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.

Multiple chikungunya virus introductions in Lao PDR from 2014 to 2020

The first documented chikungunya virus (CHIKV) outbreak in Lao People’s Democratic Republic (Lao PDR) occurred in 2012–2013. Since then, several imported and a few autochthonous cases were identified by the national arbovirus surveillance network. The present study aimed to summarize the main genetic features of the CHIKV strains detected in Lao PDR between 2014 and 2020. Samples from Lao patients presenting symptoms compatible with a CHIKV infection were centralized in Vientiane Capital city for real-time RT-PCR screening. Molecular epidemiology was performed by sequencing the E2-6K-E1 region. From 2014 to 2020, two Asian lineage isolates (e.g. French Polynesia; Indonesia), one ECSA-IOL lineage isolate (e.g. Thailand) and one unclassified (e.g. Myanmar) were imported in Vientiane Capital city. Sequences from the autochthonous cases recorded in the Central and Southern parts of the country between July and September 2020 belonged to the ECSA-IOL lineage and clustered with CHIKV strains recently detected in neighboring countries. These results demonstrate the multiple CHIKV introductions in Lao PDR since 2014 and provide evidence for sporadic and time-limited circulation of CHIKV in the country. Even if the circulation of CHIKV seems to be geographically and temporally limited in Lao PDR, the development of international tourism and trade may cause future outbreaks of CHIKV in the country and at the regional level.

Using Background Sequencing Data to Anticipate DENV-1 Circulation in the Lao PDR

Since its first detection in 1979, dengue fever has been considered a major public health issue in the Lao People’s Democratic Republic (PDR). Dengue virus (DENV) serotype 1 was the cause of an epidemic in 2010–2011. Between 2012 and 2020, major outbreaks due successively to DENV-3, DENV-4 and recently DENV-2 have been recorded. However, DENV-1 still co-circulated in the country over this period. Here, we summarize epidemiological and molecular data of DENV-1 between 2016 and 2020 in the Lao PDR. Our data highlight the continuous circulation of DENV-1 in the country at levels ranging from 16% to 22% among serotyping tests. In addition, the phylogenetic analysis has revealed the circulation of DENV-1 genotype I at least since 2008 with a co-circulation of different clusters. Sequence data support independent DENV-1 introductions in the Lao PDR correlated with an active circulation of this serotype at the regional level in Southeast Asia. The maintenance of DENV-1 circulation over the last ten years supports a low level of immunity against this serotype within the Lao population. Thereby, the risk of a DENV-1 epidemic cannot be ruled out in the future, and this emphasizes the importance of maintaining an integrated surveillance approach to prevent major outbreaks.

Low seroprevalence of COVID-19 in Lao PDR, late 2020

BACKGROUND

In 2020 Lao PDR had low reported COVID-19 cases but it was unclear whether this masked silent transmission. A seroprevalence study was done August - September 2020 to determine SARS-CoV-2 exposure.

METHODS

Participants were from the general community (n=2433) or healthcare workers (n=666) in five provinces and bat/wildlife contacts (n=74) were from Vientiane province. ELISAs detected anti- SARS-CoV-2 Nucleoprotein (N; n=3173 tested) and Spike (S; n=1417 tested) antibodies. Double-positive samples were checked by IgM/IgG rapid tests. Controls were confirmed COVID-19 cases (n=15) and pre-COVID-19 samples (n=265). Seroprevalence for the general community was weighted to account for complex survey sample design, age and sex.

FINDINGS

In pre-COVID-19 samples, 5·3%, [95% CI=3·1-8·7%] were anti-N antibody single-positive and 1·1% [0·3-3·5%] were anti-S antibody single positive. None were double positive. Anti-N and anti-S antibodies were detected in 5·2% [4·2-6·5%] and 2·1% [1·1-3·9%] of the general community, 2·0% [1·1-3·3%] and 1·4% [0·5-3·7%] of healthcare workers and 20·3% [12·6-31·0%] and 6·8% [2·8-15·3%] of bat/wildlife contacts. 0·1% [0·02-0·3%] were double positive for anti-N and anti-S antibodies (rapid test negative).

INTERPRETATION

We find no evidence for significant SARS-CoV-2 circulation in Lao PDR before September 2020. This likely results from early decisive measures taken by the government, social behavior, and low population density. High anti-N /low anti-S seroprevalence in bat/wildlife contacts may indicate exposure to cross-reactive animal coronaviruses with threat of emerging novel viruses.

FUNDING

Agence Française de Développement. Additional; Institut Pasteur du Laos, Institute Pasteur, Paris and Luxembourg Ministry of Foreign and European Affairs ("PaReCIDS II").

First probable case of congenital Zika syndrome in Lao People's Democratic Republic

Zika virus (ZIKV) is a Flavivirus transmitted by Aedes mosquitoes, and was responsible for a worldwide outbreak between 2013 and 2016. However, no ZIKV outbreak has been described in Southeast Asia since 2017. In this study, we report the first microcephaly case with probable ZIKV infection during pregnancy in Lao People's Democratic Republic.

Trends of the Dengue Serotype-4 Circulation with Epidemiological, Phylogenetic, and Entomological Insights in Lao PDR between 2015 and 2019

Dengue outbreaks have regularly been recorded in Lao People's Democratic Republic (PDR) since the first detection of the disease in 1979. In 2012, an integrated arbovirus surveillance network was set up in Lao PDR and an entomological surveillance has been implemented since 2016 in Vientiane Capital. Here, we report a study combining epidemiological, phylogenetic, and entomological analyzes during the largest DENV-4 epidemic ever recorded in Lao PDR (2015-2019). Strikingly, from 2015 to 2019, we reported the DENV-4 emergence and spread at the country level after two large epidemics predominated by DENV-3 and DENV-1, respectively, in 2012-2013 and 2015. Our data revealed a significant difference in the median age of the patient infected by DENV-4 compared to the other serotypes. Phylogenetic analysis demonstrated the circulation of DENV-4 Genotype I at the country level since at least 2013. The entomological surveillance showed a predominance of Aedesaegypti compared to Aedesalbopictus and high abundance of these vectors in dry and rainy seasons between 2016 and 2019, in Vientiane Capital. Overall, these results emphasized the importance of an integrated approach to evaluate factors, which could impact the circulation and the epidemiological profile of dengue viruses, especially in endemic countries like Lao PDR.

Rapid genotyping protocol to improve dengue virus serotype 2 survey in Lao PDR

Dengue fever is one of the major public health problems in Lao PDR. Over the last decade, dengue virus (DENV) epidemics were characterized by a novel predominant serotype accompanied by at least two other serotypes. Since 2008, DENV-2 circulated at a low level in Lao PDR but its epidemiologic profile changed at the end of 2018. Indeed, the number of confirmed DENV-2 cases suddenly increased in October 2018 and DENV-2 became predominant at the country level in early 2019. We developed a Genotype Screening Protocol (GSP) to determine the origin(s) of the Lao DENV-2 and study their genetic polymorphism. With a good correlation with full envelope gene sequencing data, this molecular epidemiology tool evidence the co-circulation of two highly polymorphic DENV-2 genotypes, i.e. Asian I and Cosmopolitan genotypes, over the last five years, suggesting multiple introductions of DENV-2 in the country. GSP approach provides relevant first line information that may help countries with limited laboratory resources to reinforce their capabilities to DENV-2 and to follow the epidemics progresses and assess situations at the regional level.

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes

In New Caledonia (NC), Aedes aegypti is the only proven vector of dengue virus (DENV), which is the most prevalent arbovirosis in NC. Since World War II, the four DENV serotypes have circulated regularly in NC. The epidemiological profile, however, has evolved over the last ten years, with the persistence of DENV-1 circulation and the co-circulation of several DENV serotypes. The current study evaluated the ability of Ae. aegypti from NC to transmit four DENV serotypes (and two DENV-1 genotypes) isolated during recent outbreaks in NC. An Ae. aegypti F1 generation was twice independently orally challenged with each DENV strain (10⁷ FFU/ml). Infection, dissemination and transmission rates and transmission efficiency were measured at day 7 and 14 post-exposure, as well as the quantity of infectious virus particles. Mosquito infection was observed as early as 7 days post-infection. Infection rates between 18 and 58% were measured for all DENV serotypes/genotypes tested. Although dissemination rates ranged from 78 to 100%, transmission efficiencies were low, with values not exceeding 21% at 14 days post-infection for all DENV strains. This study shows that NC Ae. aegypti are moderately competent for DENV in laboratory conditions. In link with epidemiological data, these results suggest implication of other factors in the sustained circulation of DENV-1 in New Caledonia.

Aedes aegypti is the only known vector for dengue virus (DENV) in New Caledonia (NC). DENV are divided into four serotypes (DENV-1 to -4), based on their antigenic properties, these being subdivided into different genotypes. All four DENV serotypes have regularly circulated in New Caledonia in the past. An unusual persistence of DENV-1 has been observed during the last ten years, suggesting a possible preferential transmission of this DENV serotype by Ae. aegypti. In this study, we examine for the first time the ability of Ae. aegypti from New Caledonia to transmit the four circulating DENV serotypes, and more precisely two genotypes of DENV-1. Our results demonstrate that this vector is moderately competent for DENV, with slight differences observed between DENV serotype/genotype in terms of transmission. These findings suggest that other factors are at play in the sustained circulation of DENV-1 and that further vector-virus interactions studies should be undertaken to better understand the DENV epidemiological profile in NC.

Assessing entomological risk factors for arboviral disease transmission in the French Territory of the Wallis and Futuna Islands

Background

The French overseas Territory of the Wallis and Futuna Islands has been affected by several dengue epidemics. Aedes polynesiensis is the main mosquito vector described in this territory. Other Aedes species have been reported, but recent entomological data are missing to infer the presence of other potential arbovirus vectors and to assess the entomological risk factors for transmission of arboviral diseases.

Methodology/ Principal findings

An entomological prospective study was conducted on the three main islands of the territory to determine the presence and distribution of Aedes spp. Larvae, pupae and adult mosquitoes were collected from 54 sampling points in different environments, with a final sampling of 3747 immature stages and 606 adults. The main identified breeding sites were described. Ae. polynesiensis was found in every sampled site in peridomestic and wild habitats. Ae. aegypti was only found on the island of Wallis in peridomestic environments with a limited distribution. Two other Aedes species endemic to the Pacific were recorded, Aedes oceanicus and Aedes futunae. To evaluate the ability of local Ae. polynesiensis to transmit the chikungunya virus (CHIKV), two field populations were analyzed for vector competence using experimental oral exposure of females to CHIKV and infection, dissemination and transmission assays. Results showed that both populations of Ae. polynesiensis were competent for CHIKV (30% at 7 days post-infection).

Conclusions/Significance

This study showed the ubiquitous distribution and abundance of Ae. polynesiensis on the three islands and demonstrated that local populations were able to transmit CHIKV. Combined with the presence and expansion of Ae. aegypti on the main island of Wallis, these data highlight the risk of transmission of arboviral diseases in the territory of Wallis and Futuna and provide relevant information for entomological surveillance and vector control programs.

The French overseas Territory of the Wallis and Futuna Islands, located in the South Pacific, has been affected by several dengue epidemics, but did not face Zika or chikungunya outbreaks, unlike other neighboring islands. The near-exclusive presence of the Aedes polynesiensis mosquito in the islands of Wallis and Futuna confirmed the role played by this mosquito as a vector of dengue fever. A local Ae. polynesiensis population was recently shown to be able to transmit the Zika virus under experimental conditions, but its susceptibility to the chikungunya virus was still unknown, and recent data on the presence of other potential arbovirus vectors were missing. Therefore, we investigated the entomological risk factors for the transmission of arboviral diseases in the Wallis and Futuna Islands. We reported the occurrence and distribution of different Aedes species, especially the abundant presence of Ae. polynesiensis across the territory and the spread of Ae. aegypti in the island of Wallis. Our results demonstrated the ability of local Ae. polynesiensis populations to transmit the chikungunya virus. These findings highlight the risk of arbovirus transmission in the Wallis and Futuna Islands and provide relevant data to guide prevention and vector control strategies in the territory.

Risk of arbovirus emergence via bridge vectors: case study of the sylvatic mosquito Aedes malayensis in the Nakai district, Laos

Many emerging arboviruses of global public health importance, such as dengue virus (DENV) and yellow fever virus (YFV), originated in sylvatic transmission cycles involving wild animals and forest-dwelling mosquitoes. Arbovirus emergence in the human population typically results from spillover transmission via bridge vectors, which are competent mosquitoes feeding on both humans and wild animals. Another related, but less studied concern, is the risk of 'spillback' transmission from humans into novel sylvatic cycles. We colonized a sylvatic population of Aedes malayensis from a forested area of the Nakai district in Laos to evaluate its potential as an arbovirus bridge vector. We found that this Ae. malayensis population was overall less competent for DENV and YFV than an urban population of Aedes aegypti. Olfactometer experiments showed that our Ae. malayensis colony did not display any detectable attraction to human scent in laboratory conditions. The relatively modest vector competence for DENV and YFV, combined with a lack of detectable attraction to human odor, indicate a low potential for this sylvatic Ae. malayensis population to act as an arbovirus bridge vector. However, we caution that opportunistic blood feeding on humans by sylvatic Ae. malayensis may occasionally contribute to bridge sylvatic and human transmission cycles.

Zika virus outbreak in the Pacific: Vector competence of regional vectors

BACKGROUND

In 2013, Zika virus (ZIKV) emerged in French Polynesia and spread through the Pacific region between 2013 and 2017. Several potential Aedes mosquitoes may have contributed to the ZIKV transmission including Aedes aegypti, the main arbovirus vector in the region, and Aedes polynesiensis, vector of lymphatic filariasis and secondary vector of dengue virus. The aim of this study was to analyze the ability of these two Pacific vectors to transmit ZIKV at a regional scale, through the evaluation and comparison of the vector competence of wild Ae. aegypti and Ae. polynesiensis populations from different Pacific islands for a ZIKV strain which circulated in this region during the 2013-2017 outbreak.

METHODOLOGY/PRINCIPAL FINDINGS

Field Ae. aegypti (three populations) and Ae. polynesiensis (two populations) from the Pacific region were collected for this study. Female mosquitoes were orally exposed to ZIKV (107 TCID50/mL) isolated in the region in 2014. At 6, 9, 14 and 21 days post-infection, mosquito bodies (thorax and abdomen), heads and saliva were analyzed to measure infection, dissemination, transmission rates and transmission efficiency, respectively. According to our results, ZIKV infection rates were heterogeneous between the Ae. aegypti populations, but the dissemination rates were moderate and more homogenous between these populations. For Ae. polynesiensis, infection rates were less heterogeneous between the two populations tested. The transmission rate and efficiency results revealed a low vector competence for ZIKV of the different Aedes vector populations under study.

CONCLUSION/SIGNIFICANCE

Our results indicated a low ZIKV transmission by Ae. aegypti and Ae. polynesiensis tested from the Pacific region. These results were unexpected and suggest the importance of other factors especially the vector density, the mosquito lifespan or the large immunologically naive fraction of the population that may have contributed to the rapid spread of the ZIKV in the Pacific region during the 2013-2017 outbreak.

Introduction of the Anopheles bancroftii Mosquito, a Malaria Vector, into New Caledonia

In June 2017, an Anopheles mosquito species was detected in New Caledonia. Morphologic identification and genomic sequencing revealed that the specimens tested belong to An. bancroftii genotype A1. This introduction underscores the risk for local malaria transmission and the vulnerability of New Caledonia to vector introduction.

Genetic Diversity and Phylogeny of Aedes aegypti, the Main Arbovirus Vector in the Pacific

Background

The Pacific region is an area unique in the world, composed of thousands of islands with differing climates and environments. The spreading and establishment of the mosquito Aedes aegypti in these islands might be linked to human migration. Ae. aegypti is the major vector of arboviruses (dengue, chikungunya and Zika viruses) in the region. The intense circulation of these viruses in the Pacific during the last decade led to an increase of vector control measures by local health authorities. The aim of this study is to analyze the genetic relationships among Ae. aegypti populations in this region.

Methodology/Principal Finding

We studied the genetic variability and population genetics of 270 Ae. aegypti, sampled from 9 locations in New Caledonia, Fiji, Tonga and French Polynesia by analyzing nine microsatellites and two mitochondrial DNA regions (CO1 and ND4). Microsatellite markers revealed heterogeneity in the genetic structure between the western, central and eastern Pacific island countries. The microsatellite markers indicate a statistically moderate differentiation (F_ST = 0.136; P < = 0.001) in relation to island isolation. A high degree of mixed ancestry can be observed in the most important towns (e.g. Noumea, Suva and Papeete) compared with the most isolated islands (e.g. Ouvea and Vaitahu). Phylogenetic analysis indicated that most of samples are related to Asian and American specimens.

Conclusions/Significance

Our results suggest a link between human migrations in the Pacific region and the origin of Ae. aegypti populations. The genetic pattern observed might be linked to the island isolation and to the different environmental conditions or ecosystems.

Aedes aegypti is the major arbovirus vector in the Pacific region. The spread of this mosquito in the different islands seems to be linked to human activities at the beginning of the twentieth century. Since 2010, occurrence of arbovirus outbreaks increased in this region, with the co-circulation of dengue, chikungunya and Zika viruses. The lack of vaccines and treatments for these pathogens led the health authorities to implement vector control measures. In this study, we present the genetic structure and the phylogenetic data obtained from the analysis of 270 Ae. aegypti collected in the Pacific region. The infestation of the islands seems to have American and Asian origins. The genetic structure of the vector populations indicates a differentiation of the mosquitoes between the western, central and eastern Pacific island countries and the specific island isolation context. This differentiation could be related to the different environmental conditions in each island country.

Detection of Zika virus in urine

We describe the kinetics of Zika virus (ZIKV) detection in serum and urine samples of 6 patients. Urine samples were positive for ZIKV >10 days after onset of disease, which was a notably longer period than for serum samples. This finding supports the conclusion that urine samples are useful for diagnosis of ZIKV infections.