A generic nested-RT-PCR followed by sequencing for detection and identification of members of the alphavirus genus

First isolation of the Sindbis virus in mosquitoes from southwestern Spain reveals a new recent introduction from Africa

Sindbis virus (SINV), is an Alphavirus of the family Togaviridae. This zoonotic arbovirus is transmitted by mosquitoes, primarily from the Culex genus, with bird species acting as amplifying vertebrate hosts. Occasionally it can also affect humans that are accidental hosts. SINV genotype I (SINV-I) has been isolated in mosquitoes and birds in South Africa and Northern Europe, producing fever outbreaks. In the last decades, there were several detections of SINV in Europe. In 2022, during the West Nile virus (WNV) mosquito surveillance program in Andalucía (Spain) implemented by the regional health administration, we detected the presence of both SINV and WNV in a Culex perexiguus pool, representing the first detection of SINV in Spain. After this finding, we screened 1149 mosquito pools to determine the status of SINV circulation in western Andalucía. We identified for the first time the presence of SINV in five different mosquito species. Culex perexiguus presented the highest infection rate by SINV. In addition, SINV was geographically widespread and distributed in four out of the five Andalucía's provinces studied, with Cadiz presenting the highest infection rate. All SINV genomes from Southwestern Spain characterised in this study belonged to SINV-I, previously detected in Europe and Africa. These isolated SINV-I strains presented low molecular variation among them and in the phylogenomic analyses they formed a monophyletic group that clustered with strains from Algeria and Kenya. These results suggest that, around 2017, a single new SINV introduction into the European continent occurred, probably from Northern (Algeria) or Central Africa.

Low capacity for molecular detection of Alphaviruses other than Chikungunya virus in 23 European laboratories, March 2022

Alphaviruses comprise over 30 identified species spread worldwide and carry a large global health burden. With vector expansion occurring in and around Europe, it is anticipated this burden will increase. Therefore, regular assessment of the diagnostic capabilities in Europe is important, e.g., by conducting external quality assessments (EQAs). Here we evaluated molecular detection of alphaviruses in expert European laboratories by conducting an EQA in March 2022. Molecular panels included 15 samples: nine alphaviruses, Barmah Forest virus (BFV), chikungunya virus (CHIKV), Eastern equine encephalitis virus (EEEV), Mayaro virus (MAYV), o'nyong-nyong virus (ONNV), Ross River virus (RRV), Sindbis virus (SINV), Venezuelan equine encephalitis virus (VEEV), and Western equine encephalitis virus (WEEV) and four negative control samples. Alphavirus detection was assessed among 23 laboratories in 16 European countries. Adequate capabilities were lacking for several viruses, and approximately half of the laboratories (11/23) relied on pan-alphavirus assays with varying sensitivity and specificity. Only 46% of laboratories characterized all EQA samples correctly. Correct result rates were > 90% for CHIKV, RRV and SINV, but laboratories lacked specificity for ONNV and MAYV and sensitivity for VEEV, BFV, and EEEV. Only two alphaviruses causing human disease circulate or have circulated in Europe, CHIKV and SINV. Molecular detection was satisfactory with both CHIKV and SINV, but < 50% correct for the entire alphaviruses panel. With continued imported cases, and a growing global concern about climate change and vector expansion, focus on progress toward rapid, accurate alphavirus diagnostics in Europe is recommended, as well as regular EQAs to monitor quality.

Excellent capability for molecular detection of Aedes-borne dengue, Zika, and chikungunya viruses but with a need for increased capacity for yellow fever and Japanese encephalitis viruses: an external quality assessment in 36 European laboratories

Mosquito-borne viruses represent a large global health burden. With geographic expansion of competent vectors for chikungunya virus (CHIKV), dengue virus (DENV), and Zika virus (ZIKV) in Europe, it is anticipated that the number of autochthonous cases of these tropical viruses in Europe will increase. Therefore, regular assessment of diagnostic capabilities in Europe is important. Our aim was to evaluate the mosquito-borne virus molecular detection capability of expert European laboratories by conducting an external quality assessment in October 2023. Molecular panels included 12 plasma samples: one alphavirus (CHIKV), four orthoflaviviruses (ZIKV, yellow fever virus [YFV], DENV, and Japanese encephalitis virus [JEV]), and two negative control samples. Mosquito-borne virus detection was assessed among 36 laboratories in 24 European countries. Adequate capabilities were lacking for YFV and JEV. Many laboratories relied on a mix of laboratory-developed tests (some of which were pan-orthoflavivirus or pan-alphavirus in combination with sequencing) and commercial assays. 47.2% of laboratories characterized all external quality assessment (EQA) samples correctly. Correct result rates were 100% for CHIKV and ZIKV and >99% for DENV, but laboratories lacked capacity, specificity, and sensitivity for JEV and YFV. Three of the viruses in this panel emerged and transiently circulated in Europe: CHIKV, ZIKV, and DENV. Molecular detection was excellent for those viruses, but <50% is accurate for the remainder of the panel. With the possibility or continuation of imported cases and a growing global concern about climate change and vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended, as well as regular EQAs to monitor it.IMPORTANCEThe external quality assessment (EQA) focused on Aedes-borne viruses: chikungunya virus (CHIKV), dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV). Japanese encephalitis virus, an orthoflavivirus that is spread by mosquito species belonging to the genus Culex, was included in the quality assessment as well. CHIKV, DENV, and ZIKV have proven potential for transient and limited circulation in Europe upon introduction of viremic travelers returning to Aedes albopictus-endemic regions. Results of this EQA were excellent for those viruses, but <50% is accurate for the remainder of the panel (YFV and Japanese encephalitis virus). Considering imported cases and the threat of climate change and competent vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended.

Equine Encephalomyelitis Outbreak, Uruguay, 2023-2024

We report the genomic analysis from early equine cases of the Western equine encephalitis virus outbreak during 2023-2024 in Uruguay. Sequences are related to a viral isolate from an outbreak in 1958 in Argentina. A viral origin from South America or continuous enzootic circulation with infrequent spillover is possible.

Diagnosis and genomic characterization of the largest western equine encephalitis virus outbreak in Uruguay during 2023-2024

The Western equine encephalitis virus is transmitted between mosquitoes and wild birds. Mosquitoes spread the virus to horses and human populations, causing severe encephalitis and death. The most recent large outbreak occurred in South America from November 2023 to April 2024. We identified and genetically characterized Uruguayan strains during this outbreak to understand their evolutionary trends and rapid expansion. We obtained genomes from 15 strains using a novel multiplex PCR assay combined with next-generation Illumina sequencing. The phylogenetic analysis revealed that viruses from Uruguay and Brazil collected during the outbreak and an Argentine strain from 1958 share a common evolutionary origin and are distinct from North American strains. Phylogenetic and epidemiological data suggest that the outbreak originated in Argentina and spread to Uruguay and Brazil, likely by movements of infected birds. Genomic analysis also revealed mispairing in real-time PCR primers and probes that may affect official diagnostic protocols.

Prevalence of Flavivirus and A lphavirus in bats captured in the state of Yucatan, southeastern Mexico

Flavivirus (family Flaviviridae) and Alphavirus (family Togaviridae) are mosquito-borne viruses that poses a significant risk to public health worldwide. Examples of these viruses include Dengue virus (DENV) and Zika virus (ZIKV) in the Flavivirus genus, and Chikungunya virus (CHIKV) in the Alphavirus genus. The potential contribution of bats in the mosquito-to-human transmission cycle of these viral genera in the tropics has not been studied. Here, a total of 144 bats belonging to three families (Emballonuridae, Phyllostomidae, and Molossidae) and six species were captured for one year using mist nets in sites with different landscapes (forest and grassland) in the state of Yucatan, southeastern Mexico. Blood samples and rectal and oral swabs were collected to detect Flavivirus and Alphavirus RNA genomes through RT-PCR. Flavivirus RNA was detected in 53 individuals (36.8%; 95% CI: 29.4%-44.9%), and Alphavirus RNA was detected in 59 individuals (40.1%; 95% CI: 33.2%-49.2%). The sequences obtained were consistent with ZIKV and DENV, into the Flavivirus, and CHIKV into the Alphavirus positive samples. The prevalence of both Flavivirus and Alphavirus was higher during the dry season compared with the rainy season. This high positivity rate, highlighted in both Flavivirus and Alphavirus, suggests a potential contribution of bats in the circulation of these viral genera in sylvatic environments. Seasonal variation in viral genera prevalence, with higher prevalence during dry seasons than rainy seasons, may suggest specific viral activity patterns in response to climatic conditions.

Outbreak of Chikungunya Fever in the Central Valley of Chiapas, Mexico

Chikungunya virus (CHIKV) was isolated from humans in an outbreak of a febrile illness during July and August 2015 in the central valleys of Chiapas, Mexico. Sera obtained from 80 patients were tested for CHIKV RNA by reverse transcriptase polymerase chain reaction (RT-PCR) and for IgM and IgG antibodies by an enzyme linked immunoassay and a commercial indirect immunofluorescence test for CHIKV and dengue virus (DENV). Of the 80 patients, 67 were positive, including 50 for RNA and 17 for IgM. In addition, one patient was coinfected with CHIKV-DENV and 40 patients were positive for IgG antibody to DENV. The clinical manifestations included a high fever, polyarthralgia, headache, myalgia, rash, digestive disorders, conjunctivitis, and adenopathy associated with cervical and axillary inguinal regions. Complete nucleotide sequences of two of the CHIKV isolates showed that they belonged to the Asian lineage but did not group with other Mexican CHIKV isolates from the Chiapas coast. Our findings documented that different Asian lineage strains of CHIKV were circulating simultaneously during the 2015 outbreak in the Central Valley of Chiapas, Mexico. The 2024 cases suggest an explosive scenario of re-emergence of thousands of new Chikungunya and dengue fever (DENF) cases associated with deaths, and a dangerous increase of the four DENV serotypes throughout the Americas, especially in South American countries that have shown a high influx of human migration to southern Mexico. In Mexico, the state of Chiapas and other southern regions are the most vulnerable.

Outbreak of Western Equine Encephalitis Virus Infection Associated with Neurological Disease in Horses Following a Nearly 40-Year Intermission Period in Argentina

Western equine encephalitis virus (WEEV) is a mosquito-borne arbovirus (genus Alphavirus, family Togaviridae) that has re-emerged in South America in late 2023, causing severe disease in both horses and humans after a nearly 40-year intermission period. We here describe the virological, serological, pathological, and molecular features of WEEV infection in horses during the 2023-2024 outbreak in Argentina. WEEV-infected horses developed neurological signs with mild to severe encephalitis associated with minimal to abundant WEEV-infected cells, as demonstrated by WEEV-specific in situ hybridization. The distribution of viral RNA was multifocal, with predominance within neuronal bodies, neuronal processes, and glial cells in the medulla oblongata and thalamic regions. Phylogenetic analysis of partial nsP4 sequences from three viral isolates obtained from three different provinces of Argentina support grouping with other temporally current WEEV strains from Uruguay and Brazil under a recently proposed novel lineage.

Mayaro Virus: An Emerging Alphavirus in the Americas

Mayaro virus (MAYV) is an arbovirus first isolated in Trinidad and Tobago in 1954. MAYV is the causative agent of Mayaro fever, which is characterised by high fever, maculopapular rash, myalgia and arthralgia. The potential for chronic arthralgia is of particular clinical concern. Currently, MAYV outbreaks are restricted to South and Central America, with some cases reported in Africa as well as several imported cases in Europe. However, in recent years, MAYV has become a growing global concern due to its potential to emerge into urban transmission cycles. Challenges faced with diagnostics, as well as a lack of specific antivirals or licensed vaccines further exacerbate the potential global health threat posed by MAYV. In this review, we discuss this emerging arboviral threat with a particular focus on the current treatment and vaccine development efforts. Overall, MAYV remains a neglected arbovirus due to its limited area of transmission. However, with the potential of its urbanisation and expanding circulation, the threat MAYV poses to global health cannot be overlooked. Further research into the improvement of current diagnostics, as well as the development of efficacious antivirals and vaccines will be crucial to help prevent and manage potential MAYV outbreaks.

An improved alphaviruses-specific RT-qPCR facilitates monitoring and prevention of alphaviruses

Molecular surveillance is vital for monitoring arboviruses, often employing genus-specific quantitative reverse-transcription polymerase chain reaction (RT-qPCR). Despite this, an overlooked chikungunya fever outbreak occurred in Yunnan province, China, in 2019 and false negatives are commonly encountered during alphaviruses screening practice, highlighting the need for improved detection methods. In this study, we developed an improved alphaviruses-specific RT-qPCR capable of detecting chikungunya virus, eastern equine encephalitis virus, western equine encephalitis virus, Venezuelan equine encephalitis virus, Sindbis virus, Mayaro virus, and Ross River virus with high sensitivity and specificity. The assay identified three chikungunya virus-positive cases out of 188 sera retrospectively. Later genetic characterization suggested that imported cases from neighboring countries may be responsible for the neglected chikungunya fever outbreak of 2019 in Yunnan. Our findings underscore the value of improved alphaviruses-specific RT-qPCR in bolstering alphaviruses surveillance and informing preventive strategies.

Epidemiological, virological and clinical characterization of a Dengue/Zika outbreak in the Caribbean region of Costa Rica 2017-2018

The increase in incidence and geographical expansion of viruses transmitted by the Aedes mosquitoes, such as dengue (DENV) and zika (ZIKV) in the Americas, represents a burden for healthcare systems in tropical and subtropical regions. These and other under-detected arboviruses co-circulate in Costa Rica, adding additional complexity to their management due to their shared epidemiological behavior and similarity of symptoms in early stages. Since diagnostics of febrile illness is mostly based on clinical symptoms alone, we gathered acute-phase serum and urine from 399 samples of acute dengue-like cases from two healthcare facilities of Costa Rica, during an outbreak of arboviruses from July 2017 to May 2018, and tested them using molecular and serological methods. The analyses showed that of the clinically presumptive arbovirus cases that were reported, only 39.4% (n=153) of the samples were confirmed positive by RT-PCR to be DENV (DENV (10.3%), CHIKV (0.2%), ZIKV (27.3%), or mixed infections (1.5%). RT-PCR for other alphaviruses and flaviviruses, and PCR for Leptospira sp were negative. Furthermore, to assess flavivirus positivity in post-acute patients, the negative sera were tested against Dengue-IgM. 20% of sera were found positive, confounding even more the definitive number of cases, and emphasizing the need of several distinct diagnostic tools for accurate diagnostics. Molecular characterization of the prM and E genes from isolated viruses revealed that the American/Asian genotype of DENV-2 and the Asian lineage of ZIKV were circulating during this outbreak. Two different clades of DENV-2 American/Asian genotype were identified to co-circulate in the same region and a difference in the platelet and leukocyte count was noted between people infected with each clade, suggesting a putative distinct virulence. Our study sheds light on the necessity for healthcare strategies in managing arbovirus outbreaks, emphasizing the importance of comprehensive molecular and serological diagnostic approaches, as well as molecular characterization. This approach aids in enhancing our understanding of the clinical and epidemiological aspects of arboviral diseases during outbreaks. Our research highlights the need to strengthen training programs for health professionals and the need to increase research-based on laboratory evidence for diagnostic accuracy, guidance, development and implementation of public health interventions and epidemiological surveillance.

Haemovigilance survey and screening strategy for arthropod-borne viruses in blood donors from Argentina

Arthropod-borne viruses (arboviruses) count among emerging infections, which represent a major challenge for transfusion safety worldwide. To assess the risk of arboviruses-transmission by transfusion (ATT), we performed a survey to evaluate the potential threat for transfusion safety. Samples were retrospectively and randomly collected from donors who donated during the peak of dengue incidence in Cordoba (years: 2016 and 2019-2022). A cost-efficient strategy for molecular screening was implemented with a nucleic acid test (NAT) configured with Flavivirus and Alphavirus-universal degenerated primers targeting conserved gene regions. Besides, we evaluated the neutralizing antibody (NAb) prevalence by plaque reduction neutralization test (PRNT). A total of 1438 samples were collected. Among the NAT-screened samples, one resulted positive for Flavivirus detection. Subsequent sequencing of the PCR product revealed Saint Louis Encephalitis Virus (SLEV) infection (GeneBank accession number OR236721). NAb prevalence was 2.95% for anti-Dengue, 9.94% anti-SLEV, 1.09% anti-West Nile Virus, and 0% anti-Chikungunya. One of the NAb-positive samples also resulted positive for IgM against SLEV but negative by ARN detection. This is the first haemovigilance study developed in Argentina that evaluates the potential risk of ATT and the first research to determine the prevalence of NAb against Flavivirus through PNRT to avoid possible cross-reactions between Ab against Flavivirus. Herein, the finding of one SLEV-viremic donor and the detection of anti-SLEV IgM in a different donor demonstrated a potential threat for transfusion safety and emphasized the need for increased vigilance and proactive measures to ensure the safety of blood supplies.

Real-time RT-PCR for Venezuelan equine encephalitis complex, Madariaga, and Eastern equine encephalitis viruses: application in human and mosquito public health surveillance in Panama

Eastern equine encephalitis virus (EEEV), Madariaga virus (MADV), and Venezuelan equine encephalitis virus complex (VEEV) are New World alphaviruses transmitted by mosquitoes. They cause febrile and sometimes severe neurological diseases in human and equine hosts. Detecting them during the acute phase is hindered by non-specific symptoms and limited diagnostic tools. We designed and clinically assessed real-time reverse transcription polymerase chain reaction assays (rRT-PCRs) for VEEV complex, MADV, and EEEV using whole-genome sequences. Validation involved 15 retrospective serum samples from 2015 to 2017 outbreaks, 150 mosquito pools from 2015, and 118 prospective samples from 2021 to 2022 surveillance in Panama. The rRT-PCRs detected VEEV complex RNA in 10 samples (66.7%) from outbreaks, with one having both VEEV complex and MADV RNAs. VEEV complex RNA was found in five suspected dengue cases from disease surveillance. The rRT-PCR assays identified VEEV complex RNA in three Culex (Melanoconion) vomerifer pools, leading to VEEV isolates in two. Phylogenetic analysis revealed the VEEV ID subtype in positive samples. Notably, 11.9% of dengue-like disease patients showed VEEV infections. Together, our rRT-PCR validation in human and mosquito samples suggests that this method can be incorporated into mosquito and human encephalitic alphavirus surveillance programs in endemic regions.

Madariaga and Venezuelan equine encephalitis virus seroprevalence in rodent enzootic hosts in Eastern and Western Panama

While rodents are primary reservoirs of Venezuelan equine encephalitis virus (VEEV), their role in Madariaga virus (MADV) transmission remains uncertain, particularly given their overlapping geographic distribution. This study explores the interplay of alphavirus prevalence, rodent diversity, and land use within Darien and Western Panama provinces. A total of three locations were selected for rodent sampling in Darien province: Los Pavitos, El Real de Santa Maria and Santa Librada. Two sites were selected in Western Panama province: El Cacao and Cirí Grande. We used plaque reduction neutralization tests to assess MADV and VEEV seroprevalences in 599 rodents of 16 species across five study sites. MADV seroprevalence was observed at higher rates in Los Pavitos (Darien province), 9.0%, 95% CI: 3.6-17.6, while VEEV seroprevalence was elevated in El Cacao (Western Panama province), 27.3%, 95% CI: 16.1-40.9, and El Real de Santa María (Darien province), 20.4%, 95% CI: 12.6-29.7. Species like Oryzomys coesi, 23.1%, 95% CI: 5.0-53.8, and Transandinomys bolivaris, 20.0%, 95% CI: 0.5-71.6 displayed higher MADV seroprevalences than other species, whereas Transandinomys bolivaris, 80.0%, 95% CI: 28.3-99.4, and Proechimys semispinosus, 27.3%, 95% CI: 17.0-39.6, exhibited higher VEEV seroprevalences. Our findings provide support to the notion that rodents are vertebrate reservoirs of MADV and reveal spatial variations in alphavirus seropositivity among rodent species, with different provinces exhibiting distinct rates for MADV and VEEV. Moreover, specific rodent species are linked to unique seroprevalence patterns for these viruses, suggesting that rodent diversity and environmental conditions might play a significant role in shaping alphavirus distribution.

Wind-assisted high-altitude dispersal of mosquitoes and other insects in East Africa

Knowledge of insect dispersal is relevant to the control of agricultural pests, vector-borne transmission of human and veterinary pathogens, and insect biodiversity. Previous studies in a malaria endemic area of the Sahel region in West Africa revealed high-altitude, long-distance migration of insects and various mosquito species. The objective of the current study was to assess whether similar behavior is exhibited by mosquitoes and other insects around the Lake Victoria basin region of Kenya in East Africa. Insects were sampled monthly from dusk to dawn over 1 year using sticky nets suspended on a tethered helium-filled balloon. A total of 17,883 insects were caught on nets tethered at 90, 120, and 160 m above ground level; 818 insects were caught in control nets. Small insects (<0.5 cm, n = 15,250) were predominant regardless of height compared with large insects (>0.5 cm, n = 2,334) and mosquitoes (n = 299). Seven orders were identified; dipteran was the most common. Barcoding molecular assays of 184 mosquitoes identified 7 genera, with Culex being the most common (65.8%) and Anopheles being the least common (5.4%). The survival rate of mosquitoes, experimentally exposed to high-altitude overnight, was significantly lower than controls maintained in the laboratory (19% vs. 85%). There were no significant differences in mosquito survival and oviposition rate according to capture height. These data suggest that windborne dispersal activity of mosquito vectors of malaria and other diseases occurs on a broad scale in sub-Saharan Africa.

Impact of different diets on the survival, pupation, and adult emergence of Culex pipiens biotype molestus larvae, and infectability with the insect-specific Culex Y virus

The current rapidly advancing climate change will affect the transmission of arthropod-borne viruses (arboviruses), mainly through changes in vector populations. Mosquitos of the Culex pipiens complex play a particularly prominent role in virus transmission in central Europe. Factors that contribute to the vector population density and the ability of those vectors to transmit viral pathogens (vector competence) can include nutrition during the larval stages. To test the influence of larval diet on larval survival and adult emergence, as well as vector competence, several diets varying in their nutritional composition were compared using a newly established assay. We tested the effects of 17 diets or diet combinations on the fitness of third-instar larvae of Culex pipiens biotype molestus. Larval survival rates at day 7 ranged from 43.33% to 94.44%. We then selected 3 of the 17 diets (Tetra Pleco, as the routine feed; JBL NovoTab, as the significantly inferior feed; and KG, as the significantly superior feed) and tested the effect of these diets, in combination with Culex Y virus infection, on larval survival rate. All Culex Y virus-infected larvae showed significantly lower larval survival, as well as low pupation and adult emergence rates. However, none of the tested diets in our study had a significant impact on larval survival in combination with viral infection. Furthermore, we were able to correlate several water quality parameters, such as phosphate, nitrate, and ammonium concentration, electrical conductivity, and low O2 saturations, with reduced larval survival. Thus, we were able to demonstrate that Culex Y virus could be a suitable agent to reduce mosquito population density by reducing larval density, pupation rate, and adult emergence rate. When combined with certain water quality parameters, these effects can be further enhanced, leading to a reduced mosquito population density, and reduce the cycle of transmission. Furthermore, we demonstrate, for the first time, the infection of larvae of the mosquito Culex pipiens biotype molestus with a viral pathogen.

Alphaviruses Detected in Mosquitoes in the North-Eastern Regions of South Africa, 2014 to 2018

The prevalence and distribution of African alphaviruses such as chikungunya have increased in recent years. Therefore, a better understanding of the local distribution of alphaviruses in vectors across the African continent is important. Here, entomological surveillance was performed from 2014 to 2018 at selected sites in north-eastern parts of South Africa where alphaviruses have been identified during outbreaks in humans and animals in the past. Mosquitoes were collected using a net, CDC-light, and BG-traps. An alphavirus genus-specific nested RT-PCR was used for screening, and positive pools were confirmed by sequencing and phylogenetic analysis. We collected 64,603 mosquitoes from 11 genera, of which 39,035 females were tested. Overall, 1462 mosquito pools were tested, of which 21 were positive for alphaviruses. Sindbis (61.9%, N = 13) and Middelburg (28.6%, N = 6) viruses were the most prevalent. Ndumu virus was detected in two pools (9.5%, N = 2). No chikungunya positive pools were identified. Arboviral activity was concentrated in peri-urban, rural, and conservation areas. A range of Culicidae species, including Culex univittatus, Cx. pipiens s.l., Aedes durbanensis, and the Ae. dentatus group, were identified as potential vectors. These findings confirm the active circulation and distribution of alphaviruses in regions where human or animal infections were identified in South Africa.

Culex Y Virus: A Native Virus of Culex Species Characterized In Vivo

Mosquitoes are vectors of various pathogens that cause diseases in humans and animals. To prevent the outbreak of mosquito-borne diseases, it is essential to control vector populations, as treatment or vaccination for mosquito-borne diseases are often unavailable. Insect-specific viruses (ISVs) have previously been described as being potentially helpful against arboviral disease outbreaks. In this study, we present the first in vivo characterization of the ISV Culex Y virus (CYV). CYV was first isolated from free-living Culex pipiens mosquitoes in 2010; then, it was found in several mosquito cell lines in a further study in 2018. For mammalian cells, we were able to confirm that CYV does not replicate as it was previously described. Additionally, we found that CYV does not replicate in honey bees or locusts. However, we detected replication in the Culex pipiens biotype molestus, Aedes albopictus, and Drosophila melanogaster, thus indicating dipteran specificity. We detected significantly higher mortality in Culex pipiens biotype molestus males and Drosophila melanogaster, but not in Aedes albopictus and female Culex pipiens biotype molestus. CYV could not be transmitted transovarially to offspring, but we detected venereal transmission as well as CYV in mosquitos' saliva, indicating that an oral route of infection would also be possible. CYV's dipteran specificity, transmission routes, and killing effect with respect to Culex males may be used as powerful tools with which to destabilize arbovirus vector populations in the future.

Epidemiological and Genomic Characterisation of Middelburg and Sindbis Alphaviruses Identified in Horses with Febrile and Neurological Infections, South Africa (2014-2018)

Although Old World alphaviruses, Middelburg- (MIDV) and Sindbis virus (SINV), have previously been detected in horses and wildlife with neurologic disease in South Africa, the pathogenesis and clinical presentation of MIDV and SINV infections in animals are not well documented. Clinical samples from horses across South Africa with acute or fatal neurologic and febrile infections submitted between 2014-2018 were investigated. In total, 69/1084 (6.36%) and 11/1084 (1.01%) horses tested positive for MIDV and SINV, respectively, by real-time reverse transcription (RT) PCR. Main signs/outcomes for MIDV (n = 69): 73.91% neurological, 75.36% fever, 28.99% icterus and anorexia, respectively, 8.70% fatalities; SINV (n = 11): 54.54% neurological, 72.73% fever, 36.36% anorexia and 18.18% fatalities. MIDV cases peaked in the late summer/autumn across most South African provinces while SINV cases did not show a clear seasonality and were detected in fewer South African provinces. MIDV could still be detected in blood samples via RT-PCR for up to 71,417 and 21 days after onset of signs in 4 horses respectively, suggesting prolonged replication relative to SINV which could only be detected in the initial sample. Phylogenetic analyses based on partial sequences of the nsP4 (MIDV n = 59 and SINV n = 7) and E1 (MIDV n = 45) genes, as well as full genome sequences (MIDV n = 6), clustered the MIDV and SINV strains from the present study with previously detected strains. MIDV infection appears to be more prevalent in horses than SINV infection based on RT-PCR results, however, prevalence estimates might be different when also considering serological surveillance data.

Behavioral-biological surveillance of emerging infectious diseases among a dynamic cohort in Thailand

Background

Interactions between humans and animals are the key elements of zoonotic spillover leading to zoonotic disease emergence. Research to understand the high-risk behaviors associated with disease transmission at the human-animal interface is limited, and few consider regional and local contexts.

Objective

This study employed an integrated behavioral–biological surveillance approach for the early detection of novel and known zoonotic viruses in potentially high-risk populations, in an effort to identify risk factors for spillover and to determine potential foci for risk-mitigation measures.

Method

Participants were enrolled at two community-based sites (n = 472) in eastern and western Thailand and two hospital (clinical) sites (n = 206) in northeastern and central Thailand. A behavioral questionnaire was administered to understand participants’ demographics, living conditions, health history, and animal-contact behaviors and attitudes. Biological specimens were tested for coronaviruses, filoviruses, flaviviruses, influenza viruses, and paramyxoviruses using pan (consensus) RNA Virus assays.

Results

Overall 61/678 (9%) of participants tested positive for the viral families screened which included influenza viruses (75%), paramyxoviruses (15%), human coronaviruses (3%), flaviviruses (3%), and enteroviruses (3%). The most salient predictors of reporting unusual symptoms (i.e., any illness or sickness that is not known or recognized in the community or diagnosed by medical providers) in the past year were having other household members who had unusual symptoms and being scratched or bitten by animals in the same year. Many participants reported raising and handling poultry (10.3% and 24.2%), swine (2%, 14.6%), and cattle (4.9%, 7.8%) and several participants also reported eating raw or undercooked meat of these animals (2.2%, 5.5%, 10.3% respectively). Twenty four participants (3.5%) reported handling bats or having bats in the house roof. Gender, age, and livelihood activities were shown to be significantly associated with participants’ interactions with animals. Participants’ knowledge of risks influenced their health-seeking behavior.

Conclusion

The results suggest that there is a high level of interaction between humans, livestock, and wild animals in communities at sites we investigated in Thailand. This study highlights important differences among demographic and occupational risk factors as they relate to animal contact and zoonotic disease risk, which can be used by policymakers and local public health programs to build more effective surveillance strategies and behavior-focused interventions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07439-7.

Identification and molecular characterization of highly divergent RNA viruses in cattle, Uganda

The risk for the emergence of novel viral zoonotic diseases in animals and humans in Uganda is high given its geographical location with high biodiversity. We aimed to identify and characterize viruses in 175 blood samples from cattle selected in Uganda using molecular approaches. We identified 8 viral species belonging to 4 families (Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae) and 6 genera (Hepacivirus, Pestivirus, Orthobunyavirus, Coltivirus, Dinovernavirus and Ephemerovirus). Four viruses were highly divergent and tetantively named Zikole virus (Family: Flaviviridae), Zeboroti virus (Family: Reoviridae), Zebtine virus (Family: Rhabdoviridae) and Kokolu virus (Family: Rhabdoviridae). In addition, Bovine hepacivirus, Obodhiang virus, Aedes pseudoscutellaris reovirus and Schmallenberg virus were identified for the first time in Ugandan cattle. We report 8 viral species belonging to 4 viral families including divergent ones in the blood of cattle in Uganda. Hence, cattle may be reservoir hosts for likely emergence of novel viruses with pathogenic potential to cause zoonotic diseases in different species with serious public health implications.

Alphavirus Identification in Neotropical Bats

Alphaviruses (Togaviridae) are arthropod-borne viruses responsible for several emerging diseases, maintained in nature through transmission between hematophagous arthropod vectors and susceptible vertebrate hosts. Although bats harbor many species of viruses, their role as reservoir hosts in emergent zoonoses has been verified only in a few cases. With bats being the second most diverse order of mammals, their implication in arbovirus infections needs to be elucidated. Reports on arbovirus infections in bats are scarce, especially in South American indigenous species. In this work, we report the genomic detection and identification of two different alphaviruses in oral swabs from bats captured in Northern Uruguay. Phylogenetic analysis identified Río Negro virus (RNV) in two different species: Tadarida brasiliensis (n = 6) and Myotis spp. (n = 1) and eastern equine encephalitis virus (EEEV) in Myotis spp. (n = 2). Previous studies of our group identified RNV and EEEV in mosquitoes and horse serology, suggesting that they may be circulating in enzootic cycles in our country. Our findings reveal that bats can be infected by these arboviruses and that chiropterans could participate in the viral natural cycle as virus amplifiers or dead-end hosts. Further studies are warranted to elucidate the role of these mammals in the biological cycle of these alphaviruses in Uruguay.

Detection and genome characterization of Middelburg virus strains isolated from CSF and whole blood samples of humans with neurological manifestations in South Africa

BACKGROUND

The Old world Alphavirus, Middelburg virus (MIDV), is not well known and although a few cases associated with animal illness have previously been described from Southern Africa, there has been no investigation into the association of the virus with human illness. The current study aimed to investigate possible association of MIDV infection with febrile or neurological manifestations in hospitalized or symptomatic patients fromGauteng, South Africa.

METHODS

This study is a descriptive retrospective and prospective laboratory based study. Archived cerebrospinal fluid (CSF) samples submitted to the National Health Laboratory Service (NHLS), Tshwane Academic division for viral investigation from public sector hospitals in Gauteng as well as EDTA (ethylenediaminetetraacetic acid) whole blood samples from ad hoc cases of veterinary students, presenting with neurological and febrile illness, were selected and screened for the presence of alphaviruses using real-time reverse transcription(rtRT) PCR.Virus isolations from rtRT-PCR positive samples were conducted in Vero cell culture and used to obtain full genome sequences. Basic descriptive statistical analysis was conducted using EpiInfo.

RESULTS

MIDV was detected by rtRT-PCR in 3/187 retrospective CSF specimens obtained from the NHLS from hospitalised patients in the Tshwane region of Gauteng and 1/2 EDTA samples submitted in the same year (2017) from ad hoc query arbovirus cases from veterinary students from the Faculty of Veterinary Science University of Pretoria.Full genome sequences were obtained for virus isolates from two cases; one from an EDTA whole blood sample (ad hoc case) and another from a CSF sample (NHLS sample).Two of the four Middelburg virus positive cases,for which clinical information was available, had other comorbidities or infections at the time of infection.

CONCLUSION

Detection of MIDV in CSF of patients with neurological manifestations suggests that the virus should be investigated as a human pathogen with the potential of causing or contributing to neurological signs in children and adults.

An Outbreak in Pigeons Caused by the Subgenotype VI.2.1.2 of Newcastle Disease Virus in Brazil

Newcastle disease virus (NDV) can infect over 250 bird species with variable pathogenicity; it can also infect humans in rare cases. The present study investigated an outbreak in feral pigeons in São Paulo city, Brazil, in 2019. Affected birds displayed neurological signs, and hemorrhages were observed in different tissues. Histopathology changes with infiltration of mononuclear inflammatory cells were also found in the brain, kidney, proventriculus, heart, and spleen. NDV staining was detected by immunohistochemistry. Twenty-seven out of thirty-four tested samples (swabs and tissues) were positive for Newcastle disease virus by RT-qPCR test, targeting the M gene. One isolate, obtained from a pool of positive swab samples, was characterized by the intracerebral pathogenicity index (ICPI) and the hemagglutination inhibition (HI) tests. This isolate had an ICPI of 0.99, confirming a virulent NDV strain. The monoclonal antibody 617/161, which recognizes a distinct epitope in pigeon NDV strains, inhibited the isolate with an HI titer of 512. A complete genome of NDV was obtained using next-generation sequencing. Phylogenetic analysis based on the complete CDS F gene grouped the detected isolate with other viruses from subgenotype VI.2.1.2, class II, including one previously reported in Southern Brazil in 2014. This study reports a comprehensive characterization of the subgenotype VI.2.1.2, which seems to have been circulating in Brazilian urban areas since 2014. Due to the zoonotic risk of NDV, virus surveillance in feral pigeons should also be systematically performed in urban areas.

Seroprevalence of arboviruses in Ecuador: Implications for improved surveillance

Introduction:

Arthropod-borne viruses (arboviruses) cause morbidity and mortality in humans and domestic animals worldwide. The percentage of population immunity or susceptibility to these viruses in Ecuador is unknown.

Objectives:

To investigate the proportion of Ecuadorian populations with IgG antibodies (Abs) (past exposure/immunity) and IgM Abs (current exposure) against flaviviruses and alphaviruses and to study the activity of these viruses in Ecuador.

Materials and methods:

During 2009-2011, we conducted a serosurvey for selected arboviruses in humans (n=1,842), equines (n=149), and sentinel hamsters (n=84) at two coastal locations and one in the Amazon basin (Eastern Ecuador) using enzyme-linked immunosorbent assay and hemagglutination inhibition test.

Results:

From 20.63% to 63.61% of humans showed IgG-antibodies for the flaviviruses: Dengue virus (DENV), yellow fever virus (YFV) Saint Louis encephalitis virus, and West Nile virus (WNV); from 4.67% to 8.63% showed IgG-Abs for the alphaviruses: Venezuelan

equine encephalitis virus, eastern equine encephalitis virus, and western equine encephalitis virus. IgM-Abs were found for DENV and WNV. Equines and hamsters showed antibodies to alphaviruses in all locations; two hamsters seroconverted to YFV in the Amazonia.

Conclusions:

The results show a YFV vaccination history and suggest the activity of arboviruses not included in the current surveillance scheme. Enhanced arbovirus and mosquito surveillance, as well as continued YFV vaccination and evaluation of its coverage/ effectiveness, are recommended.

Toscana virus associated with Guillain-Barré syndrome: a case-control study

Guillain-Barré syndrome (GBS) is an acute-onset, immune-mediated polyradiculoneuropathy, often precipitated by an antecedent infection. An association of GBS with vector-borne viral infections has been suggested, with evidence for the involvement of Zika, Dengue, Chikungunya and West Nile virus (WNV). This prospective case-control study was conducted to identify vector-borne viral infections in GBS. Thirteen individuals newly diagnosed as GBS were enrolled. Disease severity, prognostic factors and nerve conduction patterns were assessed. Eleven individuals with non-infectious conditions requiring cerebrospinal fluid (CSF) analysis were included as controls. Plasma, CSF and urine specimens were evaluated via nucleic acid amplification assays aimed to detect a broad spectrum of viruses. WNV and Toscana virus (TOSV) IgM/IgG antibodies were screened using commercial immunofluorescence assays and confirmed via virus neutralization tests (VNT). Partial TOSV nucleocapsid and genotype 1 polymerase sequences were detected in CSF of a patient with normal pressure hydrocephalus. Two control subjects had VNT-confirmed TOSV IgM in plasma. VNT-confirmed WNV and TOSV IgG were detected in 15.4% and 61.5% of GBS patients, respectively. Variations in WNV IgG and TOSV IgM detection rates were not statistically significant among study cohorts. However, TOSV IgG was significantly more frequent in GBS patients. No difference was observed for disease form or prognostic scores for virus markers. Follow-up serological profiles were identical to the initial findings. We have identified TOSV as a potential precipitating agent in GBS, with some rare clinical presentations of symptomatic TOSV infections.

Screening for Viruses and Lemur-Associated Filara in Wild-Caught Mosquitoes From Madagascar

Madagascar is a hotspot of biodiversity, but poverty and population growth provoke a high risk of conflict between food security and biodiversity conservation in this tropical country. Numerous vector-borne diseases, including viral infections, affect public health in Madagascar and a continuous expansion of anthropogenically used areas intensifies contact on the human-wildlife interface. However, data on human and animal pathogens in potential insect vectors is limited. Therefore, we conducted a parasitological and virological survey of 785 adult female mosquitoes between March and May 2016 at the Ankarafantsika National Park in northwestern Madagascar. Screening included Alpha-, Phlebo-, and Flaviviridae and the recently described filarial nematode species, Lemurfilaria lemuris. The predominant mosquito genus was Culex (91%), followed by Mansonia (4.1%), Anopheles (3.4%), and Aedes (0.9%). Viral screening revealed no arboviruses, but an insect-specific flavivirus in two Culex sitiens pools. No pools screened positive for the lemur-specific filarial nematode L. lemuris.

Endemic and Epidemic Human Alphavirus Infections in Eastern Panama: An Analysis of Population-Based Cross-Sectional Surveys

Madariaga virus (MADV) has recently been associated with severe human disease in Panama, where the closely related Venezuelan equine encephalitis virus (VEEV) also circulates. In June 2017, a fatal MADV infection was confirmed in a community of Darien Province. We conducted a cross-sectional outbreak investigation with human and mosquito collections in July 2017, where sera were tested for alphavirus antibodies and viral RNA. In addition, by applying a catalytic, force-of-infection (FOI) statistical model to two serosurveys from Darien Province in 2012 and 2017, we investigated whether endemic or epidemic alphavirus transmission occurred historically. In 2017, MADV and VEEV IgM seroprevalences were 1.6% and 4.4%, respectively; IgG antibody prevalences were MADV: 13.2%, VEEV: 16.8%, Una virus (UNAV): 16.0%, and Mayaro virus: 1.1%. Active viral circulation was not detected. Evidence of MADV and UNAV infection was found near households, raising questions about its vectors and enzootic transmission cycles. Insomnia was associated with MADV and VEEV infections, depression symptoms were associated with MADV, and dizziness with VEEV and UNAV. Force-of-infection analyses suggest endemic alphavirus transmission historically, with recent increased human exposure to MADV and VEEV in Aruza and Mercadeo, respectively. The lack of additional neurological cases suggests that severe MADV and VEEV infections occur only rarely. Our results indicate that over the past five decades, alphavirus infections have occurred at low levels in eastern Panama, but that MADV and VEEV infections have recently increased-potentially during the past decade. Endemic infections and outbreaks of MADV and VEEV appear to differ spatially in some locations of eastern Panama.

Vulnerabilities for Exposure to Emerging Infectious Disease at Urban Settlements in Nepal

In Nepal, rapid urbanization and rural-to-urban migration especially due to internal civil conflict have catalyzed the development of temporary settlements, often along rivers on undeveloped land. This study conducted surveillance for viruses in small mammals and assessed potential risks for virus transmission to people in urban settlements along rivers in Kathmandu, Nepal. We collected samples from 411 small mammals (100 rodents and 311 shrews) at four riverside settlement sites and detected six viruses from four virus families including Thottapalayam virus; a strain of murine coronavirus; two new paramyxoviruses; and two new rhabdoviruses. Additionally, we conducted surveys of 264 residents to characterize animal-human contact. Forty-eight percent of individuals reported contact with wildlife, primarily with rodents and shrews (91%). Our findings confirm that rodents and shrews should be considered a health threat for residents of temporary settlements, and that assessment of disease transmission risk coupled with targeted surveillance for emerging pathogens could lead to improved disease control and health security for urban populations. Additionally, interventions focused on disease prevention should consider the unique urban ecology and social dynamics in temporary settlements, along with the importance of community engagement for identifying solutions that address specific multi-dimensional challenges that life on the urban river margins presents.

Chikungunya virus infections in Finnish travellers 2009-2019

The mosquito-borne chikungunya virus (CHIKV) causes an acute febrile illness with rash, joint and muscle pain.A realtime RT-PCR assay for CHIKV detecting non-structural protein (nsP2; CHIKV nsP2-RT-qPCR) was set up. All the serodiagnosed CHIKV cases detected during 2009-2019 in Finland were screened with the assay, followed by isolations attempts and sequencing using Sanger and next generation sequencing (NGS). To validate the assay external and in-house quality control samples were used and all were correctly identified. Specificity of the assay was 100%. Assay was sensitive to detect CHIKV RNA in dilution of 10^-8.During years 2009-2019 34 patients were diagnosed for acute CHIKV infection. Twelve out of 34 cases were positive by CHIKV nsP2-RT-qPCR.Two CHIKV isolations succeeded from two individuals infected originally in Thailand, 2019. From 12 CHIKV nsP2-RT-qPCR positive samples, five (42%) CHIKVs were successfully sequenced. In this study, CHIKVs from year 2019 clustered with CHIKV ECSA-lineage forming sub-cluster with strains from ones detected in Bangladesh 2017, and the ones from Jamaica (2014) within Asian lineage showing highest similarity to strains detected in Caribbean outbreak 2013-15.  Majority of the CHIKV infections detected in Finland originates from Asia and virus lineages reflect the global circulation of the pathogen.

A survey of RNA viruses in mosquitoes from Mozambique reveals novel genetic lineages of flaviviruses and phenuiviruses, as well as frequent flavivirus-like viral DNA forms in Mansonia

BACKGROUND

Mosquito-borne diseases involving arboviruses represent expanding threats to sub-Saharan Africa imposing as considerable burden to human and veterinary public health. In Mozambique over one hundred species of potential arbovirus mosquito vectors have been identified, although their precise role in maintaining such viruses in circulation in the country remains to be elucidated. The aim of this study was to screen for the presence of flaviviruses, alphaviruses and bunyaviruses in mosquitoes from different regions of Mozambique.

RESULTS

Our survey analyzed 14,519 mosquitoes, and the results obtained revealed genetically distinct insect-specific flaviviruses, detected in multiple species of mosquitoes from different genera. In addition, smaller flavivirus-like NS5 sequences, frequently detected in Mansonia seemed to correspond to defective viral sequences, present as viral DNA forms. Furthermore, three lineages of putative members of the Phenuiviridae family were also detected, two of which apparently corresponding to novel viral genetic lineages.

CONCLUSION

This study reports for the first-time novel insect-specific flaviviruses and novel phenuiviruses, as well as frequent flavivirus-like viral DNA forms in several widely known vector species. This unique work represents recent investigation of virus screening conducted in mosquitoes from Mozambique and an important contribution to inform the establishment of a vector control program for arbovirus in the country and in the region.

Pathogenic viruses: Molecular detection and characterization

Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization.

Implementation of bamboo and monkey-pot traps for the sampling cavity-breeding mosquitoes in Darién, Panama

Despite the importance of Aedes, Haemagogus and Sabethes in the transmission of yellow fever virus (YFV) and the public health impacts of recent YFV epidemics in the Americas, relatively little has been reported on the biology and ecology of these vectors. Many Aedes, Haemagogus and Sabethes spp. in the American tropics inhabit and develop in the forest canopy and are difficult to sample with conventional entomological surveillance methods. We tested the utility of two previously developed phytotelmata-style oviposition traps (bamboo Guadua angustifolia) and (monkey-pot Lecythis minor), for collecting immature forms of these mosquitoes in a forest near the community of Aruza Abajo, Darién Province, Panama. Our results showed distribution of mosquito species emerging from the two types of traps was found to be significantly different (X² = 210.23; df = 14; P < 0.001), with significantly greater numbers of Sabethes (Peytonulus) aurescens (Lutz) and Sabethes (Peytonulus) undosus (Coquillett) emerging from the bamboo traps. More females of Sabethes (Sabethes) cyaneus (Fabricius) were captured in the monkey-pot traps, although the difference was not significant. No differences were observed in the average time to emergence for the two traps. These results suggest that various phytotelmata-style traps, including monkey-pot and bamboo, could be used to improve entomological surveillance of YFV vectors in the American tropic.

First Detection of Madariaga virus in Mosquitoes Collected in a Wild Environment of Northeastern Argentina

Madariaga virus (MADV), previously known as South American eastern equine encephalitis virus (SA EEEV; family Togaviridae, genus Alphavirus), is a mosquito-borne virus associated mainly with equine disease. In 2010, the first human outbreak by MADV was reported in Central America, but the mosquito vectors and vertebrate hosts involved in the outbreak were not identified. In Argentina, the first epizootic of MADV was in 1930, and since then, several epizootics by MADV have been reported. However, the potential vectors and hosts involved in the transmission cycle remain unknown. In the present study, MADV was detected in Culex (Culex) spp. mosquitoes and the phylogenetic analysis showed that the MADV fragment amplified grouped with the lineage/subtype III of the SA EEEV complex. Our results provide information about the natural infection with MADV in mosquitoes collected in a wild environment of Argentina and its genetic relatedness.

Coronaviruses Detected in Bats in Close Contact with Humans in Rwanda

Bats living in close contact with people in Rwanda were tested for evidence of infection with viruses of zoonotic potential. Mucosal swabs from 503 bats representing 17 species were sampled from 2010 to 2014 and screened by consensus PCR for 11 viral families. Samples were negative for all viral families except coronaviruses, which were detected in 27 bats belonging to eight species. Known coronaviruses detected included the betacorona viruses: Kenya bat coronaviruses, Eidolon bat coronavirus, and Bat coronavirus HKU9, as well as an alphacoronavirus, Chaerephon Bat coronavirus. Novel coronaviruses included two betacorona viruses clustering with SARS-CoV, a 2d coronavirus, and an alphacoronavirus.

Molecular and cellular evidence of natural Venezuelan equine encephalitis virus infection in frugivorous bats in Colombia

BACKGROUND AND AIM

Venezuelan equine encephalitis virus (VEEV) is an alphavirus that causes encephalitis with a high impact on public health in Latin America. However, only in Guatemala, Trinidad and Tobago, and Mexico have found antibodies in VEEV in bats, using immunohistochemistry, the sensitivity and specificity are improved; thus, it is better for demonstrating natural infection in bats as potential hosts. This study aimed to determine the presence of VEEV in tissues of frugivorous bats.

MATERIALS AND METHODS

A prospective descriptive cross-sectional study with a non-probabilistic sampling was carried out in 12 localities of Córdoba and Sucre area of the Colombian Caribbean. Two hundred and eighty-six bats were captured using fog nets, and the specimens according to taxonomic keys were classified. According to the Ethics Committee of the University of Córdoba, the bats were treated with analgesics and anesthetics. Blood samples were taken and then euthanized to obtain tissues and organs which were preserved in liquid N2 at -196°C. A portion of each organ was fixed in 10% buffered formalin for the detection of antigens by immunohistochemistry. Several pathological anatomy analyses were performed to determine the histological characteristics of tissue lesions of frugivorous bats naturally infected with the VEEV.

RESULTS

Of the 286 bats captured, 23 species were identified. In samples of the brain, spleen, and lung of two frugivorous bats (2/286=0.70%) Artibeus planirostris and Sturnira lilium, the presence of VEEV was confirmed by immunohistochemistry.

CONCLUSION

A fragment of the nsP4 non-structural protein gene corresponding to the alphavirus was amplified. Two samples were positive (2/286=0.70%) in frugivorous bats; A. planirostris (code GenBank: MG820274) and S. lilium (code GenBank: MG820275). The present study showed the first molecular evidence and cellular evidence (histopathology and immunohistochemistry) of natural VEEV infection in frugivorous bats in Colombia; these bats could be a host of this zoonosis.

Detection of flaviviruses and alphaviruses in mosquitoes in Central Macedonia, Greece, 2018

Culex mosquitoes are vectors of several flaviviruses and alphaviruses posing a potential risk to public and veterinary health. In order to gain an insight into the flaviviruses and alphaviruses circulating in the five regional units of Central Macedonia in northern Greece, 17,470 female Culex spp. mosquitoes collected during 2018 were tested for these viruses. Among 229 mosquito pools, West Nile virus (WNV) was detected in 10 (4.4%) pools, while insect-specific flavi- and alphaviruses were detected in 2 (0.9%) and 8 (3.5%) pools, respectively. WNV minimum infection rate (MIR) was 0.57. The highest MIR was identified in Thessaloniki regional unit, where several human cases of WNV infection occurred in 2018. All ten WNV sequences cluster into the Central European subclade of lineage 2. It is of note that the first WNV-positive mosquito pool was detected two weeks prior the report of the first human case in the area, suggesting that testing of mosquitoes could serve as early warning system.

A simple and rapid approach to prepare Sindbis and West Nile viral RNA controls for differentiation between positive samples and laboratory contamination

Reverse transcription-polymerase chain reaction (RT-PCR) is frequently used for surveillance and diagnosis of arboviruses and emerging viruses. A disadvantage of RT-PCR assays, especially nested assays, is the potential for false-positive results caused by laboratory contamination from either positive controls or positive samples. Positive reactors usually require sequence determination for confirmation which delay timeous reporting of a result. Thus, the aim of the study was to use a simple technique to prepare a positive control allowing true positives to be differentiated from laboratory contamination based on size differentiation for conventional PCR, or melt temperatures for real time assays. A flavivirus positive control and an alphavirus positive control were prepared for two RT-PCR assays that we are currently using for arbovirus surveillance in South Africa. Primers targeting a region of the partial genes of interest cloned in pGEM®T-easy were modified at the 5' ends with non-viral nucleotides. The resulting amplicons were circularised, resulting in pGEM®T-easy constructs with 51 and 65 non-viral bases inserted into the partial flaviviral and alphaviral genes respectively and used as template for transcribing RNA. Sequence analysis was used to confirm the manipulation of the partial genes. Using virus specific primer pairs, viral RNA could be readily differentiated from the modified positive controls either by size differentiation, or melt temperature in a SYBR®Green real time RT-PCR. This study demonstrates how simple recombinant technology can be used to produce a positive control that has application in the laboratory for surveillance studies or as a diagnostic tool using synthetic genes to abrogate the requirement for handling infectious virus.

Insect-specific flaviviruses and densoviruses, suggested to have been transmitted vertically, found in mosquitoes collected in Angola: Genome detection and phylogenetic characterization of viral sequences

This report describes a survey of RNA and DNA viruses carried out in adult mosquitoes from Angola, raised under laboratory conditions from field-collected immature forms. This viral genomic survey was performed using different sets of primers targeting groups of arboviruses with a considerable impact on human health, including flaviviruses, alphaviruses, and phleboviruses. Furthermore, the viral survey that was performed also included detection of densoviruses. The obtained results did not reveal the presence of recognizable pathogenic arboviruses but allowed the identification of insect-specific flaviviruses from two genetic lineages and a single lineage of brevidensoviruses. These viruses, collectivelly detected in Anopheles sp. and Culex pipiens s.l. mosquitoes, were most probably transmitted vertically.

Evaluation of honey-baited FTA cards in combination with different mosquito traps in an area of low arbovirus prevalence

Background

The threat of mosquito-borne diseases is increasing in continental Europe as demonstrated by several autochthonous chikungunya, dengue and West Nile virus outbreaks. In Switzerland, despite the presence of competent vectors, routine surveillance of arboviruses in mosquitoes is not being carried out, mainly due to the high costs associated with the need of a constant cold chain and laborious processing of thousands of mosquitoes. An alternative approach is using honey-baited nucleic acid preserving cards (FTA cards) to collect mosquito saliva that may be analysed for arboviruses. Here, we evaluate whether FTA cards could be used to detect potentially emerging viruses in an area of low virus prevalence in combination with an effective mosquito trap.

Methods

In a field trial in southern Switzerland we measured side-by-side the efficacy of the BG-Sentinel 2, the BG-GAT and the Box gravid trap to catch Aedes and Culex mosquitoes in combination with honey-baited FTA cards during 80 trapping sessions of 48 hours. We then screened both the mosquitoes and the FTA cards for the presence of arboviruses using reverse-transcription PCR. The efficacy of the compared trap types was evaluated using generalized linear mixed models.

Results

The Box gravid trap collected over 11 times more mosquitoes than the BG-GAT and BG-Sentinel 2 trap. On average 75.9% of the specimens fed on the honey-bait with no significant difference in feeding rates between the three trap types. From the total of 1401 collected mosquitoes, we screened 507 Aedes and 500 Culex females for the presence of arboviruses. A pool of six Cx. pipiens/Cx. torrentium mosquitoes and also the FTA card from the same Box gravid trap were positive for Usutu virus. Remarkably, only two of the six Culex mosquitoes fed on the honey-bait, emphasising the high sensitivity of the method. In addition, two Ae. albopictus collections but no FTA cards were positive for mosquito-only flaviviruses.

Conclusions

Based on our results we conclude that honey-baited FTA cards, in combination with the Box gravid trap, are an effective method for arbovirus surveillance in areas of low prevalence, particularly where resources are limited for preservation and screening of individual mosquitoes.

Field-captured Aedes vexans (Meigen, 1830) is a competent vector for Rift Valley fever phlebovirus in Europe

BACKGROUND

Aedes vexans (Meigen) is considered a nuisance species in central Europe and the Mediterranean region. It is an anthropophilic and mammalophilic floodwater mosquito involved in the transmission of several arboviruses. Rift Valley fever (RVF) is a relevant mosquito-borne zoonosis, affecting mainly humans and ruminants, that causes severe impact in public health and economic loses. Due to globalization and climate change, the European continent is threatened by its introduction. The main purpose of the present study was to evaluate the vector competence of a European field-collected Ae. vexans population.

METHODS

Aedes vexans field-collected larvae were reared in the laboratory under field-simulated conditions. To assess the vector competence for Rift Valley fever phlebovirus (RVFV) transmission, adult F0 females were exposed to infectious blood meals containing the 56/74 RVFV strain. Additionally, intrathoracic inoculations with the same virus strain were performed to evaluate the relevance of the salivary gland barriers. Natural circulation of alphavirus, flavivirus and phlebovirus was also tested.

RESULTS

To our knowledge, an autochthonous Ae. vexans population was experimentally confirmed as a competent vector for RVFV for the first time. This virus was capable of infecting and disseminating within the studied Ae. vexans mosquitoes. Moreover, infectious virus was isolated from the saliva of disseminated specimens, showing their capacity to transmit the virus. Additionally, a natural infection with a circulating Mosquito flavivirus was detected. The co-infection with the Mosquito flavivirus seemed to modulate RVFV infection susceptibility in field-collected Ae. vexans, but further studies are needed to confirm its potential interference in RVFV transmission.

CONCLUSIONS

Our results show that field-collected European Ae. vexans would be able to transmit RVFV in case of introduction into the continent. This should be taken into consideration in the design of surveillance and control programmes.

Identification of a novel alphavirus related to the encephalitis complexes circulating in southern Brazil

In early 2017, an outbreak caused by an unknown and supposedly viral agent in the Marilena region of southern Brazil was investigated. Since the etiological agent causing the outbreak was not identified from human samples, mosquitoes from this region were collected. Three out of 121 mosquito pools collected from the region tested positive for alphavirus in molecular tests. Next generation sequencing results revealed the presence of a novel alphavirus, tentatively named here as Caainguá virus (CAAV). DNA barcoding analyses indicated that different species of Culex are hosts for CAAV. This new virus was basal to the New World encephalitic alphaviruses in a comprehensive and robust phylogenetic approach using complete genomes. Viral particles were observed in the cytosol and inside of intracellular compartments of cells in mosquito-derived cell cultures. Despite being noninfectious in vertebrate derived cell cultures, primary culturing of CAAV in human mononuclear cells suggests monocytes and lymphocytes as CAAV targets. However, the epidemiological link of CAAV on the human outbreak should be further explored.

Arboviral screening of invasive Aedes species in northeastern Turkey: West Nile virus circulation and detection of insect-only viruses

BACKGROUND

The recent reports of Aedes aegypti and Ae. albopictus populations in Turkey, in parallel with the territorial expansion identified in several surrounding countries, have raised concerns about the establishment and re-establishment of these invasive Aedes mosquitoes in Turkey. This cross-sectional study was performed to detect Aedes aegypti and Ae. albopictus in regions of recent incursions, and screen for viral pathogens known to be transmitted elsewhere by these species.

METHODOLOGY

Mosquitoes were collected at several locations in Artvin, Rize and Trabzon provinces of the Black Sea region during 2016-2017, identified morphologically, pooled and analyzed via generic or specific nucleic acid amplification assays. Viruses in positive pools were identified by product sequencing, cell culture inoculation and next generation sequencing (NGS) in selected specimens.

PRINCIPAL FINDINGS

The study group comprised 791 specimens. Aedes albopictus was the most abundant species in all locations (89.6%), followed by Ae. aegypti (7.8%) and Culex pipiens (2.5%). Mosquitoes were screened for viruses in 65 pools where fifteen (23.1%) were reactive. The infecting strains was identified as West Nile virus (WNV) in 5 pools (7.7%) with Ae. albopictus or Cx. pipiens mosquitoes. The obtained WNV sequences phylogenetically grouped with local and global lineage 1 clade 1a viruses. In 4 (6.2%) and 6 (9.2%) pools, respectively, cell fusing agent virus (CFAV) and Aedes flavivirus (AEFV) sequences were characterized. NGS provided a near-complete AEFV genome in a pool of Ae. albopictus. The strain is provisionally called "AEFV-Turkey", and functional analysis of the genome revealed several conserved motifs and regions associated with virus replication. Merida-like virus Turkey (MERDLVT), a recently-described novel rhabdovirus, was also co-detected in a Cx. pipiens pool also positive for WNV.

CONCLUSIONS/SIGNIFICANCE

Invasive Aedes mosquitoes are established in certain locations of northeastern Turkey. Herein we conclusively show the role of these species in WNV circulation in the region. Biosurveillance is imperative to monitor the spread of these species further into Asia Minor and to detect possible introduction of pathogens.

Eco-epidemiology of the Venezuelan equine encephalitis virus in bats of Córdoba and Sucre, Colombia

Alphavirus infection associated encephalitis is an emerging infectious disease with a high impact on public health in Latin America.

OBJECTIVE

To study the eco-epidemiology of alphaviruses in bats of departments of Córdoba and Sucre, Colombia.

METHODOLOGY

A prospective descriptive cross-sectional study with a non-probabilistic sampling, in 12 localities of Córdoba and Sucre was carried out. Using mist nets capture of the specimens was carried out. The size of the sample was 286 bats, each specimen captured was taxonomically classified. The bats were immobilized with anesthetic and analgesic treatment according to the ethics committee of the University of Córdoba, morphometric measurements and blood samples were taken, later they were necropsied in the field to obtain a collection of tissues which were preserved in liquid N2 -190 °C. The averages of the climatic conditions of the sampling sites were extracted from the WorldClim database (http://www.worldclim.org/). The open source software QGIS (Quantum GIS Development Team.2015) was used to map and visualize bioclimatic regions of Córdoba. We used descriptive and retrospective information about the equine population and reports of foci of equine encephalitis.

RESULTS

In Córdoba and Sucre, 286 bats were captured and 23 species were classified, Artibeus and Phyllostomus discolor were the most frequent captured genus. The geographic ranges of the captured species were variable, some had a wide distribution and others were restricted to some areas. Venezuelan equine encephalitis virus RNA was detected in Artibeus planirostris and Sturnira lilium (2/286 = 0.70%) from Cordoba - Colombia. The univariate descriptive analysis showed no significant association for any of the analyzed variables climatic.

CONCLUSIONS

Frugivorous bats from the Caribbean area of Colombia may be involved in the Venezuelan equine encephalitis virus enzootic cycle.

Extreme temperature event and mass mortality of insectivorous bats

A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. This was investigated to clarify the causes of the die-off and assess the risk to public health. Field evidences, clinical signs, and gross pathology findings were consistent with a heat stress hypothesis. However, the detection of a novel bat paramyxovirus raises questions about its role as a contributing factor or a coincidental finding. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide.

Bionomics and insecticide resistance of the arboviral vector Aedes albopictus in northern Lao PDR

In the last four decades there has been a staggering increase in the geographical range of the arboviral vector Aedes albopictus (Skuse, 1894). This species is now found in every continent except Antarctica, increasing the distribution of arboviral diseases such as dengue and chikungunya. In Lao PDR dengue epidemics occur regularly, with cases of chikungunya also reported. As treatment methods for arboviral diseases is limited, the control of the vector mosquitoes are essential. There is a paucity of information on the bionomics and resistance status of this mosquito for successful vector control efforts. Here we describe the bionomics and insecticide resistance status of Ae. albopictus in Laos to identify opportunities for control. Adult Ae. albopictus were collected using human-baited double bed net (HDN) traps in forests, villages and rubber plantations and tested for alpha- and flaviviruses with RT-PCR. Surveys were also conducted to identify larval habitats. Seven adult and larval populations originating from Vientiane Capital and Luang Prabang province were tested against DDT, malathion, permethrin, deltamethrin and, temephos following WHO protocols. Aedes albopictus were found throughout the year, but were six-fold greater in the rainy season than the dry season. Adult females were active for 24 hours, with peak of behaviour at 18.00 h. The secondary forest and rubber plantation samples showed evidence of Pan-flaviviruses, while samples from the villages did not. More than half of the emerged Ae. albopictus were collected from mature rubber plantations (53.9%; 1,533/2,845). Most Ae. albopictus mosquitoes emerged from latex collection cups (19.7%; 562/2,845), small water containers (19.7%; 562/2,845) and tyres (17.4%; 495/2,845). Adult mosquitoes were susceptible to pyrethroids, apart from one population in Vientiane city. All populations were resistant to DDT (between 27-90% mortality) and all except one were resistant to malathion (20-86%). Three of the seven larval populations were resistant to temephos (42-87%), with suspected resistance found in three other populations (92-98%).This study demonstrates that rural areas in northern Laos are potential hot spots for arboviral disease transmission. Multiple-insecticide resistance was found. Aedes albopictus control efforts in villages need to expand to include secondary forests and rubber plantations, with larval source management and limited use of insecticides.

Mayaro: an emerging viral threat?

Mayaro virus (MAYV), an enveloped RNA virus, belongs to the Togaviridae family and Alphavirus genus. This arthropod-borne virus (Arbovirus) is similar to Chikungunya (CHIKV), Dengue (DENV), and Zika virus (ZIKV). The term “ChikDenMaZika syndrome” has been coined for clinically suspected arboviruses, which have arisen as a consequence of the high viral burden, viral co-infection, and co-circulation in South America. In most cases, MAYV disease is nonspecific, mild, and self-limited. Fever, arthralgia, and maculopapular rash are among the most common symptoms described, being largely indistinguishable from those caused by other arboviruses. However, severe manifestations of the infection have been reported, such as chronic polyarthritis, neurological complications, hemorrhage, myocarditis, and even death. Currently, there are no specific commercial tools for the diagnosis of MAYV, and the use of serological methods can be affected by cross-reactivity and the window period. A diagnosis based on clinical and epidemiological data alone is still premature. Therefore, new entomological research is warranted, and new highly specific molecular diagnostic methods should be developed. This comprehensive review is intended to encourage public health authorities and scientific communities to actively work on diagnosing, preventing, and treating MAYV infection.

Genomic Characterization and Seroprevalence Studies on Alphaviruses in Uruguay

Alphaviruses (Togaviridae) are arboviruses frequently associated with emerging infectious diseases. In this study, we aimed to investigate the presence of alphaviruses in Uruguay by detecting the viral genome in mosquitoes and neutralizing antibodies in equines. A total of 3,575 mosquitoes were analyzed for alphavirus genome detection. Serologic studies were performed on 425 horse sera by plaque reduction neutralization test (PRNT80) against Venezuelan equine encephalitis virus (VEEV) subtype IAB, Pixuna virus (PIXV), Rio Negro virus (RNV), western equine encephalitis virus (WEEV), and Madariaga virus (MADV). Mosquitoes belonging to six genera were captured and 82.9% were identified as Culex pipiens. Two Cx. pipiens pools collected in Fray Bentos and Las Toscas localities were alphavirus positive, and phylogenetic analyses showed that the sequences grouped into two different clusters: the lineage I of eastern equine encephalitis virus and RNV (VEEV complex), respectively. Plaque reduction neutralization test assays showed antibodies against strains of the VEEV complex, MADV, and WEEV. Rio Negro virus was the most geographically widespread virus, showing higher seroprevalences (up to 20%). Seroprevalences against VEEV IAB ranged between 4.6% and 13%; antibodies against PIXV, WEEV, and MADV were less frequent (3-4%). In conclusion, RNV exhibited the highest seroprevalence in horses, a wide geographical distribution, and viral genome was detected in Cx. pipiens mosquitoes. Madariaga virus had a low seroprevalence in equines, but an epizootic lineage typical of North America was detected in Cx. pipiens mosquitoes. Taken together, our results show that alphaviruses are present in Uruguay with variable occurrence and geographical distribution being a potential threat for human and equine health.

Emerging souvenirs-clinical presentation of the returning traveller with imported arbovirus infections in Europe

BACKGROUND

Arboviruses are an emerging group of viruses that are causing increasing health concerns globally, including in Europe. Clinical presentation usually consists of a nonspecific febrile illness that may be accompanied by rash, arthralgia and arthritis, with or without neurological or haemorrhagic syndromes. The range of differential diagnoses of other infectious and noninfectious aetiologies is broad, presenting a challenge for physicians. While knowledge of the geographical distribution of pathogens and the current epidemiological situation, incubation periods, exposure risk factors and vaccination history can help guide the diagnostic approach, the nonspecific and variable clinical presentation can delay final diagnosis.

AIMS AND SOURCES

This narrative review aims to summarize the main clinical and laboratory-based findings of the three most common imported arboviruses in Europe. Evidence is extracted from published literature and clinical expertise of European arbovirus experts.

CONTENT

We present three cases that highlight similarities and differences between some of the most common travel-related arboviruses imported to Europe. These include a patient with chikungunya virus infection presenting in Greece, a case of dengue fever in Turkey and a travel-related case of Zika virus infection in Romania.

IMPLICATIONS

Early diagnosis of travel-imported cases is important to reduce the risk of localized outbreaks of tropical arboviruses such as dengue and chikungunya and the risk of local transmission from body fluids or vertical transmission. Given the global relevance of arboviruses and the continuous risk of (re)emerging arbovirus events, clinicians should be aware of the clinical syndromes of arbovirus fevers and the potential pitfalls in diagnosis.