Re-emergence of dengue virus serotype 3 infections in Gabon in 2016-2017, and evidence for the risk of repeated dengue virus infections

Molecular surveillance for dengue serotypes among the population living in Moyen-Ogooué province, Gabon; evidence of the presence of dengue serotype 1

BACKGROUND

Despite dengue virus (DENV) outbreak in Gabon a decade ago, less is known on the potential circulation of DENV serotypes in the country. Previous studies conducted in some areas of the country, are limited to hospital-based surveys which reported the presence of some cases of serotype 2 and 3 seven years ago and more recently the serotype 1. As further investigation, we extend the survey to the community of Moyen Ogooué region with the aim to assess the presence of the dengue virus serotypes, additionally to characterize chikungunya (CHIKV) infection and describe the symptomatology associated with infections.

METHOD

A cross-sectional survey was conducted from April 2020 to March 2021. The study included participants of both sexes and any age one year and above, with fever or history of fever in the past seven days until blood collection. Eligible volunteers were clinically examined, and blood sample was collected for the detection of DENV and CHIKV using RT-qPCR. Positive samples were selected for the target sequencing.

RESULTS

A total of 579 volunteers were included. Their mean age (SD) was 20 (20) years with 55% of them being female. Four cases of DENV infection were diagnosed giving a prevalence of 0.7% (95%CI: 0.2-1.8) in our cohort while no case of CHIKV was detected. The common symptoms and signs presented by the DENV cases included fatigue, arthralgia myalgia, cough, and loss of appetite. DENV-1was the only virus detected by RT-qPCR.

CONCLUSION

Our results confirm the presence of active dengue infection in the region, particularly DENV-1, and could suggest the decline of DENV-2 and DENV-3. Continuous surveillance remains paramount to comprehensively describe the extent of dengue serotypes distribution in the Moyen-Ogooué region of Gabon.

Envelope-dimer epitope-like broadly protective antibodies against dengue in children following natural infection and vaccination

Cross-reactive antibodies (Abs) to epitopes that span envelope proteins on the virion surface are hypothesized to protect against dengue. Here, we measured Abs targeting the quaternary envelope dimer epitope (EDE) as well as neutralizing and binding Abs and evaluate their association with dengue virus (DENV) infection, vaccine response, and disease outcome in dengue vaccinated and unvaccinated children (n=252) within a longitudinal cohort in Cebu, Philippines (n=2,996). Abs targeting EDE were prevalent and strongly associated with broad neutralization of DENV1-4 in those with baseline multitypic immunity. Subsequent natural infection and vaccination boosted EDE-like, neutralizing, and binding Abs. EDE-like Abs were associated with reduced dengue risk and mediated the protective effect of binding and neutralizing Abs on symptomatic and severe dengue. Thus, Abs targeting quaternary epitopes help explain broad cross protection in those with multiple prior DENV exposures, making them useful for evaluation and development of future vaccines and therapeutics.

Genetic Diversity and Detection of Respiratory Viruses Excluding SARS-CoV-2 during the COVID-19 Pandemic in Gabon, 2020-2021

Acute respiratory infections are a major global burden in resource-limited countries, including countries in Africa. Although COVID-19 has been well studied since the pandemic emerged in Gabon, Central Africa, less attention has been paid to other respiratory viral diseases, and very little data are available. Herein, we provide the first data on the genetic diversity and detection of 18 major respiratory viruses in Gabon during the COVID-19 pandemic. Of 582 nasopharyngeal swab specimens collected from March 2020 to July 2021, which were SARS-CoV-2 negative, 156 were positive (26%) for the following viruses: enterovirus (20.3%), human rhinovirus (HRV) (4.6%), human coronavirus OC43 (1.2%), human adenovirus (0.9%), human metapneumovirus (hMPV) (0.5%), influenza A virus (IAV) (0.3%), and human parainfluenza viruses (0.5%). To determine the genetic diversity and transmission route of the viruses, phylogenetic analyses were performed using genome sequences of the detected viruses. The IAV strain detected in this study was genetically similar to strains isolated in the USA, whereas the hMPV strain belonging to the A2b subtype formed a cluster with Kenyan strains. This study provides the first complete genomic sequences of HRV, IAV, and hMPV detected in Gabon, and provides insight into the circulation of respiratory viruses in the country.

Mosquito-Borne Arboviruses Occurrence and Distribution in the Last Three Decades in Central Africa: A Systematic Literature Review

Arboviruses represent a real public health problem globally and in the Central African subregion in particular, which represents a high-risk zone for the emergence and re-emergence of arbovirus outbreaks. Furthermore, an updated review on the current arbovirus burden and associated mosquito vectors is lacking for this region. To contribute to filling this knowledge gap, the current study was designed with the following objectives: (i) to systematically review data on the occurrence and distribution of arboviruses and mosquito fauna; and (ii) to identify potential spillover mosquito species in the Central African region in the last 30 years. A web search enabled the documentation of 2454 articles from different online databases. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) and the quality of reporting of meta-analyses (QUORUM) steps for a systematic review enabled the selection of 164 articles that fulfilled our selection criteria. Of the six arboviruses (dengue virus (DENV), chikungunya virus (CHIKV), yellow fever virus (YFV), Zika virus (ZIKV), Rift Valley fever virus (RVFV), and West Nile virus (WNV)) of public health concern studied, the most frequently reported were chikungunya and dengue. The entomological records showed >248 species of mosquitoes regrouped under 15 genera, with Anopheles (n = 100 species), Culex (n = 56 species), and Aedes (n = 52 species) having high species diversity. Three genera were rarely represented, with only one species included, namely, Orthopodomyia, Lutzia, and Verrallina, but individuals of the genera Toxorhinchites and Finlayas were not identified at the species level. We found that two Aedes species (Ae. aegypti and Ae. albopictus) colonised the same microhabitat and were involved in major epidemics of the six medically important arboviruses, and other less-frequently identified mosquito genera consisted of competent species and were associated with outbreaks of medical and zoonotic arboviruses. The present study reveals a high species richness of competent mosquito vectors that could lead to the spillover of medically important arboviruses in the region. Although epidemiological studies were found, they were not regularly documented, and this also applies to vector competence and transmission studies. Future studies will consider unpublished information in dissertations and technical reports from different countries to allow their information to be more consistent. A regional project, entitled "Ecology of Arboviruses" (EcoVir), is underway in three countries (Gabon, Benin, and Cote d'Ivoire) to generate a more comprehensive epidemiological and entomological data on this topic.

Distribution of Aedes mosquito species along the rural-urban gradient in Lambaréné and its surrounding

BACKGROUND

Aedes albopictus and Aedes aegypti are known for their potential as vectors of dengue (DENV) and chikungunya (CHIKV) viruses. However, entomological surveys are mostly carried out during epidemics. In Gabon where outbreaks of both viruses have occurred, there is no vector control program targeting these arboviruses. Therefore, we assessed the presence of Aedes species along a rural-urban gradient in Lambaréné (Gabon) and its surroundings and determined ecological factors associated to their presence.

METHODS

An entomological survey was conducted in Lambaréné and its surrounding rural areas. Mosquitoes were collected with aspirators around human dwellings, and ecological and environmental data were collected from each study area. Morphological identification keys were used to identify Aedes species. RNA was extracted from pools of female mosquitoes and amplified by RT-qPCR to detect the presence of DENV and CHIKV.

RESULTS

Overall, the most common vector collected was Aedes albopictus (97%, 4236/4367 specimens), followed by Aedes aegypti (3%, 131/4367). Albopictus vectors was more abundant in the rural area (Wilcoxon signed-rank test, Z = 627, P = 0.043) than in the urban area. In the urban area, a higher number of mosquitoes (45%) were recorded in the economic zone (zone 3) than in the historical and administrative zones (zone 1 and 2). In the rural area, the proportions of species numbers were significantly higher along the south rural transect (92%) compared to the north rural transect (Wilcoxon signed-rank test, Z = 43, P ˂ 0.016). We also noted a high abundance of vectors in environments characterized by monocultures of Hevea brasiliensis (Hevea) and Manihot esculenta (cassava) (Kruskal-Wallis H-test, H = 25.7, df = 2, P < 0.001). Finally, no mosquito pools were positive for either DENV or CHIKV.

CONCLUSION

Aedes albopictus was the dominant vector across the study sites due to its high invasiveness capacity. This presence re-affirms the potential for local transmission of both DENV and CHIKV, as indicated previously by serological surveys conducted in our study area, even though no transmission was detected during the current study. These findings underscore the need for regular arbovirus surveillance in the study region, with the aim of supporting vector control efforts in the event of outbreaks.

Molecular Evolution of Dengue Virus 3 in Senegal between 2009 and 2022: Dispersal Patterns and Implications for Prevention and Therapeutic Countermeasures

Dengue fever is the most prevalent arboviral disease worldwide. Dengue virus (DENV), the etiological agent, is known to have been circulating in Senegal since 1970, though for a long time, virus epidemiology was restricted to the circulation of sylvatic DENV-2 in south-eastern Senegal (the Kedougou region). In 2009 a major shift was noticed with the first urban epidemic, which occurred in the Dakar region and was caused by DENV-3. Following the notification by Senegal, many other West African countries reported DENV-3 epidemics. Despite these notifications, there are scarce studies and data about the genetic diversity and molecular evolution of DENV-3 in West Africa. Using nanopore sequencing, phylogenetic, and phylogeographic approaches on historic strains and 36 newly sequenced strains, we studied the molecular evolution of DENV-3 in Senegal between 2009 and 2022. We then assessed the impact of the observed genetic diversity on the efficacy of preventive countermeasures and vaccination by mapping amino acid changes against vaccine strains. The results showed that the DENV-3 strains circulating in Senegal belong to genotype III, similarly to strains from other West African countries, while belonging to different clades. Phylogeographic analysis based on nearly complete genomes revealed three independent introduction events from Asia and Burkina Faso. Comparison of the amino acids in the CprM-E regions of genomes from the Senegalese strains against the vaccine strains revealed the presence of 22 substitutions (7 within the PrM and 15 within the E gene) when compared to CYD-3, while 23 changes were observed when compared to TV003 (6 within the PrM and 17 within the E gene). Within the E gene, most of the changes compared to the vaccine strains were located in the ED-III domain, which is known to be crucial in neutralizing antibody production. Altogether, these data give up-to-date insight into DENV-3 genomic evolution in Senegal which needs to be taken into account in future vaccination strategies. Additionally, they highlight the importance of the genomic epidemiology of emerging pathogens in Africa and call for the implementation of a pan-African network for genomic surveillance of dengue virus.

Phylogenetic Investigations of Dengue 2019-2021 Outbreak in Guadeloupe and Martinique Caribbean Islands

Dengue fever has been a public health problem in the Caribbean region since 1981, when it first reappeared in Cuba. In 1989, it was reported in Martinique and Guadeloupe (two French islands 200 km apart); since then, DENV has caused several epidemics locally. In 2019-2021, DENV-1, DENV-2, and DENV-3 were detected. Serotype distribution was differentiated, with DENV-2 and DENV-3 predominating in Guadeloupe and Martinique, respectively. Complete genome sequencing was carried out on 32 specimens, and phylogenic analysis identified the circulation of genotype V for DENV-1, cosmopolitan genotype for DENV-2, and genotype III for DENV-3. However, two distinct circulating groups were identified for DENV-1 and DENV-3, suggesting independent introductions. Overall, despite the context of the COVID-19 pandemic and the associated travel restrictions, these results confirm the active circulation of DENV and specific epidemiological features on each of the two islands. Such differences may be linked to the founder effect of the various introduction events, and to local factors such as the population immunity and the transmission capacity of the vectors. Further genomic and epidemiological characterization of DENV strains remains essential to understand how dengue spreads in each specific geographical context and to prevent future epidemics.

Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa

Viral hepatitis remains one of the largest public health concerns worldwide. Especially in Central Africa, information on hepatitis virus infections has been limited, although the prevalence in this region has been reported to be higher than the global average. To reveal the current status of hepatitis B and C virus (HBV and HCV) infections and the genetic diversity of the viruses, we conducted longitudinal surveillance in Gabon. We detected 22 HBV and 9 HCV infections in 2047 patients with febrile illness. Genetic analyses of HBV identified subgenotype A1 for the first time in Gabon and an insertion generating a frameshift to create an X-preC/C fusion protein. We also revealed that most of the detected HCVs belonged to the "Gabon-specific" HCV subtype 4e (HCV-4e), and the entire nucleotide sequence of the HCV-4e polyprotein was determined to establish the first reference sequence. The HCV-4e strains possessed resistance-associated substitutions similar to those of other HCV-4 strains, indicating that the use of direct-acting antiviral therapy may be complex. These results provide a better understanding of the current situation of hepatitis B and C virus infections in Central Africa and will help public health organizations develop effective countermeasures to eliminate chronic viral hepatitis in this region.

Re-Emergence of Dengue Serotype 3 in the Context of a Large Religious Gathering Event in Touba, Senegal

Dengue virus (DENV) was detected in Senegal in 1979 for the first time. Since 2017, unprecedented frequent outbreaks of DENV were noticed yearly. In this context, epidemiological and molecular evolution data are paramount to decipher the virus diffusion route. In the current study, we focused on a dengue outbreak which occurred in Senegal in 2018 in the context of a large religious gathering with 263 confirmed DENV cases out of 832 collected samples, including 25 life-threatening cases and 2 deaths. It was characterized by a co-circulation of dengue serotypes 1 and 3. Phylogenetic analysis based on the E gene revealed that the main detected serotype in Touba was DENV-3 and belonged to Genotype III. Bayesian phylogeographic analysis was performed and suggested one viral introduction around 2017.07 (95% HPD = 2016.61-2017.57) followed by cryptic circulation before the identification of the first case on 1 October 2018. DENV-3 strains are phylogenetically related, with strong phylogenetic links between strains retrieved from Burkina Faso and other West African countries. These phylogenetic data substantiate epidemiological data of the origin of DENV-3 and its spread between African countries and subsequent diffusion after religious mass events. The study also highlighted the usefulness of a mobile laboratory during the outbreak response, allowing rapid diagnosis and resulting in improved patient management.

Long-term validation of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 from March 2020 to October 2021 in Central Africa, Gabon

BACKGROUND

Despite the development of several methods for diagnosing COVID-19, long-term validation of such methods remains limited. In the early phase of the COVID-19 pandemic, we developed a rapid and sensitive diagnostic method based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) methodology, which is suitable for point-of-care application or for use in resource-limited settings to detect SARS-CoV-2. To assess the applicability of the RT-LAMP assay technique to resource-limited regions, such as rural areas in Africa, and to verify the usability of the method against various SARS-CoV-2 variants, the method was validated using clinical samples collected longitudinally during the pandemic.

METHODOLOGY/PRINCIPAL FINDINGS

First, the sensitivity of the RT-LAMP assay for detecting 10 SARS-CoV-2 variants was evaluated using viral RNA samples extracted from cell culture with a portable battery-supported device, resulting in the successful detection of 20-50 copies of the viral genome within 15 min, regardless of the variant. COVID-19 positive samples collected in Gabon between March 2020 and October 2021 were used to evaluate the sensitivity of the assay and to calculate the copy number of the SARS-CoV-2 genome. More than 292 copies of the viral genome were detected with 100% probability within 15 min in almost all tests.

CONCLUSIONS

This long-term validation study clearly demonstrated the applicability of the RT-LAMP assay for the clinical diagnosis of COVID-19 in resource-limited settings of Africa, such as rural areas in Gabon. The results show the potential of the assay as a promising COVID-19 diagnostic method, especially in rural and remote regions located far from the official diagnosis facilities in urban or semi-urban areas.

Re-emergence of dengue, chikungunya, and Zika viruses in 2021 after a 10-year gap in Gabon

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DENV-1, CHIKV, and ZIKV were detected in Gabon in 2021.

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DENV appeared to switch to serotype 1 from serotype 2 and 3 since 2010.

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Aedes albopictus‒adapted CHIKV appears to circulate repeatedly in Central Africa.

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The recent Gabonese ZIKV strain was genetically different from the previous strain.

Mosquito-borne viral infections are a major concern in endemic areas, such as Africa. Although outbreaks have been reported throughout Africa, only a few surveillance studies have been conducted in Gabon since the outbreaks of dengue virus (DENV) and chikungunya virus (CHIKV) in 2010. Therefore, the current situation is unknown. This study aimed to investigate the presence of arboviruses, especially DENV (serotypes 1–4), CHIKV, and Zika virus (ZIKV), in Gabon, Central Africa. Between 2020 and 2021, we collected 1060 serum samples from febrile patients and screened them against viruses using reverse transcription-quantitative PCR. We detected two DENV serotypes 1 (DENV-1), one CHIKV, and one ZIKV, and subsequently analyzed the genome sequences. To determine the genetic diversity and transmission route of the viruses, phylogenetic analysis was performed using complete or partial genome sequences. The DENV-1 and CHIKV strains detected in this study were closely related to the previous Gabonese strains, whereas the recent ZIKV strain was genetically different from a strain detected in 2007 in Gabon. This study provides new genomic information on DENV-1, CHIKV, and ZIKV that were detected in Gabon and insight into the circulation of the viruses in the country and their introduction from neighboring African countries.

Assessment of Dengue and Chikungunya Infections among Febrile Patients Visiting Four Healthcare Centres in Yaoundé and Dizangué, Cameroon

Dengue and chikungunya are now widely distributed in Cameroon, but there is still not enough information on their prevalence in different epidemiological settings. This study was undertaken to assess the prevalence of dengue and chikungunya in both urban and rural settings in Cameroon using three diagnostic tools. From December 2019 to September 2021, willing febrile (temperature >38 °C) outpatients visiting four healthcare facilities in the cities of Yaoundé and Dizangué were screened for dengue, and chikungunya. Clinical features of patient were recorded in a form, and their blood samples were analysed using real-time reverse transcriptase-polymerase chain reaction (rtRT-PCR), rapid diagnostic tests (RDTs) and enzyme-linked immuno-sorbent assays (ELISA). Odds ratios were used to determine the level of association between socio-demographic factors, clinical features, and infection status. The Kappa coefficient permitted to assess the level of agreement between RDTs and ELISA. Overall, 301 febrile patients were recruited in the study: 198 in Yaoundé and 103 in Dizangué. The prevalence of infection varied with the diagnostic tool used. For dengue diagnostics, 110 patients were positive to rtRT-PCR: 90 (45.45%) in Yaoundé, and 20 (19.42%) in Dizangué. The prevalence of dengue IgM using ELISA varied from 22.3% in Dizangué to 30.8% in Yaoundé. Dengue IgM rate using RDTs was 7.6% in Yaoundé and 3.9% in Dizangué. For chikungunya, one (0.5%) patient (Yaoundé, suburb) was positive to rtRT-PCR. The prevalence of chikungunya IgM according to ELISA varied from 18.4% in Dizangué to 21.7% in Yaoundé, while it was 4.5% in Yaoundé and 12.6% in Dizangué with RDTs. Only abdominal and retro-orbital pains were significantly associated with acute dengue infection. All four dengue serotypes were recorded, with a predominance of DENV-3 (35.45%) and DENV-4 (25.45%). Rapid Diagnostic Tests for either chikungunya or dengue displayed very poor sensitivity. This study further confirms the high endemicity of both dengue and chikungunya in Yaoundé and Dizangué. These data stress the need for active surveillance and the implementation of vector control measures to prevent the occurrence of outbreaks across the country.

Tracing and tracking the emergence, epidemiology and dispersal of dengue virus to Africa during the 20th century

The four mosquito-borne dengue virus serotypes (DENV1–DENV4) cause a high burden of disease throughout the tropical and sub-tropical regions of the world. Nevertheless, their precise epidemiological history in Africa, including when and where they originated and were distributed during the 20th century, remains unclear stressing the need for One Health focused research. Accordingly, we conducted a time-scaled molecular epidemiological reconstruction using publicly available and newly sequenced dengue virus genomes of African origin representing all four serotypes to deduce the most likely temporal and spatial transmission routes of each DENV serotype from their ancestral regions to, within and from Africa.

Our analyses suggest that during the 20th century, serotypes DENV1–DENV3 were introduced to Africa from South East Asia on multiple occasions. The earliest evidence recorded indicates introduction of DENV2 during the early-1940s and of DENV1 during the mid-1940s to Western Africa from South East Asia. The analysis also implies an early introduction of DENV4 during the mid-1940s to Western Africa, alongside DENV1, probably originating in South East Asia. Establishment of DENV3 in Africa appears to have occurred later in the 1960s, apparently originating from South East Asia. However, with the re-establishment of DENV in the Americas, following the cessation of the PAHO mosquito control programme during the mid-20th century, evidence of introductions of DENV1 and DENV2 from the Americas to Western Africa was also observed. The data also identify intra-regional circulation of DENV, but also inter-regional dispersal of all four serotypes within Africa, which has led to a high degree of geographical overlap among serotypes. It is also noteworthy that DENV from both Eastern and Western Africa, have been introduced into Central Africa but there is no support for the converse relationship. For serotypes DENV1–DENV3, we observed probable exports from within established African DENV clusters (≥2 sequences) primarily to Eastern and Southern Asia.

Collectively, our findings support the view that all DENV serotypes, apart from DENV4, have been introduced on multiple occasions to Africa, primarily originating from South East Asia, and subsequently to neighbouring regions within Africa.

Concurrent circulation of dengue serotype 1, 2 and 3 among acute febrile patients in Cameroon

Acute febrile patients presenting at hospitals in Douala, Cameroon between July and December 2020, were screened for dengue infections using real time RT-PCR on fragments of the 5’ and 3’ UTR genomic regions. In total, 12.8% (41/320) of cases examined were positive for dengue. Dengue virus 3 (DENV-3) was the most common serotype found (68.3%), followed by DENV-2 (19.5%) and DENV-1 (4.9%). Co-infections of DENV-3 and DENV-2 were found in 3 cases. Jaundice and headache were the most frequent clinical signs associated with infection and 56% (23/41) of the cases were co-infections with malaria. Phylogenetic analysis of the envelope gene identified DENV-1 as belonging to genotype V, DENV-2 to genotype II and DENV-3 to genotype III. The simultaneous occurrence of three serotypes in Douala reveals dengue as a serious public health threat for Cameroon and highlights the need for further epidemiological studies in the major cities of this region.

Acute febrile patients presenting at hospitals in Douala, Cameroon between July and December 2020, were screened for dengue infections by Polymerase chain reaction. In total, 12.8% (41/320) of cases examined were infected by dengue virus. Dengue virus 3 (DENV-3) was the most common serotype found (68.3%), followed by DENV-2 (19.5%) and DENV-1 (4.9%). Co-infections of DENV-3 and DENV-2 were found in 3 cases. Jaundice and headache were the most frequent clinical signs associated with infection and 56% (23/41) of the cases were co-infections with malaria. The simultaneous occurrence of three serotypes in Douala reveals dengue as a serious public health threat for Cameroon and highlights the need for further epidemiological studies in the major cities of this region.

Multifoci and multiserotypes circulation of dengue virus in Senegal between 2017 and 2018

Background

Dengue fever is a mosquito born disease associated with self-limited to life threatening illness. First detected in Senegal in the nineteenth century, and despite its growing incidence this last decade, significant knowledge gaps exist in our knowledge of genetic diversity of circulating strains. This study highlights the circulating serotypes and genotypes between January 2017 and December 2018 and their spatial and temporal distribution throughout all regions of Senegal.

Methods

We used 56 dengue virus (DENV) strains for the analysis collected from 11 sampling areas: 39 from all regions of Senegal, and 17 isolates from Thiès, a particular area of the country. Two real time RT-qPCR systems were used to confirm dengue infection and corresponding serotypes. For molecular characterization, CprM gene was sequenced and submitted to phylogenetic analysis for serotypes and genotypes assignment.

Results

Three dengue virus serotypes (DENV-1–3) were detected by all used methods. DENV-3 was detected in 50% (28/56) of the isolates, followed by DENV-1 and DENV-2, each representing 25% (14/56) of the isolates. DENV-3 belongs to genotype III, DENV-1 to genotype V and DENV-2 to Cosmopolitan genotype. Serotype 3 was detected in 7 sampling locations and a co-circulation of different serotypes was observed in Thiès, Fatick and Richard-toll.

Conclusions

These results emphasize the need of continuous DENV surveillance in Senegal to detect DENV cases, to define circulating serotypes/genotypes and to prevent the spread and the occurrence of severe cases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06580-z.

Dengue Virus Infection in Sub-Saharan Africa Between 2010 and 2020: A Systematic Review and Meta-Analysis

Dengue virus (DENV) infection has garnered a global interest in the past few decades. Nevertheless, its epidemiology in certain developing and low-income regions remains poorly understood, due to the absence of comprehensive surveillance and reporting systems. This systematic review and meta-analysis aimed to determine the prevalence of DENV infection in the population of Sub-Saharan Africa using DENV infection markers, and to track any changes in its prevalence during the past ten years. It was conducted in accordance with the PRISMA guidelines, targeting the literature available at MEDLINE/PubMed, ScienceDirect, Cochrane library and Google Scholar. All articles published in English language between January 2010 and June 2020 were screened for eligibility. Random effects model was used to calculate the pooled prevalence of all infection markers. The Inconsistency Index (I²) was used to assess the level of heterogeneity between studies. Subgroup analysis according to country and time-frame of studies was conducted to provide possible explanations to substantial heterogeneity. The critical appraisal tool for prevalence studies designed by the Joanna Briggs Institute (JBI) was used to assess the risk of bias in all included studies. A total of 84 articles, covering 21 countries, were included in this review. Quantitative meta-analysis estimated a pooled IgG prevalence of 25% (95% CI: 21-29%, I² = 99%), a pooled IgM prevalence of 10% (95% CI: 9-11%, I² = 98%) and a pooled DENV RNA prevalence of 14% (95% CI: 12-16%, I² = 99%). Evidence for possible publication bias was also found in all three meta-analyses. Subgroup analysis according to the time of sample collection was performed to closely track the changing prevalence of DENV infection markers between 2010 and 2019. This meta-analysis estimates a high prevalence of DENV infection in Sub-Saharan Africa. More cost-efficient vector control strategies should be designed and implemented in order to adapt to the low-resource nature of this region.

Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018

Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we report complete viral genomes from 17 previously undetected DENV cases from the city of Thiès. In total we identified 19 cases of DENV in a cohort of 198 individuals with fever collected in October and November 2018. We detected 3 co-circulating serotypes; DENV 3 was the most frequent accounting for 11/17 sequences (65%), 4 (23%) were DENV2 and 2 (12%) were DENV1. Sequences were most similar to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.

Surveillance of the major pathogenic arboviruses of public health concern in Gabon, Central Africa: increased risk of West Nile virus and dengue virus infections

BACKGROUND

Increasing arbovirus infections have been a global burden in recent decades. Many countries have experienced the periodic emergence of arbovirus diseases. However, information on the prevalence of arboviruses is largely unknown or infrequently updated because of the lack of surveillance studies, especially in Africa.

METHODS

A surveillance study was conducted in Gabon, Central Africa, on arboviruses, which are a major public health concern in Africa, including: West Nile virus (WNV), dengue virus (DENV), Zika virus (ZIKV), yellow fever virus (YFV), chikungunya virus (CHIKV), and Rift Valley fever virus (RVFV). Serological and molecular assays were performed to investigate past infection history and the current status of infection, using serum samples collected from healthy individuals and febrile patients, respectively.

RESULTS

The overall seroprevalence during 2014-2017 was estimated to be 25.3% for WNV, 20.4% for DENV, 40.3% for ZIKV, 60.7% for YFV, 61.2% for CHIKV, and 14.3% for RVFV. No significant differences were found in the seroprevalence of any of the viruses between the male and female populations. However, a focus on the mean age in each arbovirus-seropositive individual showed a significantly younger age in WNV- and DENV-seropositive individuals than in CHIKV-seropositive individuals, indicating that WNV and DENV caused a relatively recent epidemic in the region, whereas CHIKV had actively circulated before. Of note, this indication was supported by the detection of both WNV and DENV genomes in serum samples collected from febrile patients after 2016.

CONCLUSIONS

This study revealed the recent re-emergence of WNV and DENV in Gabon as well as the latest seroprevalence state of the major arboviruses, which indicated the different potential risks of virus infections and virus-specific circulation patterns. This information will be helpful for public health organizations and will enable a rapid response towards these arbovirus infections, thereby preventing future spread in the country.

Identification of potential novel hosts and the risk of infection with lymphocytic choriomeningitis virus in humans in Gabon, Central Africa

OBJECTIVES

Lymphocytic choriomeningitis virus (LCMV), a human pathogenic arenavirus, is distributed worldwide. However, no human cases have been reported in Africa. This study aimed to investigate the current situation and potential risks of LCMV infection in Gabon, Central Africa.

METHODS

A total of 492 human samples were screened to detect LCMV genome RNA and anti-LCMV IgG antibodies using reverse transcription-quantitative PCR and enzyme-linked immunosorbent assay (ELISA), respectively. ELISA-positive samples were further examined using a neutralization assay. Viral RNAs and antibodies were also analyzed in 326 animal samples, including rodents, shrews, and bushmeat.

RESULTS

While no LCMV RNA was detected in human samples, the overall seroprevalence was 21.5% and was significantly higher in male and adult populations. The neutralization assay identified seven samples with neutralizing activity. LCMV RNA was detected in one species of rodent (Lophuromys sikapusi) and a porcupine, and anti-LCMV IgG antibodies were detected in four rodents and three shrews.

CONCLUSIONS

This study determined for the first time the seroprevalence of LCMV in Gabon, and revealed that local rodents, shrews, and porcupines in areas surrounding semi-urban cities posed an infection risk. Hence, LCMV infection should be considered a significant public health concern in Africa.

Epidemiology of dengue fever in Gabon: Results from a health facility-based fever surveillance in Lambaréné and its surroundings

Background

In Africa, information on dengue is limited to outbreak reports and focused on some countries with continuing transmission in West and East Africa. To estimate the proportion of dengue-positive cases among febrile patients and identify clinical indicators of dengue cases, we conducted passive facility-based fever surveillance in a catchment area population of 70,000 residents of Lambaréné and its surroundings in Gabon.

Methods

Non-malarial febrile patients with current fever or history of fever (≤7 days) between 1 and 55 years of age, were enrolled at Albert Schweitzer Hospital (ASH). Acute (visit 1, day of enrollment) and convalescent blood samples were collected between 10 and 21 days after enrollment. Acute/convalescent samples were tested with IgM/IgG ELISA, and a selected subset of acute samples with RT-PCR.

Results

Among 682 non-malarial febrile patients enrolled, 119 (17.4%) were identified as dengue-positive (94 dengue-confirmed and 25 dengue-probable cases). Of these dengue-positive cases, 14 were confirmed with PCR, and based on serotyping, two infections were identified to be DENV-2 and two were DENV-3. The majority of our enrolled patients were <25 years of age and close to 80% of our dengue-positive cases were <15 years of age. In adjusted analyses, retro-orbital pain and abdominal pain were 2.7 and 1.6 times more frequently found among dengue-positive cases, compared to non-dengue cases.

Conclusion

Lambaréné is not considered dengue-endemic. However, one in six non-malarial febrile episodes was found to be dengue-positive in the study period. Dengue should be considered more frequently in clinicians’ diagnosis among non-malarial febrile patients in Lambaréné. Given the lack of data on dengue in Gabon, additional prospective and longitudinal studies would help to further define the burden and patterns of dengue for improved case detection.

In Africa, information on dengue is limited to outbreak reports focused on some countries in West and East Africa. To estimate the proportion of dengue-positive cases among febrile patients and identify clinical indicators of dengue cases, we conducted passive health facility-based fever surveillance in a catchment area population of 70,000 residents of Lambaréné and its surroundings, Gabon. Among the patients with negative malaria RDT results, those with current fever or history of fever (≤7 days) between 1 and 55 years of age were enrolled at Albert Schweitzer Hospital (ASH). Two samples were collected with an interval of 10 to 21 days after enrollment. Samples underwent different testing for dengue confirmation. Among 682 febrile patients enrolled, 17.4% were identified as dengue-positive. Of these dengue-positive cases, we found DENV-2 and DENV-3 serotypes. Close to 80% of our dengue-positive cases were < 15 years old. Retro-orbital pain and abdominal pain were more commonly found among dengue-positive cases, compared to non-dengue cases. Lambaréné is not considered dengue-endemic. However, one in six non-malarial febrile episodes was found to be dengue-positive in the study period. Clinicians should consider dengue more frequently among non-malarial febrile patients. Given the lack of data on dengue in Gabon, more data should be generated to understand the burden and patterns of dengue for improved case detection.

Development and evaluation of a rapid and simple diagnostic assay for COVID-19 based on loop-mediated isothermal amplification

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic novel coronavirus that has caused a worldwide outbreak. Here we describe a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay that uses a portable device for efficient detection of SARS-CoV-2. This RT-LAMP assay specifically detected SARS-CoV-2 without cross-reacting with the most closely related human coronavirus, SARS-CoV. Clinical evaluation of nasal swab samples from suspected SARS-CoV-2 pneumonia (COVID-19) patients showed that the assay could detect over 23.7 copies within 15 min with a 100% probability. Since the RT-LAMP assay can be performed with a portable battery-supported device, it is a rapid, simple, and sensitive diagnostic assay for COVID-19 that can be available at point-of-care. We also developed the RT-LAMP assay without the RNA extraction step–Direct RT-LAMP, which could detect more than 1.43 x 10³ copies within 15 min with a 100% probability in clinical evaluation test. Although the Direct RT-LAMP assay was less sensitive than the standard RT-LAMP, the Direct RT-LAMP assay can be available as the rapid first screening of COVID-19 in poorly equipped areas, such as rural areas in developing countries.

Rapid, accurate and simple diagnostic assay is required to provide an appropriate treatment and establish a surveillance system to prevent the spread of COVID-19. In this study, we developed the RT-LAMP assay using a portable platform equipped with a battery for detection of SARS-CoV-2 in clinical specimens. It could detect over 23.7 copies within 15 min. Since RNA extraction step is one of the main obstacles for rapid diagnosis, we also developed the RT-LAMP assay without this step, Direct RT-LAMP. This assay could detect over 203 copies of viral RNA in virus-spiked swab solution within 10.5 min. Since our RT-LAMP assay is a rapid, simple and highly sensitive diagnostic system for identifying COVID-19 case, it would be useful for the detection of SARS-CoV-2, especially in the field or the settings with insufficient infrastructure.

First evidence for continuous circulation of hepatitis A virus subgenotype IIA in Central Africa

Although a high seroprevalence of antibodies against hepatitis A virus (HAV) has been estimated in Central Africa, the current status of both HAV infections and seroprevalence of anti-HAV antibodies remains unclear due to a paucity of surveillance data available. We conducted a serological survey during 2015-2017 in Gabon, Central Africa, and confirmed a high seroprevalence of anti-HAV antibodies in all age groups. To identify the currently circulating HAV strains and to reveal the epidemiological and genetic characteristics of the virus, we conducted molecular surveillance in a total of 1007 patients presenting febrile illness. Through HAV detection and sequencing, we identified subgenotype IIA (HAV-IIA) infections in the country throughout the year. A significant prevalence trend emerged in the young child population, presenting several infection peaks which appeared to be unrelated to dry or rainy seasons. Whole-genome sequencing and phylogenetic analyses revealed local HAV-IIA evolutionary events in Central Africa, indicating the circulation of HAV-IIA strains of a region-specific lineage. Recombination analysis of complete genome sequences revealed potential recombination events in Gabonese HAV strains. Interestingly, Gabonese HAV-IIA possibly acquired the 5'-untranslated region (5'-UTR) of the rare subgenotype HAV-IIB in recent years, suggesting the present existence of HAV-IIB in Central Africa. These findings indicate a currently stable HAV-IIA circulation in Gabon, with a high risk of infections in children aged under 5 years. Our findings will enhance the understanding of the current status of HAV infections in Central Africa and provide new insight into the molecular epidemiology and evolution of HAV genotype II.

Production of dengue virus-like particles serotype-3 in silkworm larvae and their ability to elicit a humoral immune response in mice

To develop monovalent dengue virus-like particle for serotype 3 (DENV-LP/3), we prepared and expressed two structural polyprotein constructs using silkworm and Bm5 cells: DENV-3 Capsid-premembrane-envelope (DENV-3CprME) and premembrane-envelope (DENV-3prME). The expressed PA-tagged 3CprME and 3prME polypeptides were partially purified by PA-tag affinity chromatography and had molecular weights of 85 and 75 kDa, respectively. Expressed proteins were separately verified using the following primary antibodies: the anti-PA tag antibody, DENV premembrane polyclonal antibody, and DENV envelope polyclonal antibody. Transmission electron microscopy revealed that these DENV-3CprME and 3prME formed rough, spherical DENV-LPs (DENV-LP/3CprME and DENV-LP/3prME), respectively, with a diameter of 30–55 nm. The heparin-binding assay demonstrated that these DENV-LPs contained the envelope protein domain III on their surfaces. Both DENV-LPs showed an affinity to sera from human dengue patients and immunized mice. Immunization of mice with DENV-LP/3prME significantly induced the level of antibodies compared with DENV-LP/3CprME. These results indicate that DENV-LP/3prME is suitable as a vaccine candidate compared with DENV-LP/3CprME.

Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti

Although specific interactions between host and pathogen genotypes have been well documented in invertebrates, the identification of host genes involved in discriminating pathogen genotypes remains a challenge. In the mosquito Aedes aegypti, the main dengue virus (DENV) vector worldwide, statistical associations between host genetic markers and DENV types or strains were previously detected, but the host genes underlying this genetic specificity have not been identified. In particular, it is unknown whether DENV type- or strain-specific resistance relies on allelic variants of the same genes or on distinct gene sets. Here, we investigated the genetic architecture of DENV resistance in a population of Ae. aegypti from Bakoumba, Gabon, which displays a stronger resistance phenotype to DENV type 1 (DENV-1) than to DENV type 3 (DENV-3) infection. Following experimental exposure to either DENV-1 or DENV-3, we sequenced the exomes of large phenotypic pools of mosquitoes that are either resistant or susceptible to each DENV type. Using variation in single-nucleotide polymorphism (SNP) frequencies among the pools, we computed empirical p values based on average gene scores adjusted for the differences in SNP counts, to identify genes associated with infection in a DENV type-specific manner. Among the top 5% most significant genes, 263 genes were significantly associated with resistance to both DENV-1 and DENV-3, 287 genes were only associated with DENV-1 resistance and 290 were only associated with DENV-3 resistance. The shared significant genes were enriched in genes with ATP binding activity and sulfur compound transmembrane transporter activity, whereas the genes uniquely associated with DENV-3 resistance were enriched in genes with zinc ion binding activity. Together, these results indicate that specific resistance to different DENV types relies on largely non-overlapping sets of genes in this Ae. aegypti population and pave the way for further mechanistic studies.

Compatibility between hosts and pathogens is often genetically specific in invertebrates but host genes underlying this genetic specificity have not been elucidated. We investigated the genetic architecture of dengue virus type-specific resistance in the mosquito vector Aedes aegypti. We used a natural population of Ae. aegypti from Bakoumba, Gabon, which is differentially resistant to dengue virus type 1 and dengue virus type 3. We surveyed genetic variation in protein-coding regions of the mosquito genome and compared the frequency of genetic polymorphisms between groups of mosquitoes that are either resistant or susceptible to each dengue virus type. We found that the Ae. aegypti genes associated with resistance to dengue virus type 1 or dengue virus type 3 were largely non-overlapping. This finding indicates that different sets of host genes, rather than different variants of the same genes, confer pathogen-specific resistance in this population. This study is an important step towards identification of mechanisms underlying the genetic specificity of invertebrate host-pathogen interactions.