Evolution of endemic and sylvatic lineages of dengue virus

Recent disease outbreaks have raised awareness of tropical pathogens, especially mosquito-borne viruses. Dengue virus (DENV) is a widely studied mammalian pathogen transmitted by various species of mosquito in the genus Aedes, especially Aedes aegypti and Aedes albopictus. The prevailing view of the research community is that endemic viral lineages that cause epidemics of DENV in humans have emerged over time from sylvatic viral lineages, which persist in wild, non-human primates. These notions have been examined by researchers through phylogenetic analyses of the envelope gene (E) from the four serotypes of DENV (serotypes DENV-1 to DENV-4). In these previous reports, researchers used visual inspection of a phylogeny in order to assert that sylvatic lineages lead to endemic clades. In making this assertion, these researchers also reasserted the model of periodic sylvatic to endemic disease outbreaks. Since that study, there has been a significant increase in data both in terms of metadata (e.g., place and host of isolation) and genetic sequences of DENV. Here, we re-examine the model of sylvatic to endemic shifts in viral lineages through a phylogenetic tree search and character evolution study of metadata on the tree. We built a dataset of nucleotide sequences for 188 isolates of DENV that have metadata on sylvatic or endemic sampling along with three orthologous sequences from West Nile virus as the outgroup for the phylogenetic analysis. In contrast to previous research, we find that there are several shifts from endemic to sylvatic lineages as well as sylvatic to endemic lineages, indicating a much more dynamic model of evolution. We propose that a model that allows oscillation between sylvatic and endemic hosts better captures the dynamics of DENV transmission.     

Evolutionary processes among sylvatic dengue type 2 viruses

Sylvatic dengue viruses (DENV) are transmitted in an enzootic cycle between nonhuman primates and arboreal Aedes mosquitoes in Southeast Asia and West Africa. Although previous analyses have revealed the evolutionary processes among endemic (human) DENV, little is known about viral evolution in the sylvatic cycle. Through an analysis of 14 complete coding regions of sylvatic Dengue type 2 virus sampled over a 33-year period, we show that both the rate of evolutionary change and the pattern of natural selection are similar among endemic and sylvatic DENV, although the latter have a uniquely high frequency of positive selection in the NS4B protein gene. Our findings support a recent cross-species transmission event and suggest the possibility of future DENV reemergence from the sylvatic cycle.     

Dengue-1 virus clade replacement in Thailand associated with enhanced mosquito transmission

Dengue viruses (DENV) are characterized by extensive genetic diversity and can be organized in multiple, genetically distinct lineages that arise and die out on a regular basis in regions where dengue is endemic. A fundamental question for understanding DENV evolution is the relative extent to which stochastic processes (genetic drift) and natural selection acting on fitness differences among lineages contribute to lineage diversity and turnover. Here, we used a set of recently collected and archived low-passage DENV-1 isolates from Thailand to examine the role of mosquito vector-virus interactions in DENV evolution. By comparing the ability of 23 viruses isolated on different dates between 1985 and 2009 to be transmitted by a present-day Aedes aegypti population from Thailand, we found that a major clade replacement event in the mid-1990s was associated with virus isolates exhibiting increased titers in the vector's hemocoel, which is predicted to result in a higher probability of transmission. This finding is consistent with the hypothesis that selection for enhanced transmission by mosquitoes is a possible mechanism underlying major DENV clade replacement events. There was significant variation in transmission potential among isolates within each clade, indicating that in addition to vector-driven selection, other evolutionary forces act to maintain viral genetic diversity. We conclude that occasional adaptive processes involving the mosquito vector can drive major DENV lineage replacement events.     

Emergence of dengue virus serotype 2 in Mauritania and molecular characterization of its circulation in West Africa

The number of sporadic and epidemic dengue fever cases have reportedly been increasing in recent years in some West African countries, such as Senegal and Mali. The first epidemic of laboratory-confirmed dengue occurred in Nouakchott, the capital city of Mauritania situated in the Saharan desert, in 2014. On-site diagnosis of dengue fever was established using a rapid diagnostic test for dengue. In parallel, the presence of Aedes aegypti mosquitoes in the city was confirmed. The initial diagnosis was confirmed by RT-PCR, which showed that all samples from the 2014 dengue epidemic in Nouakchott were dengue virus serotype 2 (DENV-2). The whole genome or envelope protein gene of these strains, together with other DENV-2 strains obtained from travelers returning from West African countries to France between 2016 and 2019 (including two Mauritanian strains in 2017 and 2018), were sequenced. Phylogenetic analysis suggested a recent emergence of an epidemic strain from the cosmopolitan genotype belonging to West African cosmopolitan lineage II, which is genetically distinct from African sylvatic genotype. The origin of this DENV-2 lineage is still unknown, but our data seem to suggest a recent and rapid dispersion of the epidemic strain throughout the region. More complete genome sequences of West African DENV-2 are required for a better understanding of the dynamics of its circulation. Arboviral surveillance and outbreak forecasting are urgently needed in West Africa.     

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century

Zika virus (ZIKV) is a mosquito-borne flavivirus first isolated in Uganda in 1947. Although entomological and virologic surveillance have reported ZIKV enzootic activity in diverse countries of Africa and Asia, few human cases were reported until 2007, when a Zika fever epidemic took place in Micronesia. In the context of West Africa, the WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever at Institut Pasteur of Dakar (http://www.pasteur.fr/recherche/banques/CRORA/) reports the periodic circulation of ZIKV since 1968. Despite several reports on ZIKV, the genetic relationships among viral strains from West Africa remain poorly understood. To evaluate the viral spread and its molecular epidemiology, we investigated 37 ZIKV isolates collected from 1968 to 2002 in six localities in Senegal and Côte d''Ivoire. In addition, we included strains from six other countries. Our results suggested that these two countries in West Africa experienced at least two independent introductions of ZIKV during the 20^th century, and that apparently these viral lineages were not restricted by mosquito vector species. Moreover, we present evidence that ZIKV has possibly undergone recombination in nature and that a loss of the N154 glycosylation site in the envelope protein was a possible adaptive response to the Aedes dalzieli vector.     

The Gr family of candidate gustatory and olfactory receptors in the yellow-fever mosquito Aedes aegypti

The gustatory receptor (Gr) protein family contains most of the diversity in the insect chemoreceptor superfamily, including within it not only taste receptors but select olfactory receptors as well. Manual annotation of the Gr family in the genome sequence of the yellow-fever mosquito, Aedes aegypti, yielded a total of 114 potential proteins encoded by 79 genes. In the sequenced genome, 23 of these genes and protein isoforms are pseudogenic, leaving 91 putatively functional Grs. Comparison with our previously published set of 76 Grs encoded by 52 genes in the distantly related Anopheles gambiae mosquito revealed 13 new AgGrs encoded by 8 genes. Phylogenetic analysis reveals the conservation of carbon dioxide, sugar, and several orphan receptors in these 2 mosquitoes and Drosophila flies. On the other hand, most of these Grs are unique to mosquitoes and many are specific to the Aedes or Anopheles lineages, indicating their involvement in mosquito-specific aspects of both gustatory and olfactory perception. In particular, most instances of alternative splicing in orthologous loci appear to have evolved after the culicine-anopheline split +/-150 million years ago.     

Specific genetic markers for detecting subtypes of dengue virus serotype-2 in isolates from the states of Oaxaca and Veracruz,Mexico

Background  

Dengue (DEN) is an infectious disease caused by the DEN virus (DENV), which belongs to the Flavivirus genus in the family Flaviviridae. It has a (+) sense RNA genome and is mainly transmitted to humans by the vector mosquito Aedes aegypti. Dengue fever (DF) and dengue hemorrhagic fever (DHF) are caused by one of four closely related virus serotypes (DENV-1, DENV-2, DENV-3 and DENV-4). Epidemiological and evolutionary studies have indicated that host and viral factors are involved in determining disease outcome and have proved the importance of viral genotype in causing severe epidemics. Host immune status and mosquito vectorial capacity are also important influences on the severity of infection. Therefore, an understanding of the relationship between virus variants with altered amino acids and high pathogenicity will provide more information on the molecular epidemiology of DEN. Accordingly, knowledge of the DENV serotypes and genotypes circulating in the latest DEN outbreaks around the world, including Mexico, will contribute to understanding DEN infections.     

Diversity and seasonal abundances of mosquitoes at potential arboviral transmission sites in two different climate zones in Switzerland

Pathogens of medical or veterinary significance that are transmitted by mosquitoes (Diptera: Culicidae) are (re‐)emerging in Europe [e.g. West Nile virus (WNV), Dirofilaria nematodes]. Little is known about the spatiotemporal abundances of mosquito species in Switzerland. Therefore, mosquito population dynamics were investigated, focusing on areas of risk for sylvatic or synanthropic transmission, such as natural sites and suburban sites on either side of the Alpine crest. Repeated collections were made using Centers for Disease Control (CDC) traps, juvenile sampling and ovitrapping. A total of 122 831 mosquito specimens of 21 taxa were identified. Levels of mosquito species richness were similar at suburban sites and in natural zones in Switzerland. Mosquito abundances and seasonality were analysed with generalized linear mixed models based on 382 CDC trap samples (29 454 females) and revealed Aedes annulipes/cantans, Aedes geniculatus, Aedes japonicus, Aedes sticticus, Aedes vexans, Coquillettidia richiardii and Culex pipiens/torrentium as the dominant species overall. Abundances of these species were season‐dependent in most cases. There was an effect of site with regard to abundance (higher in natural zones), but not with respect to seasonality. Together with data on vector competence and the host preferences of different species, the present data contribute to assessments of risk for pathogen transmission. For example, both natural and suburban environments seem feasible as sites for amplification cycles of WNV and transmission to mammals.     

Human isolates of dengue type 1 virus induce apoptosis in mouse neuroblastoma cells.

Human isolates of dengue (DEN) type 1 viruses FGA/89 and BR/90 differ in their membrane fusion properties in mosquito cell lines (P. Desprès et al., Virology 196:209-216, 1993). FGA/89 and BR/90 were assayed for their neurovirulence in newborn mice, and neurons were the major target cells for both DEN-1 virus strains within the central nervous system. To study the susceptibility of neurons to DEN virus infection, DEN virus replication was analyzed in the murine neuroblastoma cell line Neuro 2a. Infection of Neuro 2a cells with FGA/89 or BR/90 induced apoptotic DNA degradation after 25 h of infection. Studies of DEN protein synthesis revealed that accumulation of viral proteins leads to apoptotic cell death. The apoptotic process progressed more rapidly following BR/90 infection than it did after FGA/89 infection. The higher cytotoxicity of BR/90 for Neuro 2a cells was linked to an incomplete maturation of the envelope proteins, resulting in abortive virus assembly. Accumulation of viral proteins in the endoplasmic reticulum may induce stress and thereby activate the apoptotic pathway in mouse neuroblastoma cells.     

High Efficiency of Temperate Aedes albopictus to Transmit Chikungunya and Dengue Viruses in the Southeast of France

Background

Since 2005, cases of chikungunya (CHIK) were caused by an unusual vector, Aedes albopictus. This mosquito, present in Europe since 1979, has gained importance since its involvement in the first CHIK outbreak in Italy in 2007. The species is capable of transmitting experimentally 26 arboviruses. However, the vectorial status of its temperate populations has remained little investigated. In 2010, autochthonous cases of CHIK and dengue (DEN) were reported in southeastern France. We evaluated the potential of a French population of Ae. albopictus in the transmission of both viruses.

Methodology and Principal Findings

We used two strains of each virus, CHIK and DEN: one strain was isolated from an imported case, and one from an autochthonous case. We used as controls Aedes aegypti from India and Martinique, the source of the imported cases of CHIK and DEN, respectively. We showed that Ae. albopictus from Cagnes-sur-Mer (AL-CSM) was as efficient as the typical tropical vector Ae. aegypti from India to experimentally transmit both CHIK strains isolated from patients in Fréjus, with around 35–67% of mosquitoes delivering up to 14 viral particles at day 3 post-infection (pi). The unexpected finding came from the high efficiency of AL-CSM to transmit both strains of DENV-1 isolated from patients in Nice. Almost 67% of Ae. albopictus AL-CSM which have ensured viral dissemination were able to transmit at day 9 pi when less than 21% of the typical DEN vector Ae. aegypti from Martinique could achieve transmission.

Conclusions/Significance

Temperate Ae. albopictus behaves differently compared to its counterpart from tropical regions, where recurrent epidemic outbreaks occur. Its potential responsibility for outbreaks in Europe should not be minimized.     

Antigenic analysis of Giardia duodenalis strains isolated in Alberta

Giardia duodenalis is a common intestinal parasite in most parts of the world. In Canada it is associated with both endemic and epidemic infections that are often transmitted by the waterborne route. Although G. duodenalis strains have been isolated from several animals, the role of other mammals in human infection is unclear. We have isolated and cultured G. duodenalis trophozoites from domestic and wild animals in Alberta and compared them with a human isolate by protein gel electrophoresis and immunoblot analysis. All strains examined share a similar polypeptide profile and important protein antigens. Prominent antigens of 62, 52, 38, and 31 kilodaltons are conserved. The 52- and 31-kilodalton proteins are the major surface-exposed trophozoite components. The high degree of antigenic sharing among strains from different hosts suggests that there may be a wide range of potential reservoirs for G. duodenalis infections.     

S-phase-dependent enhancement of dengue virus 2 replication in mosquito cells, but not in human cells

Dengue virus (DEN) is the most prevalent cause of arthropod-borne viral illness in humans. We determined the influence of cellular growth state on DEN type 2 (DEN2) replication in mosquito and human cells, based on the hypothesis that manipulation of cellular growth state will facilitate identification of viral and cellular determinants of productive infection. Comparison of density-arrested and cycling C6/36 Aedes albopictus cells infected with a low-passage DEN2 isolate revealed that cycling cells generated higher virus titers per cell. When C6/36 cells were stalled in S-phase via a thymidine (THY) block, titers of low-passage DEN2 isolates and a high-passage strain, 16681, were increased approximately 30-fold and 10-fold, respectively. Moreover, virus release was earlier in THY-treated cells than in asynchronously cycling cells. Adsorption, entry, genome uncoating, and translation were not responsible for increased titers of virus from S-phase C6/36 cells. In contrast to the 30-fold increase in virus titers, intracellular levels of viral RNA were increased approximately 2-fold, suggesting that the S-phase-responsive step is late in the DEN2 replication cycle. Analysis of viral RNA and protein released from the cells indicated that enhanced DEN2 assembly is largely responsible for increased virus titers produced during S-phase. In contrast to C6/36 cells, DEN2 titers from S-phase human hepatoma cells or primary human fibroblasts were not increased. These results demonstrate a differential response of DEN2 to the mosquito and human cell cycle and provide a framework for detailed studies into the mechanisms mediating virus assembly.     

Association mapping of segregating sites in the early trypsin gene and susceptibility to dengue-2 virus in the mosquito Aedes aegypti

Evidence suggests that midgut trypsins in Aedes aegypti condition the mosquito's ability to become infected with the dengue-2 flavivirus (DEN2). The activity of early trypsin protein peaks approximately 3 h after blood feeding and then drops within a few hours. We use association mapping to test the hypothesis that segregating sites in early trypsin condition midgut susceptibility to DEN2 virus. A total of 1642 females from throughout Mexico and the southern US were fed an artificial blood meal containing DEN2. After 2 weeks, mosquito heads and midguts were tested for DEN2. Mosquitoes with an infected head were classified as susceptible, those without a midgut infection had an infection barrier, and those with an infected gut but no head infection had an escape barrier. The early trypsin gene was amplified in two overlapping pieces from each mosquito and analyzed for single strand conformation polymorphisms (SSCPs). Unique SSCP genotypes were sequenced and 90 segregating sites were found. The dataset was divided into the four geographic regions within which Ae. aegypti is panmictic in Mexico. Heterogeneity chi2 analyses between alleles or genotypes and infection phenotypes demonstrated significant associations but allelic and genotypic effects were inconsistent among geographic regions. No consistent associations were found between segregating sites in early trypsin and susceptibility to DEN2 in Ae. aegypti in Mexico.     

Vector Competence of American Mosquitoes for Three Strains of Zika Virus

In 2015, Zika virus (ZIKV; Flaviviridae; Flavivirus) emerged in the Americas, causing millions of infections in dozens of countries. The rapid spread of the virus and the association with disease outcomes such as Guillain-Barré syndrome and microcephaly make understanding transmission dynamics essential. Currently, there are no reports of vector competence (VC) of American mosquitoes for ZIKV isolates from the Americas. Further, it is not clear whether ZIKV strains from other genetic lineages can be transmitted by American Aedes aegypti populations, and whether the scope of the current epidemic is in part facilitated by viral factors such as enhanced replicative fitness or increased vector competence. Therefore, we characterized replication of three ZIKV strains, one from each of the three phylogenetic clades in several cell lines and assessed their abilities to be transmitted by Ae. aegypti mosquitoes. Additionally, laboratory colonies of different Culex spp. were infected with an American outbreak strain of ZIKV to assess VC. Replication rates were variable and depended on virus strain, cell line and MOI. African strains used in this study outcompeted the American strain in vitro in both mammalian and mosquito cell culture. West and East African strains of ZIKV tested here were more efficiently transmitted by Ae. aegypti from Mexico than was the currently circulating American strain of the Asian lineage. Long-established laboratory colonies of Culex mosquitoes were not efficient ZIKV vectors. These data demonstrate the capacity for additional ZIKV strains to infect and replicate in American Aedes mosquitoes and suggest that neither enhanced virus replicative fitness nor virus adaptation to local vector mosquitoes seems likely to explain the extent and intensity of ZIKV transmission in the Americas.     

Oral susceptibility to yellow fever virus of Aedes aegypti from Brazil

The oral susceptibility to yellow fever virus was evaluated in 23 Aedes aegypti samples from Brazil. Six Ae. aegypti samples from Africa, America and Asia were also tested for comparison. Mosquito samples from Asia showed the highest infection rates. Infection rates for the Brazilian Ae. aegypti reached 48.6%, but were under 13% in 60% of sample tested. We concluded that although the low infection rates estimated for some Brazilian mosquito samples may not favor the establishment of urban cycle of yellow fever in some parts of the country, the founding of Ae. aegypti of noteworthy susceptibility to the virus in cities located in endemic and transition areas of sylvatic yellow fever, do pose a threat of the re-emergence of the urban transmission of the disease in Brazil.     

Fitness advantage and cytoplasmic incompatibility in Wolbachia single- and superinfected Aedes albopictus

Wolbachia are obligate, maternally inherited, intracellular bacteria that infect numerous insects and other invertebrates. Wolbachia infections have evolved multiple mechanisms to manipulate host reproduction and facilitate invasion of naive host populations. One such mechanism is cytoplasmic incompatibility (CI) that occurs in many insect species, including Aedes albopictus (Asian tiger mosquito). The multiple Wolbachia infections that occur naturally in A. albopictus make this mosquito a useful system in which to study CI. Here, experiments employ mosquito strains that have been introgressed to provide genetically similar strains that harbor differing Wolbachia infection types. Cytoplasmic incompatibility levels, host longevity, egg hatch rates, and fecundity are examined. Crossing results demonstrate a pattern of additive unidirectional cytoplasmic incompatibility. Furthermore, relative to uninfected females, infected females are at a reproductive advantage due to both cytoplasmic incompatibility and a fitness increase associated with Wolbachia infection. In contrast, no fitness difference was observed in comparisons of single- and superinfected females. We discuss the observed results in regard to the evolution of the Wolbachia/A. albopictus symbiosis and the observed pattern of Wolbachia infection in natural populations.     

Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue‐endemic and non‐endemic areas of Rajasthan,India

Dengue viruses are transmitted to humans through the bites of infected female aedine mosquitoes. Differences in the composition and structure of bacterial communities in the midguts of mosquitoes may affect the vector's ability to transmit the disease. To investigate and analyse the role of midgut bacterial communities in viral transmission, midgut bacteria from three species, namely Stegomyia aegypti (= Aedes aegypti), Fredwardsius vittatus (= Aedes vittatus) and Stegomyia albopicta (= Aedes albopictus) (all: Diptera: Culicidae), from dengue‐endemic and non‐endemic areas of Rajasthan, India were compared. Construction and analyses of six 16S rRNA gene libraries indicated that Serratia spp.‐related phylotypes dominated all clone libraries of the three mosquito species from areas in which dengue is not endemic. In dengue‐endemic areas, phylotypes related to Aeromonas, Enhydrobacter spp. and uncultivated bacterium dominated the clone libraries of S. aegypti, F. vittatus and S. albopicta, respectively. Diversity indices analysis and real‐time TaqMan polymerase chain reaction assays showed bacterial diversity and abundance in the midguts of S. aegypti to be higher than in the other two species. Significant differences observed among midgut bacterial communities of the three mosquito species from areas in which dengue is and is not endemic, respectively, may be related to the vectorial capacity of mosquitoes to carry dengue viruses and, hence, to the prevalence of disease in some areas.     

Pathogenicity of Spiroplasma taiwanense for larval Aedes aegypti mosquitoes

Helical replicative forms, but not the persistent non-replicative forms, of Spiroplasma taiwanense Abalain-Colloc et al. (isolated from the mosquito Anopheles sinensis Wiedemann in Taiwan) were shown to reduce significantly the survival of Aedes aegypti (L.) mosquito larvae reared in 10 ml of water with 0.3 ml of S.taiwanense suspensions added on days 0 and 3. The suspensions contained, respectively, helical forms at a concentration of 10(9) Colour Change Units (CCU)/ml and persistent forms at 10(6) CCU/ml. It is suggested that S.taiwanense, or toxins produced from it, are potentially useful for use in integrated mosquito control programmes.     

Landscape ecology of sylvatic chikungunya virus and mosquito vectors in southeastern Senegal

The risk of human infection with sylvatic chikungunya (CHIKV) virus was assessed in a focus of sylvatic arbovirus circulation in Senegal by investigating distribution and abundance of anthropophilic Aedes mosquitoes, as well as the abundance and distribution of CHIKV in these mosquitoes. A 1650 km(2) area was classified into five land cover classes: forest, barren, savanna, agriculture and village. A total of 39,799 mosquitoes was sampled from all classes using human landing collections between June 2009 and January 2010. Mosquito diversity was extremely high, and overall vector abundance peaked at the start of the rainy season. CHIKV was detected in 42 mosquito pools. Our data suggest that Aedes furcifer, which occurred abundantly in all land cover classes and landed frequently on humans in villages outside of houses, is probably the major bridge vector responsible for the spillover of sylvatic CHIKV to humans.     

Dengue 1 Diversity and Microevolution,French Polynesia 2001–2006: Connection with Epidemiology and Clinics

Background

Dengue fever (DF) is an emerging infectious disease in the tropics and subtropics. Determinants of DF epidemiology and factors involved in severe cases—dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS)—remain imperfectly characterized. Since 2000, serotype 1 (DENV-1) has predominated in the South Pacific. The aim of this study was (i) to determine the origin and (ii) to study the evolutionary relationships of DENV-1 viruses that have circulated in French Polynesia (FP) from the severe 2001 outbreak to the recent 2006 epidemic, and (iii) to analyse the viral intra-host genetic diversity according to clinical presentation.

Methodology/Principal Findings

Sequences of 181 envelope gene and 12 complete polyproteins of DENV-1 viruses obtained from human sera in FP during the 2001–2006 period were generated. Phylogenetic analysis showed that all DENV-1 FP strains belonged to genotype IV–“South Pacific” and derived from a single introduction event from South-East Asia followed by a 6-year in situ evolution. Although the ratio of nonsynonymous/synonymous substitutions per site indicated strong negative selection, a mutation in the envelope glycoprotein (S222T) appeared in 2002 and was subsequently fixed. It was noted that genetic diversification was very significant during the 2002–2005 period of endemic DENV-1 circulation. For nine DF sera and eight DHF/DSS sera, approximately 40 clones/serum of partial envelope gene were sequenced. Importantly, analysis revealed that the intra-host genetic diversity was significantly lower in severe cases than in classical DF.

Conclusions/Significance

First, this study showed that DENV-1 epidemiology in FP was different from that described in other South-Pacific islands, characterized by a long sustained viral circulation and the absence of new viral introduction over a 6-year period. Second, a significant part of DENV-1 evolution was observed during the endemic period characterized by the rapid fixation of S222T in the envelope protein that may reflect genetic drift or adaptation to the mosquito vector. Third, for the first time, it is suggested that clinical outcome may be correlated with intra-host genetic diversity.