Genetic characterization of Chikungunya virus in the Central African Republic

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.

Arboviral Risk Associated with Solid Organ and Hematopoietic Stem Cell Grafts: The Prophylactic Answers Proposed by the French High Council of Public Health in a National Context

Diseases caused by arboviruses are on the increase worldwide. In addition to arthropod bites, most arboviruses can be transmitted via accessory routes. Products of human origin (labile blood products, solid organs, hematopoietic stem cells, tissues) present a risk of contamination for the recipient if the donation is made when the donor is viremic. Mainland France and its overseas territories are exposed to a complex array of imported and endemic arboviruses, which differ according to their respective location. This narrative review describes the risks of acquiring certain arboviral diseases from human products, mainly solid organs and hematopoietic stem cells, in the French context. The main risks considered in this study are infections by West Nile virus, dengue virus, and tick-borne encephalitis virus. The ancillary risks represented by Usutu virus infection, chikungunya, and Zika are also addressed more briefly. For each disease, the guidelines issued by the French High Council of Public Health, which is responsible for mitigating the risks associated with products of human origin and for supporting public health policy decisions, are briefly outlined. This review highlights the need for a "One Health" approach and to standardize recommendations at the international level in areas with the same viral epidemiology.

Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification

Total RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as the predominant template from which sequences are generated, meaning that the desired host and viral templates are sequenced far less. Second, mosquito specimens captured in the field must be correctly identified, in some cases to the sub-species level. Here, we generate mosquito rRNA datasets which will substantially mitigate both of these problems. We describe a strategy to assemble novel rRNA sequences from mosquito specimens and produce an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). These sequences will allow both physical and computational removal of rRNA from specimens during RNA-seq protocols. We also assess the utility of rRNA sequences for molecular taxonomy and compare phylogenies constructed using rRNA sequences versus those created using the gold standard for molecular species identification of specimens-the mitochondrial cytochrome c oxidase I (COI) gene. We find that rRNA- and COI-derived phylogenetic trees are incongruent and that 28S and concatenated 28S+18S rRNA phylogenies reflect evolutionary relationships that are more aligned with contemporary mosquito systematics. This significant expansion to the current rRNA reference library for mosquitoes will improve mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader range of species and streamlining species identification by rRNA sequence and phylogenetics.

Molecular characterization of chikungunya virus from the first cluster of patients during the 2020 outbreak in Chad

We sequenced a portion of the E1 envelope protein gene of two of four CHIKV RT-PCR-positive samples from the first cluster of chikungunya patients during the 2020 Chad outbreak. Phylogenetic analysis revealed that the viruses belonged to the East/Central/South/African genotype but lacked the E1 A226V and K211E mutations associated with viral adaptability and transmission, suggesting an autochthonous transmission. These sequences are a useful basis for tracking viral evolution in subsequent outbreaks in Chad.

Genetic characterization of chikungunya virus isolates from Aedes aegypti mosquitoes collected during a recent outbreak in Bangkok, Thailand

Chikungunya virus (CHIKV) is a mosquito-borne emerging pathogen that is transmitted to humans through the bite of female Aedes mosquitoes. CHIKV infection has become a major public health concern worldwide, as it has a significant impact on the healthcare system. Since 2004, the virus has emerged in Africa and subsequently spread to countries located near the Indian Ocean, including India, and to Europe, the Americas, and Asia. In Thailand, a large CHIKV outbreak occurred during 2008-2009 and was caused by a virus originating from the east/central/south African (ECSA) CHIKV genotype. Since then, the ECSA genotype of CHIKV has continued to circulate and has caused sporadic cases in different areas in Thailand. Approximately 20,000 reported cases have been confirmed by the Bureau of Epidemiology, Ministry of Public Health, Thailand, from January 1, 2018 to July 31, 2020. However, the causes of this CHIKV re-emergence remain unclear. To obtain a better understanding of CHIKV circulation during the recent outbreak in Bangkok, Thailand, complete genome analysis of CHIKV isolates from field-caught mosquitoes collected in outbreak areas was performed. A total of 28 Ae. aegypti samples (21 females and 7 males) were collected, and individual mosquitoes were used for CHIKV detection and isolation. Eleven of 28 (39.29%) female and three of 28 (10.71%) male mosquitoes were positive for CHIKV by E1 nested RT-PCR. Four CHIKV isolates were successfully isolated from four female Ae. aegypti mosquitoes. Based on complete genome analysis, several amino acid substitutions were identified in the protein coding region. The E1:K211E and E2:V264A mutations in the background of the E1:226A mutation were observed in all four CHIKV isolates. An important observation was the presence of one amino acid substitution, leading to an E1:K245R change. This mutation was found in all four CHIKV isolates from mosquitoes in this study and in Thai patients described previously. Additionally, phylogenetic analysis indicated that the four CHIKV isolates belonged to the Indian Ocean clade of the ECSA genotype. The results obtained in this study provide detailed information on the molecular characteristics and evolution of currently circulating CHIKV strains in Thailand, which are useful for developing prevention and control strategies.

Fast Expansion of the Asian-Pacific Genotype of the Chikungunya Virus in Indonesia

Chikungunya is repeatedly affecting Indonesia through successive outbreaks. The Asian genotype has been present in Asia since the late 1950s while the ECSA-IOL (East/Central/South Africa - Indian Ocean Lineage) genotype invaded Asia in 2005. In order to determine the extension of the circulation of the chikungunya virus (CHIKV) in Indonesia, mosquitoes were collected in 28 different sites from 12 Indonesian provinces in 2016-2017. The E1 subunit of the CHIKV envelope gene was sequenced while mosquitoes were genotyped using the mitochondrial cox1 (cytochrome C oxidase subunit 1) gene to determine whether a specific population was involved in the vectoring of CHIKV. A total of 37 CHIKV samples were found in 28 Aedes aegypti, 8 Aedes albopictus and 1 Aedes butleri out of 15,362 samples collected and tested. These viruses, like all Indonesian CHIKV since 2000, belonged to a genotype we propose to call the Asian-Pacific genotype. It also comprises the Yap isolates and viruses having emerged in Polynesia, the Caribbean and South America. They differ from the CHIKV of the Asian genotype found earlier in Indonesia indicating a replacement. These results raise the question of the mechanisms behind this fast and massive replacement.

Chikungunya fever in Africa: a systematic review

Since the identification of chikungunya virus (CHIKV), sporadic cases and outbreaks were reported in several African countries, on the Indian subcontinent, and in south-east Asia. In the last 20 years, there is a growing number of reports of CHIKV infections from African countries, but the overall picture of its circulation at the continent level remains ill-characterized because of under-diagnosis and under-reporting. Moreover, the public health impact of the infection in Africa is generally poorly understood, especially during outbreak situations. Our work has the aim to review available data on CHIKV circulation in Africa to facilitate the understanding of underlying reasons of its increased detection in the African continent.

Geographical distribution of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) and genetic diversity of invading population of Ae. albopictus in the Republic of the Congo

Background: The arbovirus vector, Aedes albopictus, originating from Asia, has recently invaded African countries, including the Republic of the Congo, where it was associated with a chikungunya outbreak. Up until now, little was known about its distribution in relation to the native Aedes aegypti and how the invasion will modify the epidemiology of arboviral diseases. Here, we assessed the current distribution of Ae. albopictus and Ae. aegypti in the Republic of the Congo and explored the genetic diversity of the invading species, Ae. albopictus.

Methods: Immature stages of Aedes were collected in nine locations in the Republic of the Congo in 2017 following a north-south transect and reared to adult stage. Adults were morphologically identified, counted and grouped according to species and location. Genetic diversity of Ae. albopictus was assessed by analyzing the cytochrome oxidase I ( COI) gene.

Results: Ae. albopictus and Ae. aegypti were found together across the country in all the locations investigated. The invasive species is predominant over the native species in all locations except Brazzaville, suggesting that Ae. albopictus is displacing Ae. aegypti across Congo. When comparing the species distributions across the two largest cities, Brazzaville and Pointe Noire, Ae. albopictus was more prevalent than Ae. aegypti in the suburbs whereas the opposite situation was reported in the city centre. Mitochondrial DNA analysis revealed very low genetic diversity of Ae. albopictus with only three haplotypes recorded across the country supporting the recent introduction of this species in the Republic of the Congo. Phylogenetic tree analysis revealed that Ae. albopictus from Congo originated from other tropical Asian countries such as China, likely as a result of increasing trade links.

Conclusion: These findings are important for the implementation of vector control strategies and can serve as a foundation for further research on these vectors in the country.

Geographical distribution of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) and genetic diversity of invading population of Ae. albopictus in the Republic of the Congo

Background:The arbovirus vector,Aedes albopictus,originating from Asia, has recently invaded African countries, including the Republic of the Congo, where it was associated with a chikungunya outbreak. Up until now, little was known about its distribution in relation to the nativeAedes aegyptiand how the invasion will modify the epidemiology of arboviral diseases. Here, we assessed the current distribution ofAe. albopictusandAe. aegyptiin the Republic of the Congo and explored the genetic diversity of the invading species,Ae. albopictus.Methods:Immature stages ofAedeswere collected in nine locations in the Republic of the Congo in 2017 following a north-south transect and reared to adult stage. Adults were morphologically identified, counted and grouped according to species and location. Genetic diversity ofAe. albopictuswas assessed by analyzing the cytochrome oxidase I (COI) gene.Results:Ae.albopictusandAe. aegyptiwere found together across the country in all the locations investigated. The invasive species is predominant over the native species in all locations except Brazzaville, suggesting thatAe. albopictusis displacingAe. aegyptiacross Congo. When comparing the species distributions across the two largest cities, Brazzaville and Pointe Noire,Ae. albopictuswas more prevalent thanAe. aegyptiin the suburbs whereas the opposite situation was reported in the city centre. Mitochondrial DNA analysis revealed very low genetic diversity ofAe. albopictuswith only three haplotypes recorded across the country supporting the recent introduction of this species in the Republic of the Congo. Phylogenetic tree analysis revealed thatAe. albopictusfrom Congo originated from other tropical Asian countries such as China, likely as a result of increasing trade links.Conclusion:These findings are important for the implementation of vector control strategies and can serve as a foundation for further research on these vectors in the country.

Geographical distribution of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) and genetic diversity of invading population of Ae. albopictus in the Republic of the Congo

Background: The arbovirus vector, Aedes albopictus, originating from Asia, has recently invaded African countries, including the Republic of the Congo, where it was associated with a chikungunya outbreak. Up until now, little was known about its distribution in relation to the native Aedes aegypti and how the invasion will modify the epidemiology of arboviral diseases. Here, we assessed the current distribution of Ae. albopictus and Ae. aegypti in the Republic of the Congo and explored the genetic diversity of the invading species, Ae. albopictus. Methods: Immature stages of Aedes were collected in nine locations in the Republic of the Congo in 2017 following a north-south transect and reared to adult stage. Adults were morphologically identified, counted and grouped according to species and location. Genetic diversity of Ae. albopictus was assessed by analyzing the cytochrome oxidase I (COI) gene. Results: Ae. albopictus and Ae. aegypti were found together across the country in all the locations investigated. The invasive species is predominant over the native species in all locations except Brazzaville, suggesting that Ae. albopictus is displacing Ae. aegypti across Congo. When comparing the species distributions across the two largest cities, Brazzaville and Pointe Noire, Ae. albopictus was more prevalent than Ae. aegypti in the suburbs whereas the opposite situation was reported in the city centre. Mitochondrial DNA analysis revealed very low genetic diversity of Ae. albopictus with only three haplotypes recorded across the country supporting the recent introduction of this species in the Republic of the Congo. Phylogenetic tree analysis revealed that Ae. albopictus from Congo originated from other tropical Asian countries such as China, likely as a result of increasing trade links. Conclusion: These findings are important for the implementation of vector control strategies and can serve as a foundation for further research on these vectors in the country.

Chikungunya: Its History in Africa and Asia and Its Spread to New Regions in 2013-2014

Chikungunya virus (CHIKV) is transmitted by Aedes aegypti and Aedes albopictus mosquitoes and causes febrile illness with severe arthralgia in humans. There are 3 circulating CHIKV genotypes, Asia, East/Central/South Africa, and West Africa. CHIKV was first reported in 1953 in Tanzania, and up until the early 2000s, a few outbreaks and sporadic cases of CHIKV were mainly reported in Africa and Asia. However, from 2004 to 2005, a large epidemic spanned from Kenya over to the southwestern Indian Ocean region, India, and Southeast Asia. Identified in 2005, the E1 glycoprotein A226V mutation of the East/Central/South Africa genotype conferred enhanced transmission by the A. albopictus mosquito and has been implicated in CHIKV's further spread in the last decade. In 2013, the Asian CHIKV genotype emerged in the Caribbean and quickly took the Americas by storm. This review will discuss the history of CHIKV as well as its expanding geographic distribution.

Potential of Aedes aegypti and Aedes albopictus populations in the Central African Republic to transmit enzootic chikungunya virus strains

Background

Major chikungunya outbreaks have affected several Central African countries during the past decade. The chikungunya virus (CHIKV) was isolated from humans and sylvan mosquitoes in the Central African Republic (CAR) during the 1970 and 1980s but has not been found recently, despite the presence of Aedes albopictus since 2010. The risk of a massive chikungunya epidemic is therefore potentially high, as the human populations are immunologically naïve and because of the presence of the mosquito vector. In order to estimate the risk of a large outbreak, we assessed the vector competence of local Ae. aegypti and Ae. albopictus populations for ancient local strains of CHIKV in CAR. Mosquitoes were orally infected with the virus, and its presence in mosquito saliva was analysed 7 and 14 days post-infection (dpi) by quantitative reverse transcriptase polymerase chain reaction.

Results

The two species had similar infection rates at 7 and 14 days, and the dissemination rate of both vectors was ≥ 80% at 14 dpi. Only females followed up to 14 dpi had CHKV in their saliva.

Conclusion

These results confirm the risk of transmission of enzootic CHIKV by anthropophilic vectors such as Ae. aegypti and Ae. albopictus.

Global expansion of chikungunya virus: mapping the 64-year history

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that is emerging as a global threat because of the highly debilitating nature of the associated disease and unprecedented magnitude of its spread. Chikungunya originated in Africa and has since spread across the entire globe causing large numbers of epidemics that have infected millions of people in Asia, the Indian subcontinent, Europe, the Americas, and Pacific Islands. Phylogenetic analysis has identified four different genotypes of CHIKV: Asian, West African, East/Central/South African (ECSA), and Indian Ocean Lineage (IOL). In the absence of well-designed epidemiological studies, the aim of this review article was to summarize the global epidemiology of CHIKV and to provide baseline data for future research on the treatment, prevention, and control of this life-threatening disease.

Complete Genome Sequences of Two Chikungunya Viruses Isolated in the Central African Republic in the 1970s and 1980s

Some arboviruses threaten human global health with potentially explosive emergence. Analysis of whole-genome sequences of decades-old isolates might contribute to the understanding of the complex dynamics which drive their circulation and emergence. Here, we report the whole-genome sequences of two Chikungunya viruses isolated in the Central African Republic in the 1970s and 1980s.