a fatal human case of Lassa fever in the Bangolo District of western Côte d'Ivoire during 2015.

DETECTION OF NON-INFLUENZA VIRUSES IN ACUTE RESPIRATORY INFECTIONS IN CHILDREN UNDER FIVE-YEAR-OLD IN COTE D'IVOIRE (JANUARY - DECEMBER 2013).

BACKGROUND: Influenza sentinel surveillance in Cote d'Ivoire showed that 70% of Acute Respiratory Infections (ARI) cases remained without etiology. This work aims to describe the epidemiological, clinical, and virological pattern of ARI that tested negative for influenza virus, in children under five years old. MATERIALS AND METHODS: one thousand and fifty nine samples of patients presenting influenza Like Illness (ILI) or Severe Acute Respiratory Infections (SARI) symptoms were tested for other respiratory viruses using multiplex RT-PCR assays targeting 10 respiratory viruses. RESULTS: The following pathogens were detected as follows, hRV 31,92% (98/307), hRSV 24.4% (75/329), PIV 20.5% (63/307), HCoV 229E 12,05% (37/307), hMPV 6.2% (19/307), HCoVOC43 1.0% (3/307) and EnV 1.0% (3/307). Among the 1,059 specimens analyzed, 917 (86.6%) were ILI samples and 142 (23.4%) were SARI samples. The proportion of children infected with at least one virus was 29.8% (273/917) in ILI cases and 23.9% (34/142) in SARI cases. The most prevalent viruses, responsible for ILI cases were hRV with 35.89% (98/273) and hRSV in SARI cases with 41.2% (14/34) of cases. Among the 1,059 patients, only 22 (2.1%) children presented risk factors related to the severity of influenza virus infection. CONCLUSION: This study showed that respiratory viruses play an important role in the etiology of ARI in children. For a better understanding of the epidemiology of ARI and improved case management, it would be interesting in this context to expand the surveillance of influenza to other respiratory viruses.

Epidemiology of rubella infection and genotyping of rubella virus in Cote d'Ivoire, 2012-2016.

Rubella is a contagious disease caused by the rubella virus (RuV) that can lead to serious birth defects when women are infected in early pregnancy. This study aimed to describe the epidemiology and genetic diversity of rubella viruses in Cote d'Ivoire (CIV). Blood or oral fluid samples collected from suspected measles cases were first tested for the presence of measles specific IgM antibodies by enzyme-linked immunosorbent assay (ELISA). All measles IgM negative or indeterminate samples were tested for rubella IgM antibody using ELISA. Rubella-IgM-positive samples were tested by real-time reverse transcription polymerase chain reaction (RT-PCR) for the presence of rubella virus RNA. Real-time RT-PCR-positive RNA samples were used as template to amplify the 739 nt region used for rubella genotyping. PCR-positive samples were sequenced and phylogenetic analysis performed. Between 2012 and 2016, 4121 serums and 126 oral fluids were collected through the measles surveillance system. Of these, 3823 and 108 respectively were measles IgM negative or indeterminate. Subsequent testing for rubella found that 690 of 3823 (18%) serum samples and 25 of 108 (23%) oral fluid samples were rubella IgM-positive. The 739 nt segment of the E1 glycoprotein gene was amplified and sequenced for two serums and seven oral fluids samples. Phylogenetic analysis showed that the rubella viruses from CIV belonged to genotypes 1G (eight samples) and 2B (one sample). Rubella virus genotype 2B was found in CIV for the first time. These data contribute to baseline information on rubella virus strains found in CIV before the introduction of rubella vaccine.

Novel polyomaviruses of nonhuman primates: genetic and serological predictors for the existence of multiple unknown polyomaviruses within the human population.

Polyomaviruses are a family of small non-enveloped DNA viruses that encode oncogenes and have been associated, to greater or lesser extent, with human disease and cancer. Currently, twelve polyomaviruses are known to circulate within the human population. To further examine the diversity of human polyomaviruses, we have utilized a combinatorial approach comprised of initial degenerate primer-based PCR identification and phylogenetic analysis of nonhuman primate (NHP) polyomavirus species, followed by polyomavirus-specific serological analysis of human sera. Using this approach we identified twenty novel NHP polyomaviruses: nine in great apes (six in chimpanzees, two in gorillas and one in orangutan), five in Old World monkeys and six in New World monkeys. Phylogenetic analysis indicated that only four of the nine chimpanzee polyomaviruses (six novel and three previously identified) had known close human counterparts. To determine whether the remaining chimpanzee polyomaviruses had potential human counterparts, the major viral capsid proteins (VP1) of four chimpanzee polyomaviruses were expressed in E. coli for use as antigens in enzyme-linked immunoassay (ELISA). Human serum/plasma samples from both Côte d'Ivoire and Germany showed frequent seropositivity for the four viruses. Antibody pre-adsorption-based ELISA excluded the possibility that reactivities resulted from binding to known human polyomaviruses. Together, these results support the existence of additional polyomaviruses circulating within the human population that are genetically and serologically related to existing chimpanzee polyomaviruses.

Sentinel surveillance for influenza and other respiratory viruses in Côte d'Ivoire, 2003-2010.

BACKGROUND: Many countries in Africa have lacked sentinel surveillance systems for influenza and are under-represented in data used for global vaccine strain selection. OBJECTIVES: We describe 8 years of sentinel surveillance data and the contribution of influenza and other viruses to medically attended influenza-like illness (ILI) in Côte d'Ivoire. METHODS: Sentinel surveillance was established in 2003. Nasopharyngeal (NP) specimens and epidemiologic data are collected from persons of all ages presenting with ILI at sentinel sites. Respiratory specimens have been tested for influenza using various viral and molecular diagnostic methods. A subset of 470 specimens collected from children aged 0-5 years were tested for multiple respiratory viruses using RT-PCR. RESULTS: From 2003 to 2010, 5074 NP specimens were collected from patients with ILI. Overall, 969/5074 (19%) of these specimens tested positive for influenza. Seasonal influenza A(H1N1) viruses predominated during 5 years and influenza A(H3N2) viruses predominated during 3 years. Influenza B viruses cocirculated with influenza A viruses during each year from 2004 to 2010. Seasonal peaks in influenza circulation were observed during the months of May, June, and October, with the largest peak corresponding with the primary rainfall season. Of 470 specimens collected from children under aged 5 who were tested for multiple respiratory viruses, a viral respiratory pathogen was detected in 401/470 (85%) of specimens. Commonly detected viruses were RSV (113 of 470 specimens, 24%), rhinoviruses (85/470, 18%), influenza (77/470, 16%), and parainfluenza (75/470, 16%). CONCLUSION: In Côte d'Ivoire, there is a significant annual contribution of influenza and other respiratory viruses to medically attended ILI.

Diversity of parvovirus 4-like viruses in humans, chimpanzees, and monkeys in hunter-prey relationships.

During 2010-2011, we investigated interspecies transmission of partetraviruses between predators (humans and chimpanzees) and their prey (colobus monkeys) in Côte d'Ivoire. Despite widespread infection in all species investigated, no interspecies transmission could be detected by PCR and genome analysis. All sequences identified formed species- or subspecies (chimpanzee)-specific clusters, which supports a co-evolution hypothesis.

Origin of human T-lymphotropic virus type 1 in rural Côte d'Ivoire.

Simian T-lymphotropic virus type 1 (STLV-1) strains occasionally infect humans. However, the frequency of such infections is unknown. We show that direct transmission of STLV-1 from nonhuman primates to humans may be responsible for a substantial proportion of human T-lymphotropic virus type 1 infections in rural Côte d'Ivoire, where primate hunting is common.

Balamuthia and Acanthamoeba-binding antibodies in West African human sera.

Little is known about the prevalence of Balamuthia mandrillaris amoebae and Balamuthia amoebic encephalitis in Africa. As an approach, relative concentrations of amoebae-binding serum antibodies (Ab) were assessed by flow cytometry using formaldehyde-fixed B. mandrillaris, Acanthamoeba lenticulata 72-2 and Acanthamoeba castellanii 1BU amoebae for specific Ab capture (B.m.-Ab, A.l.-Ab, A.c.-Ab). One hundred and ninety-two sera from West African (Côte d'Ivoire) donors aged 11-95years (mean 38 a; 51% males), and living in villages surrounded by rainforest near the Liberian border, were tested and related to reference sera from Berlin. While B.m.-Ab tended to increase with donor age, A.l.-Ab and A.c.-Ab did not. Accordingly, B.m.-Ab correlated only weakly with A.l.-Ab or A.c.-Ab. Of the nine individuals with the highest B.m.-Ab concentrations, most were elderly (mean 58 a), male (78%), and professed intensive outdoor activity (hunting, farming). Only three of these sera also showed elevated A.l.-Ab, and none elevated A.c.-Ab.

Evolutionary history and dynamics of dog rabies virus in western and central Africa.

The burden of rabies in Africa is estimated at 24,000 human deaths year(-1), almost all of which result from infection with dog rabies viruses (RABV). To investigate the evolutionary dynamics of RABV in western and central Africa, 92 isolates sampled from 27 African countries over 29 years were collected and sequenced. This revealed that RABV currently circulating in dogs in this region fell into a single lineage designated 'Africa 2'. A detailed analysis of the phylogeographical structure of this Africa 2 lineage revealed strong population subdivision at the country level, with only limited movement of virus among localities, including a possible east-to-west spread across Africa. In addition, Bayesian coalescent analysis suggested that the Africa 2 lineage was introduced into this region of Africa only recently (probably <200 years ago), in accordance with the timescale of expanding European colonial influence and urbanization, and then spread relatively slowly, perhaps occupying the entire region in a 100 year period.

Global distribution of novel rhinovirus genotype.

Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years.