A real-time RT-PCR method for the universal detection and identification of flaviviruses

Connectivity at the human-wildlife interface: starling movements relate to carriage of E. coli

Synanthropic bird species in human, poultry or livestock environments can increase the spread of pathogens and antibiotic-resistant bacteria between wild and domestic animals. We present the first telemetry-based spatial networks for a small songbird. We quantified landscape connectivity exerted by spotless starling movements, and aimed to determine if connectivity patterns were related to carriage of potential pathogens. We captured 28 starlings on a partridge farm in 2020 and tested them for Avian influenza virus, West Nile virus WNV, Avian orthoavulavirus 1, Coronavirus, Salmonella spp. and Escherichia coli. We did not detect any viruses or Salmonella, but one individual had antibodies against WNV or cross-reacting Flaviviruses. We found E. coli in 61 % (17 of 28) of starlings, 76 % (13 of 17) of which were resistant to gentamicin, 12 % (2 of 17) to cefotaxime/enrofloxacin and 6 % (1 of 17) were phenotypic extended spectrum beta-lactamase (ESBL) carriers. We GPS-tracked 17 starlings and constructed spatial networks showing how their movements (i.e. links) connect different farms with nearby urban and natural habitats (i.e. nodes with different attributes). Using E. coli carriage as a proxy for acquisition/dispersal of bacteria, we found differences across spatial networks constructed for E. coli positive (n = 7) and E. coli negative (n = 9) starlings. We used Exponential Random Graph Models to reveal significant differences between networks. In particular, an urban roost was more connected to other sites by movements of E. coli positive than by movements of E. coli negative starlings. Furthermore, an open pine forest used mainly for roosting was more connected to other sites by movements of E. coli negative than by movements of E. coli positive starlings. Using E. coli as a proxy for a potential pathogen carried by starlings, we reveal the pathways of spread that starlings could provide between farms, urban and natural habitats.

Pentobarbital intoxication as a potential underlying cause for electrocution in a bearded vulture

A bearded vulture (Gypaetus barbatus) found dead in northern Spain presented external lesions consistent with electrocution as the cause of death. During forensic examination, macroscopic lesions suggested potential comorbidity, so samples were collected for molecular and toxicological analyses. Gastric content and liver were analysed for toxic substances, and pentobarbital (a common pharmaceutical used for euthanasia in domestic animals) was detected at a concentration of 37.3 and 0.05 µg/g, respectively. Other toxicological, viral and endoparasite analyses (avian malaria, avian influenza and flaviviruses) were negative. Thus, although the cause of death was electrocution, pentobarbital intoxication likely impaired the equilibrium and reflexes of the individual, possibly causing the bird to contact energized wires that it would not have otherwise. These results underline the importance of comprehensive analysis of forensic cases of wildlife deaths and reveal barbiturate poisoning as an additional threat for the conservation of the bearded vulture in Europe.

Epidemiology and risk factors of Japanese encephalitis in Taiwan, 2010-2022

INTRODUCTION

Taiwan introduced a two-dose inactivated Japanese encephalitis (JE) mouse brain-derived (JE-MB) vaccine into routine childhood immunization in 1968, with booster vaccination implemented in 1974 and 1983. In 2017, JE-MB vaccine was replaced by a two-dose live-attenuated chimeric vaccine (JE-CV). After implementation of JE vaccination programs, JE cases have shifted from children to adults. In this study, we described the JE epidemiology and identify high-risk groups to further inform vaccine policy.

METHODOLOGY/PRINCIPAL FINDINGS

We extracted data from Taiwan's notifiable disease surveillance database, vital statistics, and employment statistics from 2010 to 2022. Diagnosis of JE was confirmed by JE seroconversion, a four-fold increase in virus-specific antibodies, a positive JE viral nucleic-acid test, or JE virus isolation. From 2010 to 2022, a total of 313 cases of JE were diagnosed, resulting in an overall incidence rate of 0.10 cases per 100,000 person-years and a mortality rate of 0.006 per 100,000 population per year. Among these patients, 64% were male, and the median age was 51 years (range 0-82). Compared with people born in or after 1976 (vaccinated with four doses of JE-MB vaccine or two doses of JE-CV), those born in or before 1962 (unvaccinated) and those born during 1963-1975 (vaccinated with two or three doses of JE-MB vaccine) had a 4.2-fold (95% confidence interval [CI] 3.0-5.7) and 5.9-fold (95% CI 4.3-8.1) higher risk of JE, respectively. The relative risk of working in agriculture, forestry, fishing, or animal husbandry, compared to other occupations, was 5.0 (95% CI 3.5-7.0).

CONCLUSIONS/SIGNIFICANCE

In Taiwan, individuals born before 1976 and those employed in agriculture, forestry, fishing, or animal husbandry had a higher risk of JE. We recommend JE vaccination for people in these high-risk groups who have not been fully vaccinated or have an unknown vaccination history.

Mosquito community composition shapes virus prevalence patterns along anthropogenic disturbance gradients

Previously unknown pathogens often emerge from primary ecosystems, but there is little knowledge on the mechanisms of emergence. Most studies analyzing the influence of land-use change on pathogen emergence focus on a single host-pathogen system and often observe contradictory effects. Here, we studied virus diversity and prevalence patterns in natural and disturbed ecosystems using a multi-host and multi-taxa approach. Mosquitoes sampled along a disturbance gradient in Côte d'Ivoire were tested by generic RT-PCR assays established for all major arbovirus and insect-specific virus taxa including novel viruses previously discovered in these samples based on cell culture isolates enabling an unbiased and comprehensive approach. The taxonomic composition of detected viruses was characterized and viral infection rates according to habitat and host were analyzed. We detected 331 viral sequences pertaining to 34 novel and 15 previously identified viruses of the families Flavi-, Rhabdo-, Reo-, Toga-, Mesoni- and Iflaviridae and the order Bunyavirales. Highest host and virus diversity was observed in pristine and intermediately disturbed habitats. The majority of the 49 viruses was detected with low prevalence. However, nine viruses were found frequently across different habitats of which five viruses increased in prevalence towards disturbed habitats, in congruence with the dilution effect hypothesis. These viruses were mainly associated with one specific mosquito species (Culex nebulosus), which increased in relative abundance from pristine (3%) to disturbed habitats (38%). Interestingly, the observed increased prevalence of these five viruses in disturbed habitats was not caused by higher host infection rates but by increased host abundance, an effect tentatively named abundance effect. Our data show that host species composition is critical for virus abundance. Environmental changes that lead to an uneven host community composition and to more individuals of a single species are a key driver of virus emergence.

Analyses of Mosquito Species Composition, Blood-Feeding Habits and Infection with Insect-Specific Flaviviruses in Two Arid, Pastoralist-Dominated Counties in Kenya

Insect-specific flaviviruses (ISFs), although not known to be pathogenic to humans and animals, can modulate the transmission of arboviruses by mosquitoes. In this study, we screened 6665 host-seeking, gravid and blood-fed mosquitoes for infection with flaviviruses and assessed the vertebrate hosts of the blood-fed mosquitoes sampled in Baringo and Kajiado counties; both dryland ecosystem counties in the Kenyan Rift Valley. Sequence fragments of two ISFs were detected. Cuacua virus (CuCuV) was found in three blood-fed Mansonia (Ma.) africana. The genome was sequenced by next-generation sequencing (NGS), confirming 95.8% nucleotide sequence identity to CuCuV detected in Mansonia sp. in Mozambique. Sequence fragments of a potential novel ISF showing nucleotide identity of 72% to Aedes flavivirus virus were detected in individual blood-fed Aedes aegypti, Anopheles gambiae s.l., Ma. africana and Culex (Cx.) univittatus, all having fed on human blood. Blood-meal analysis revealed that the collected mosquitoes fed on diverse hosts, primarily humans and livestock, with a minor representation of wild mammals, amphibians and birds. The potential impact of the detected ISFs on arbovirus transmission requires further research.

Northern and Central Chile still free of emerging flaviviruses in mosquitoes (Diptera: Culicidae)

Geographic isolation and strict control limits in border areas have kept Chile free from various pathogens, including Flavivirus. However, the scenario is changing mainly due to climate change, the reintroduction of more aggressive mosquitoes, and the great wave of migration of people from endemic countries in recent years. Hence, it is necessary to surveillance mosquitoes to anticipate a possible outbreak in the population and take action to control it. This study aimed to investigate the presence of Flavivirus RNA by molecular tools with consensus primers in mosquitoes collected in the extreme north and central Chile. From 2019 to 2021, a prospective study was carried out in localities of Northern and part of Central Chile. Larvae, pupae, and adults of mosquitoes were collected in rural and urban sites in each locality. The collected samples were pooled by species and geographical location and tested using RT-PCR and RT-qPCR to determine presence of Flavivirus. 3085 specimens were collected, the most abundant specie Culex quinquefasciatus in the North and Aedes (Ochlerotatus) albifasciatus in the Center of Chile. Both genera are associated with Flavivirus transmission. However, PCR and RT-PCR did not detect Flavivirus RNA in the mosquitoes studied. These negative results indicate we are still a free Flavivirus country, which is reaffirmed by the non-existence of endemic human cases. Despite this, routine surveillance of mosquitoes and the pathogens they carry is highly recommended to evaluate each area-specific risk of vector-borne transmission.

One Health Surveillance Highlights Circulation of Viruses with Zoonotic Potential in Bats, Pigs, and Humans in Viet Nam

A One Health cross-sectoral surveillance approach was implemented to screen biological samples from bats, pigs, and humans at high-risk interfaces for zoonotic viral spillover for five viral families with zoonotic potential in Viet Nam. Over 1600 animal and human samples from bat guano harvesting sites, natural bat roosts, and pig farming operations were tested for coronaviruses (CoVs), paramyxoviruses, influenza viruses, filoviruses and flaviviruses using consensus PCR assays. Human samples were also tested using immunoassays to detect antibodies against eight virus groups. Significant viral diversity, including CoVs closely related to ancestors of pig pathogens, was detected in bats roosting at the human-animal interfaces, illustrating the high risk for CoV spillover from bats to pigs in Viet Nam, where pig density is very high. Season and reproductive period were significantly associated with the detection of bat CoVs, with site-specific effects. Phylogeographic analysis indicated localized viral transmission among pig farms. Our limited human sampling did not detect any known zoonotic bat viruses in human communities living close to the bat cave and harvesting bat guano, but our serological assays showed possible previous exposure to Marburg virus-like (Filoviridae), Crimean-Congo hemorrhagic fever virus-like (Bunyaviridae) viruses and flaviviruses. Targeted and coordinated One Health surveillance helped uncover this viral pathogen emergence hotspot.

Clinical and epidemiologic evaluation of a 2020 chikungunya outbreak in Cambodia

BACKGROUND

In 2020, the Kingdom of Cambodia experienced a nationwide outbreak of chikungunya virus (CHIKV). Despite an increase in the frequency of outbreaks and expanding geographic range of CHIKV, diagnostic challenges remain, and limited surveillance data of sufficient granularity are available to characterize epidemiological profiles and disease dynamics of the virus.

METHODS

An ongoing and long-standing cross-sectional study of acute undifferentiated febrile illness (AUFI) in Cambodia was leveraged to describe the disease epidemiology and characterize the clinical presentation of patients diagnosed with CHIKV during the 2020 outbreak. Participants presenting with AUFI symptoms at ten study locations provided acute and convalescent blood samples and were tested for CHIKV using a reverse transcription-polymerase chain reaction (RT-PCR) and serological diagnostic methods including IgM and IgG. Acute and follow-up clinical data were also collected.

RESULTS

From 1194 participant blood samples tested, 331 (27.7%) positive CHIKV cases were detected. Most CHIKV positive individuals (280, 84.6%) reported having a fever 3 to 4 days prior to visiting a health facility. Symptoms including chills, joint pain, nausea, vomiting, and lesions were all statistically significant among CHIKV positive participants compared to CHIKV negative AUFI participants. Cough was negatively associated with CHIKV positive participants. Positivity proportions were significantly higher among adults compared to children. No significant difference was found in positivity proportion between rainy and dry seasons during the outbreak. Positive CHIKV cases were detected in all study site provinces, with the highest test positivity proportion recorded in the rural northeast province of Kratie.

CONCLUSIONS

Surveillance data captured in this study provided a clinical and epidemiological characterization of positive CHIKV patients presenting at selected health facilities in Cambodia in 2020, and highlighted the widespread distribution of the outbreak, impacting both urban and rural locations. Findings also illustrated the importance of utilizing both RT-PCR and serological testing for effective CHIKV surveillance.

Screening of West Nile Virus, Herpesvirus, and Parvovirus in Rattus spp. in Klang Valley, Malaysia

Free-roaming and scavenging lifestyles of Rattus spp. in densely populated urban areas expose them to multiple pathogens that facilitate the transmission of infection to the human population more rapidly, raising public health concerns. There is limited information on the status of rat susceptibility to virus infection, particularly West Nile virus (WNV), herpesvirus, and parvovirus, to prepare for emerging zoonosis. A total of 23 (n = 23) blood samples collected from Rattus spp. in the wet market areas of Klang Valley, Malaysia, were subjected to molecular assay using a one-step reverse transcription-polymerase chain reaction (RT-PCR) to detect the highly conserved region of the WNV capsid and pre-membrane protein via nested polymerase chain reaction (PCR) assay targeting highly conserved amino acid motifs within the herpesviral DNA-directed DNA polymerase gene (DPOL) and polymerase chain reaction (PCR) assay targeting the parvovirus non-structural (NS) protein. As a result, 4 out of 23 (17.39%) rats were positive for herpesvirus DNA, but none were positive for WNV RNA and parvovirus DNA. The positive PCR amplicons of herpesvirus DNA were subjected to partial DNA sequencing analysis, 100% identical to Acomys herpesvirus SVMS 226,222 from Betaherpesvirinae, which is highly suggestive of rat cytomegalovirus (RCMV). This study has successfully demonstrated the presence of RCMV from Rattus spp. in the Klang Valley. The RCMV potentially crosses species barriers and establishes infection, raising public health concerns. The non-viraemic state of WNV or parvovirus infection, low sample size, and limited niche distribution emphasise the need for the expansion of this study in the future.

Bagaza virus and Plasmodium spp. coinfection in red-legged partridges (Alectoris rufa), in Southern Spain 2019

Flaviviruses such as West Nile (WNV), Usutu (USUV) and Bagaza (BAGV) virus and avian malaria parasites are vector borne pathogens that circulate naturally between avian and mosquito hosts. WNV and USUV and potentially also BAGV constitute zoonoses. Temporal and spatial cocirculation and coinfection with Plasmodium spp., and West Nile virus has been documented in birds and mosquito vectors, and fatally USUV-infected passerines coinfected with Plasmodium spp. had more severe lesions. Also, WNV, USUV and BAGV have been found to cocirculate. Yet little is known about the interaction of BAGV and malaria parasites during consecutive or coinfections of avian hosts. Here we report mortality of free-living red-legged partridges in a hunting estate in Southern Spain that were coinfected with BAGV and Plasmodium spp. The outbreak occurred in the area where BAGV first emerged in Europe in 2010 and where cocirculation of BAGV, USUV and WNV was confirmed in 2011 and 2013. Partridges were found dead in early October 2019. Birds had mottled locally pale pectoral muscles, enlarged, congestive greenish-black tinged livers and enlarged kidneys. Microscopically congestion and predominantly mononuclear inflammatory infiltrates were evident and Plasmodium phanerozoites were present in the liver, spleen, kidneys, muscle and skin. Molecular testing and sequencing detected Plasmodium spp. and BAGV in different tissues of the partridges, and immunohistochemistry confirmed the presence and colocalization of both pathogens in the liver and spleen. Due to the importance of the red-legged partridge in the ecosystem of the Iberian Peninsula and as driver of regional economy such mortalities are of concern. Such outbreaks may reflect climate change related shifts in host, vector and pathogen ecology and interactions that could emerge similarly for other pathogens.

Monitoring Urban Zoonotic Virus Activity: Are City Rats a Promising Surveillance Tool for Emerging Viruses?

Urban environments represent unique ecosystems where dense human populations may come into contact with wildlife species, some of which are established or potential reservoirs for zoonotic pathogens that cause human diseases. Finding practical ways to monitor the presence and/or abundance of zoonotic pathogens is important to estimate the risk of spillover to humans in cities. As brown rats (Rattus norvegicus) are ubiquitous in urban habitats, and are hosts of several zoonotic viruses, we conducted longitudinal sampling of brown rats in Vienna, Austria, a large population center in Central Europe. We investigated rat tissues for the presence of several zoonotic viruses, including flaviviruses, hantaviruses, coronaviruses, poxviruses, hepatitis E virus, encephalomyocarditis virus, and influenza A virus. Although we found no evidence of active infections (all were negative for viral nucleic acids) among 96 rats captured between 2016 and 2018, our study supports the findings of others, suggesting that monitoring urban rats may be an efficient way to estimate the activity of zoonotic viruses in urban environments.

Coronavirus and Paramyxovirus Shedding by Bats in a Cave and Buildings in Ethiopia

Bats are important hosts of zoonotic viruses with pandemic potential, including filoviruses, MERS-Coronavirus (CoV), SARS-CoV -1, and likely SARS-CoV-2. Viral infection and transmission among wildlife are dependent on a combination of factors that include host ecology and immunology, life history traits, roosting habitats, biogeography, and external stressors. Between 2016 and 2018, four species of insectivorous bats from a readily accessed roadside cave and buildings in Ethiopia were sampled and tested for viruses using consensus PCR assays for five viral families/genera. Previously identified and novel coronaviruses and paramyxoviruses were identified in 99 of the 589 sampled bats. Bats sampled from the cave site were more likely to test positive for a CoV than bats sampled from buildings; viral shedding was more common in the wet season; and rectal swabs were the most common sample type to test positive. A previously undescribed alphacoronavirus was detected in two bat species from different taxonomic families, sampling interfaces, geographic locations, and years. These findings expand knowledge of the range and diversity of coronaviruses and paramyxoviruses in insectivorous bats in Ethiopia and reinforce that an improved understanding of viral diversity and species-specific shedding dynamics is important for designing informed zoonotic disease surveillance and spillover risk reduction efforts.

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.

Molecular Characterization of Herpesviral Encephalitis in Cetaceans: Correlation with Histopathological and Immunohistochemical Findings

Simple Summary

In this study we describe the molecular and pathological characteristics of alpha- and gamma-herpesvirus infection of the central nervous system of stranded cetaceans and correlate them with viral load, immunohistochemical findings and biological data such as age, sex, and the presence of co-infections. The viruses (alpha- and gamma-herpesvirus) were detected in twelve out of 103 analysed stranded cetaceans and were associated with a wide range of histopathological lesions, as previously described for these and other species. In five out the twelve animals, lesions were severe enough (malacia, neuronal necrosis and neuronophagia) to cause death. Intranuclear inclusions bodies were present in brain tissue samples from half of the HV-positive animals, indicating that the injury was due to an infective agent belonging to a group of filterable viruses. These results are in accordance with immunohistochemical findings, as all the brain tissue samples with INIBs were immunolabeled with Anti-HSV1. Males, juveniles, and calves were predominantly infected among the analysed cetaceans and a 41.6% (5/12) incidence of co-infections in the brain was detected, with three animals co-infected with Dolphin Morbillivirus (DMV). In this study, we present, to the best of our knowledge, the first histopathological evidence of superinfection between HV and DMV pathogens in brain tissue.

Abstract

Herpesviruses are causative agents of meningitis and encephalitis in cetaceans, which are among the main leading known natural causes of death in these species. Brain samples from 103 stranded cetaceans were retrospectively screened for the presence of herpesvirus DNA in the brain. Molecular detection of Cetacean Morbillivirus was performed in HV positive brain cases. Histopathologic evaluation of brain samples included the presence or absence of the following findings (n = 7): meningitis, perivascular cuffings, microgliosis, intranuclear inclusion bodies, malacia, neuronal necrosis and neurophagic nodules, and haemorrhages. Histological evidence of the involvement of other etiological agents led to complementary analysis. We detected the presence of alpha and gamma-HVs in 12 out of 103 (11.6%) brain samples from stranded cetaceans of five different species: one bottlenose dolphin, six striped dolphins, three Atlantic spotted dolphins, one Cuvier’s beaked whale, and one common dolphin. Pathogenic factors such as viral strain, age, sex, and the presence of co-infections were analysed and correlated with the brain histopathological findings in each case. Herpesvirus was more prevalent in males, juveniles, and calves and a 41.6% incidence of co-infections in the brain was detected in our study: three with Dolphin Morbillivirus, one with Staphilococcus aureus septicaemia and one with Brucella spp.

Surveillance for potentially zoonotic viruses in rodent and bat populations and behavioral risk in an agricultural settlement in Ghana

BACKGROUND

In Ghana, the conversion of land to agriculture, especially across the vegetative belt has resulted in fragmented forest landscapes with increased interactions among humans, domestic animals, and wildlife.

METHODS

We investigated viruses in bats and rodents, key reservoir hosts for zoonotic viral pathogens, in a small agricultural community in the vegetation belt of Ghana. We also administered questionnaires among the local community members to learn more about people's awareness and perceptions of zoonotic disease risks and the environmental factors and types of activities in which they engage that might influence pathogen transmission from wildlife.

RESULTS

Our study detected the RNA from paramyxoviruses and coronaviruses in rodents and bats, including sequences from novel viruses with unknown zoonotic potential. Samples collected from Epomophorus gambianus bats were significantly more likely to be positive for coronavirus RNA during the rainy season, when higher numbers of young susceptible individuals are present in the population. Almost all community members who responded to the questionnaire reported contact with wildlife, especially bats, rodents, and non-human primates in and around their homes and in the agricultural fields. Over half of the respondents were not aware or did not perceive any zoonotic disease risks associated with close contact with animals, such as harvesting and processing animals for food. To address gaps in awareness and mitigation strategies for pathogen transmission risks, we organized community education campaigns using risk reduction and outreach tools focused around living safely with bats and rodents.

CONCLUSIONS

These findings expand our knowledge of the viruses circulating in bats and rodents in Ghana and of the beliefs, perceptions, and practices that put community members at risk of zoonotic virus spillover through direct and indirect contact with bats and rodents. This study also highlights the importance of community engagement in research and interventions focused on mitigating risk and living safely with wildlife.

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.

Development of Real-Time Molecular Assays for the Detection of Wesselsbron Virus in Africa

Wesselsbron is a neglected, mosquito-borne zoonotic disease endemic to Africa. The virus is mainly transmitted by the mosquitoes of the Aedes genus and primarily affects domestic livestock species with teratogenic effects but can jump to humans. Although no major outbreak or fatal case in humans has been reported as yet worldwide, a total of 31 acute human cases of Wesselsbron infection have been previously described since its first isolation in 1955. However, most of these cases were reported from Sub-Saharan Africa where resources are limited and a lack of diagnostic means exists. We describe here two molecular diagnostic tools suitable for Wesselsbron virus detection. The newly established reverse transcription-quantitative polymerase chain reaction and reverse-transcription-recombinase polymerase amplification assays are highly specific and repeatable, and exhibit good agreement with the reference assay on the samples tested. The validation on clinical and veterinary samples shows that they can be accurately used for Wesselsbron virus detection in public health activities and the veterinary field. Considering the increasing extension of Aedes species worldwide, these new assays could be useful not only in laboratory studies for Wesselsbron virus, but also in routine surveillance activities for zoonotic arboviruses and could be applied in well-equipped central laboratories or in remote areas in Africa, regarding the reverse-transcription-recombinase polymerase amplification assay.

Detection and Molecular Characterization of Canine Alphacoronavirus in Free-Roaming Dogs, Bangladesh

Canine coronavirus (CCoV) is widespread among the dog population and causes gastrointestinal disorders, and even fatal cases. As the zoonotic transmission of viruses from animals to humans has become a worldwide concern nowadays, it is necessary to screen free-roaming dogs for their common pathogens due to their frequent interaction with humans. We conducted a cross-sectional study to detect and characterize the known and novel Corona, Filo, Flavi, and Paramyxoviruses in free-roaming dogs in Bangladesh. Between 2009-10 and 2016-17, we collected swab samples from 69 dogs from four districts of Bangladesh, tested using RT-PCR and sequenced. None of the samples were positive for Filo, Flavi, and Paramyxoviruses. Only three samples (4.3%; 95% CI: 0.9-12.2) tested positive for Canine Coronavirus (CCoV). The CCoV strains identified were branched with strains of genotype CCoV-II with distinct distances. They are closely related to CCoVs from the UK, China, and other CoVs isolated from different species, which suggests genetic recombination and interspecies transmission of CCoVs. These findings indicate that CCoV is circulating in dogs of Bangladesh. Hence, we recommend future studies on epidemiology and genetic characterization with full-genome sequencing of emerging coronaviruses in companion animals in Bangladesh.

Novel alphaherpesvirus in a wild South American sea lion (Otaria byronia) with pulmonary tuberculosis

In 2017, an adult male South American sea lion (Otaria byronia), presenting emaciation and a cervical abscess, stranded alive in Florianópolis, southern Brazil. The animal was directed to a rehabilitation center, dying a few days later. On necropsy, the main gross findings were necrotizing lymphadenitis of the right prescapular lymph node and nodular bronchopneumonia. A novel alphaherpesvirus, tentatively named Otariid alphaherpesvirus 1, was amplified in several tissue samples. No histopathologic findings associated with viral infection were observed. Additionally, pulmonary tuberculosis by Mycobacterium pinnipedii was diagnosed by histopathological, immunohistochemical, and molecular techniques. Several bacteria were cultured from antemortem and postmortem samples, including Proteus mirabilis from the cervical abscess and cardiac blood, and Escherichia coli from the cervical abscess and pericardial effusion. Flavivirus, morbillivirus, and Apicomplexa were not detected by molecular techniques. Herein, we report a novel alphaherpesvirus in a pinniped species of the family Otariidae. Although previously described in Southern Hemisphere pinniped species, including South American sea lions, there is limited information regarding M. pinnipedii impact over this group. Further research is required to determine the associated pathogenesis of this novel herpesvirus, and prevalence of Otariid alphaherpesvirus 1 and M. pinnipedii in the reproductive colonies.

A new cluster of rhabdovirus detected in field-caught sand flies (Diptera: Psychodidae: Phlebotominae) collected from southern Thailand

BACKGROUND

The distribution of phlebotomine sand flies is changing rapidly due to climate change. This issue has implications for the epidemiology of sand fly-borne diseases, especially sand fly-associated viruses. Few studies concerning sand fly-associated viruses have been conducted in Thailand. Therefore, this study aimed to perform a molecular survey of groups of pathogenic RNA viruses belonging to the Orbivirus, Phlebovirus, and Flavivirus genera and family Rhabdoviridae in sand fly samples collected from southern Thailand.

METHODS

Sand flies were collected at two locations in Trang and Songkhla provinces of southern Thailand, and individual sand fly samples were processed for species identification and virus detection. The Orbivirus, Phlebovirus, and Flavivirus genera and family Rhabdoviridae molecular determination was performed by RT-PCR, and positive samples were identified by cloning and sequencing, cell culture inoculation, and phylogenetic analysis.

RESULTS

The results presented in this study were based on the analysis of a total of 331 female sand flies. This molecular study revealed evidence of Rhabdoviridae family virus presence in Phlebotomus papatasi (3/331, 0.9%). The findings demonstrated a new cluster of rhabdovirus that was closely related to Bactrocera dorsalis sigmavirus strain BDSV.abc5 and the lineages of insect-specific Rhabdoviridae. In addition, the Bayesian tree suggested that the common ancestor of this group was the dimarhabdovirus clade. It was assumed that the virus may have switched hosts during its evolution. However, the detection of Orbivirus, Phlebovirus, and Flavivirus genera using specific primers for RT-PCR was negative in the collected sand flies.

CONCLUSIONS

There is limited knowledge on the genetic diversity and ecology of Rhabdoviridae in Thailand. This is the first data regarding the circulation of Rhabdoviridae in Ph. papatasi from Thailand. We found a new cluster of rhabdoviruses that was close to the new B. dorsalis sigmavirus. It is possible that there is a great deal of diversity in this family yet to be discovered, and a more extensive survey for new rhabdoviruses may uncover viruses from a wide diversity of host taxa and broaden our understanding of the relationships among the Rhabdoviridae.

CLINICO-PATHOLOGIC FINDINGS AND PATHOGEN SCREENING IN FUR SEALS (ARCTOCEPHALUS AUSTRALIS AND ARCTOCEPHALUS TROPICALIS) STRANDED IN SOUTHEASTERN BRAZIL, 2018

Among pinnipeds, four Otariidae species (eared seals) have been reported as occasional or frequent vagrants along the coast of Brazil, mainly in the southern region. These animals usually arrive debilitated during winter and are directed to rehabilitation. Nevertheless, available information on sanitary aspects of stranded pinnipeds in Brazil is limited. Increased fur seal strandings (n=23) were recorded during the 2018 winter season in southeast Brazil (Iguape, Ilha Comprida, and Ilha do Cardoso, Sao Paulo State) compared to 2017 (n=2). Of these 23 fur seals, two were found dead and were in a good postmortem condition, and four died during rehabilitation and were subsequently necropsied. The remaining fur seals were not analyzed due to advanced decomposition (9/23) or successful rehabilitation (8/23). Herein, we report the antemortem hematology (n=4) and postmortem pathologic, parasitologic, and molecular analysis results as well as the most likely cause of stranding and/or death (CSD) in five free-ranging juvenile South American fur seals (Arctocephalus australis) and one free-ranging juvenile subantarctic fur seal (Arctocephalus tropicalis). All animals were males, and all but one had poor body condition. Pathologic examinations revealed a variety of lesions, predominantly hemodynamic disturbances, endoparasitism, and inflammatory disease processes of suspected infectious nature. Molecular analyses detected gammaherpesvirus infections in two South American seals and one subantarctic fur seal, Sarcocystis sp. in one subantarctic fur seal, and Neospora sp. in two South American fur seals. All seals were PCR-negative for morbillivirus, flavivirus, and Toxoplasma gondii. The most likely CSDs were: starvation (2), aspiration pneumonia (1), asphyxia (1), predator attack (1), and presumed systemic infectious disease (1). These findings expand the geographic range of various pathogens of pinnipeds and may be of value to first responders, clinicians, and diagnosticians.

Molecular Characterization of Imported and Autochthonous Dengue in Northeastern Spain

Dengue is the most significant arbovirus worldwide and a public health threat to non-endemic areas in which Aedes vectors are present. Autochthonous dengue transmission has been reported in several European countries in the last decade. Infected travelers from endemic regions arriving to areas colonized by Aedes albopictus in Europe need to be monitored in surveillance and control programs. We aimed to perform molecular characterization of RT-PCR-positive dengue cases detected in Catalonia, northeastern Spain, from 2013 to 2018. The basic demographic information and the geographical regions of importation were also analyzed. One-hundred four dengue cases were studied (103 imported infections and the first autochthonous case in our region). The dengue virus strains detected were serotyped and genotyped using molecular methods, and phylogenetic analyses were conducted. All four dengue serotypes were detected in travelers, including up to 10 different genotypes, reflecting the global circulation of dengue in endemic areas. The primary travel-related case of the 2018 autochthonous transmission was not identified, but the molecular analysis revealed dengue serotype 1, genotype I of Asian origin. Our results highlight the diversity of imported dengue virus strains and the role of molecular epidemiology in supporting arbovirus surveillance programs.

Host selection pattern and flavivirus screening of mosquitoes in a disturbed Colombian rainforest

Studies on the feeding behavior of hematophagous insects, particularly those of medical importance, are relevant for tracking possible pathogen transmission routes and identifying biases in the choice of vertebrates. We evaluated host selection of blood-feeding mosquitoes in a disturbed forest in the Magdalena Medio valley in Colombia from March 2017 to April 2018, after the introduction of Zika virus to the Americas from the 2015-2016 outbreak. We estimated vertebrate diversity and collected blood-engorged female mosquitoes. Genomic DNA/RNA was extracted from the mosquito's abdomen for vertebrate host identification and pathogen detection. We performed conventional PCR and sequencing, using universal primers targeting vertebrate regions of the eukaryotic mitochondrial genome to determine bloodmeal host. Additionally, we tested for the presence of flaviviruses in all mosquito samples with RT-PCR. Based on the identity and quantity of detected bloodmeals, we performed mosquito-vertebrate interaction network analysis and estimated topology metrics. In total, we collected 292 engorged female mosquitoes representing 20 different species. Bloodmeal analyses identified 26 vertebrate species, the majority of which were mammals (N = 16; 61.5%). No flaviviruses of medical importance were detected from the samples. Although feeding patterns varied, network analyses showed a high degree of specialization by mosquitoes and revealed ecological and phylogenetic relationships among the host community. We conclude that host selection or preference by mosquitoes is species specific.

Japanese encephalitis virus live attenuated vaccine strains display altered immunogenicity, virulence and genetic diversity

Japanese encephalitis virus (JEV) is the etiological agent of Japanese encephalitis (JE). The most commonly used vaccine used to prevent JE is the live-attenuated strain SA14-14-2, which was generated by serial passage of the wild-type (WT) JEV strain SA14. Two other vaccine candidates, SA14-5-3 and SA14-2-8 were derived from SA14. Both were shown to be attenuated but lacked sufficient immunogenicity to be considered effective vaccines. To better contrast the SA14-14-2 vaccine with its less-immunogenic counterparts, genetic diversity, ribavirin sensitivity, mouse virulence and mouse immunogenicity of the three vaccines were investigated. Next generation sequencing demonstrated that SA14-14-2 was significantly more diverse than both SA14-5-3 and SA14-2-8, and was slightly less diverse than WT SA14. Notably, WT SA14 had unpredictable levels of diversity across its genome whereas SA14-14-2 is highly diverse, but genetic diversity is not random, rather the virus only tolerates variability at certain residues. Using Ribavirin sensitivity in vitro, it was found that SA14-14-2 has a lower fidelity replication complex compared to SA14-5-3 and SA14-2-8. Mouse virulence studies showed that SA14-2-8 was the most virulent of the three vaccine strains while SA14-14-2 had the most favorable combination of safety (virulence) and immunogenicity for all vaccines tested. SA14-14-2 contains genetic diversity and sensitivity to the antiviral Ribavirin similar to WT parent SA14, and this genetic diversity likely explains the (1) differences in genomic sequences reported for SA14-14-2 and (2) the encoding of major attenuation determinants by the viral E protein.

Feline morbillivirus-1 in dogs with respiratory diseases

Feline morbillivirus-1 (FeMV-1) is a viral pathogen associated with kidney disease in domestic cats and wild felids. We initially identified the FeMV-1 from the lung of a necropsied dog with severe pulmonary disease by the reverse transcription polymerase chain reaction (RT-PCR). Thereafter, we investigated FeMV-1 in nasal and oral swab samples from 73 healthy and 113 dogs with respiratory illnesses. We found polymerase chain reaction (PCR)-positive FeMV-1 from only 14/113 (12.39%) dogs with respiratory disease (p = .001). Of these 14 dogs, six were co-infected with other canine respiratory viruses (6/14; 42.86%). Two independent immunohistochemistry procedures, using antibodies against matrix and phosphoprotein of FeMV-1, confirmed the presence of FeMV-1 in lung tissues of two necropsied dogs (out of a total of 22 dogs, 9.09%) that died from respiratory disease. This finding corresponded to transmission electron microscopy findings that paramyxoviral particles exist in lung epithelia. FeMV-1 antigen localization was also evident in the kidney, lymphoid and brain tissues of two deceased dogs. FeMV-1 was successfully isolated from a necropsied dog and from two living dogs, all with respiratory illnesses, which supports FeMV infection in dogs. The detection of FeMV-1 in dog tissues expands the known tropism of this virus to a non-felid host. Our findings indicate that FeMV-1, alone or in co-infection with other viral pathogens, might contribute to respiratory illness and death in dogs.

Japanese encephalitis virus infection in meerkats (Suricata suricatta)

Japanese encephalitis virus (JEV) infection has been recognized as a serious disease in humans. Wildlife animal infections due to JEV have not been well described. This study identified JEV infection in two deceased meerkats in Thailand, with clinical signs of neurological disease. Histopathology of brains revealed severe lymphoplasmacytic necrotizing meningoencephalitis, while similar inflammation was observed in the lung and liver. Partial JEV sequences were identified from the formalin-fixed paraffin-embedded-derived brain sections of two meerkats and were found to be genetically similar to a JEV strain detected in China but not from a local strain. Using immunohistochemistry, the virus was identified in neurons and glial cells, and also found in bronchial glands, Kupffer's cells in liver, lymphocytes in the spleen and pancreatic acini, which suggests extraneural infection. Transmission electron microscopy confirmed the presence of spheroid viral particles in the lungs. These findings may suggest that infection of extraneural organs in meerkats is similar to that described in JEV-infected humans. In conclusion, this study identified the first JEV infection in meerkats as an interesting case study. The JEV should be considered as an important differential diagnosis in meerkats with encephalitis. Further surveillance on JEV infection in meerkats and other wildlife species in a large cohort is needed in the future study.

Lack of Zika Virus and Other Recognized Flaviviruses among the Mosquito Vectors during and Post the Hajj Mass Gathering

Makkah city, Kingdom of Saudi Arabia (KSA), contains many of the world’s mosquito vectors of parasitic and arboviral disease and is the site of the Hajj mass gathering. As such there is a risk of exportation and globalization of vector-borne viruses, including the re-emerging Zika virus (ZIKV). There was international concern regarding the introduction of ZIKV to KSA and potential international spread of the virus following the 2016 Hajj which took place few days after the Rio summer Olympics at the height of the ZIKV pandemic. We aimed to detect flaviviruses, including ZIKV, circulating among mosquito hosts in the city of Makkah during and post the 2016 Hajj pilgrimage. Mosquitos (adults and larvae) were sampled from 15 sites in Makkah city during and post the 2016 Hajj and identified to species by morphological keys. Mosquitos were pooled according to date of collection, location, and species. A Pan-Flaviviruses RT-PCR assay that enables identification of 51 flaviviruses species and three tentative species was used to detect flavivirus RNA directly from mosquito homogenates. Between the 10 September and 6 October 2016, 9412 female mosquitos were collected. Of these, 81.3% were Aedes aegypti, 18.6% were Culex species, and 0.1% were Anopheles species. Of the total 493 mosquito pools generated, 242 (49%) were positive by the Pan-Flaviviruses primer set. Sequence analysis revealed that none of the mosquitos carried a pathogenic flavivirus, including ZIKV, but were infected with a novel insect-specific flavivirus. We found no pathogenic flaviviruses circulating in Makkah city during and post the 2016 Hajj and no evidence of introduction of ZIKV through the pilgrimage. Enhanced vector-borne diseases surveillance, prevention, and control are crucial in KSA especially during international mass gatherings such as the annual Hajj to prevent outbreaks and the spread of viruses with epidemic and pandemic potentials.

Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats

Hepatitis is a major global health concern. However, the etiology of 10-20% hepatitis cases remains unclear. Some hepatitis-associated viruses, like the hepatitis E virus, are zoonotic pathogens. Rats, shrews, and bats are reservoirs for many zoonotic pathogens. Therefore, understanding the virome in the liver of these animals is important for the investigation of the etiologies of hepatitis and monitoring the emerging zoonotic viruses. In this study, viral metagenomics and PCR methods were used to investigate viral communities in rats, mice, house shrews, and bats livers. Viral metagenomic analysis showed a diverse set of sequences in liver samples, comprising: sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses. Using PCR methods, we first detected hepatovirus sequences in Hipposideros larvatus (3.85%). We also reported the first detection of Zika virus-related sequences in rats and house shrews. Sequences related to influenza A virus and herpesviruses were detected in liver. Higher detection rates of pegivirus sequences were found in liver tissue and serum samples from rats (7.85% and 15.79%, respectively) than from house shrews. Torque teno virus sequences had higher detection rates in the serum samples of rats and house shrews (52.72% and 5.26%, respectively) than in the liver. Near-full length genomes of pegivirus and torque teno virus were amplified. This study is the first to compare the viral communities in the liver of bats, rats, mice, and house shrews. Its findings expand our understanding of the virome in the liver of these animals and provide an insight into hepatitis-related viruses.

West Nile and Usutu viruses co-circulation in central Italy: outcomes of the 2018 integrated surveillance

BACKGROUND

West Nile (WNV) and Usutu (USUV) are emerging vector-borne zoonotic flaviviruses. They are antigenically very similar, sharing the same life cycle with birds as amplification host, Culicidae as vector, and man/horse as dead-end host. They can co-circulate in an overlapping geographic range. In Europe, surveillance plans annually detect several outbreaks.

METHODS

In Italy, a WNV/USUV surveillance plan is in place through passive and active surveillance. After a 2018 WNV outbreak, a reinforced integrated risk-based surveillance was performed in four municipalities through clinical and serological surveillance in horses, Culicidae catches, and testing on human blood-based products for transfusion.

RESULTS

Eight WNV cases in eight equine holdings were detected. Twenty-three mosquitoe catches were performed and 2367 specimens of Culex pipiens caught; 17 pools were USUV positive. A total of 8889 human blood donations were tested, and two asymptomatic donors were USUV positive.

CONCLUSIONS

Different surveillance components simultaneously detected WNV only in horses and USUV only in humans and mosquitoes. While in endemic areas (i.e. northern Italy) entomological surveillance is successfully used as an early detection warning, this method in central Italy seems ineffective. To achieve a high level of sensitivity, the entomological trapping effort should probably exceed a reasonable balance between cost and performance. Besides, WNV/USUV early detection can be addressed by horses and birds. Further research is needed to adapt the surveillance components in different epidemiological contexts.

Simultaneous circulation of two West Nile virus lineage 2 clades and Bagaza virus in the Zambezi region, Namibia

Flaviviruses include a great diversity of mosquito-borne arboviruses with epidemic potential and high global disease burden. Several flaviviruses are circulating in southern Africa affecting humans and livestock, among them West Nile virus (WNV) and Wesselsbron virus. Despite their high relevance, no arbovirus surveillance study has been conducted for more than 35 years in Namibia. In this study we assessed the diversity of flaviviruses circulating in mosquitoes in the densely populated, semi-tropical Zambezi region of north-eastern Namibia. In total, 10,206 mosquitoes were sampled in Bwabwata and Mudumu national parks and Mashi and Wuparo conservancies and screened for flavivirus infections. A high infection rate with insect-specific flaviviruses was found with 241 strains of two previously known and seven putative novel insect-specific flaviviruses. In addition, we identified ten strains of WNV in the main vector Cx. univittatus sampled in the Mashi conservancy. Surprisingly, the strains fell into two different clades of lineage 2, 2b and 2d. Further, three strains of Bagaza Virus (BAGV) were found in Cx. univittatus mosquitoes originating from Mudumu national park. Assessment of BAGV growth in different cell lines showed high replication rates in mosquito and duck cells and about 100,000fold lower replication in human, primate and rodent cells. We demonstrate a wide genetic diversity of flaviviruses is circulating in mosquitoes in the Zambezi region. Importantly, WNV and BAGV can cause outbreaks including severe disease and mortality in humans and birds, respectively. Future studies should focus on WNV and BAGV geographic distribution, as well as on their potential health impacts in and the associated social and economic implications for southern Africa.

Mosquitoes serve as vectors for the transmission of infectious diseases. Some of the most important mosquito-borne arboviruses belong to the genus Flavivirus, which can induce severe disease in humans and livestock. Surveillance of vector populations provide information on circulating arboviruses and may help to identify local outbreaks. Here we sampled mosquitoes over three wet seasons in the densely populated, semi-tropical Zambezi region of north-eastern Namibia and tested them for infections with flaviviruses. We observed simultaneous circulation of two different West Nile virus clades in the main vector species Cx. univittatus. Humans infected with West Nile virus can develop flu-like symptoms or in rare cases meningoencephalitis. Further, we detected Bagaza virus in Cx. univittatus from another locality and season. Bagaza virus infects birds leading to high mortality rates and may also infect humans. Our data suggest that both viruses are endemic in the Zambezi region and may affect human health and well-being in Namibia.

First investigation of pathogenic bacteria, protozoa and viruses in rodents and shrews in context of forest-savannah-urban areas interface in the city of Franceville (Gabon)

Rodents are reservoirs of numerous zoonotic diseases caused by bacteria, protozoans, or viruses. In Gabon, the circulation and maintenance of rodent-borne zoonotic infectious agents are poorly studied and are often limited to one type of pathogen. Among the three existing studies on this topic, two are focused on a zoonotic virus, and the third is focused on rodent Plasmodium. In this study, we searched for a wide range of bacteria, protozoa and viruses in different organs of rodents from the town of Franceville in Gabon. Samples from one hundred and ninety-eight (198) small mammals captured, including two invasive rodent species, five native rodent species and 19 shrews belonging to the Soricidae family, were screened. The investigated pathogens were bacteria from the Rickettsiaceae and Anaplasmataceae families, Mycoplasma spp., Bartonella spp., Borrelia spp., Orientia spp., Occidentia spp., Leptospira spp., Streptobacillus moniliformis, Coxiella burnetii, and Yersinia pestis; parasites from class Kinetoplastida spp. (Leishmania spp., Trypanosoma spp.), Piroplasmidae spp., and Toxoplasma gondii; and viruses from Paramyxoviridae, Hantaviridae, Flaviviridae and Mammarenavirus spp. We identified the following pathogenic bacteria: Anaplasma spp. (8.1%; 16/198), Bartonella spp. (6.6%; 13/198), Coxiella spp. (5.1%; 10/198) and Leptospira spp. (3.5%; 7/198); and protozoans: Piroplasma sp. (1%; 2/198), Toxoplasma gondii (0.5%; 1/198), and Trypanosoma sp. (7%; 14/198). None of the targeted viral genes were detected. These pathogens were found in Gabonese rodents, mainly Lophuromys sp., Lemniscomys striatus and Praomys sp. We also identified new genotypes: Candidatus Bartonella gabonensis and Uncultured Anaplasma spp. This study shows that rodents in Gabon harbor some human pathogenic bacteria and protozoans. It is necessary to determine whether the identified microorganisms are capable of undergoing zoonotic transmission from rodents to humans and if they may be responsible for human cases of febrile disease of unknown etiology in Gabon.

Detection of Changuinola virus (Reoviridae: Orbivirus) in field-caught sand flies in southern Thailand

BACKGROUND

Phlebotomine sand flies are vectors for several pathogenic bacteria, parasites and viruses that have significant impacts on public health. Sand fly-associated viruses that cause diseases in humans and animals have recently received more attention. This study aimed to detect pathogenic viruses belonging to the Orbivirus genus, Phlebovirus genus, Flavivirus genus and family Rhabdoviridae in several field-caught sand fly species in southern Thailand.

METHODS

Sand flies were collected in southern Thailand using CDC light traps. Each sample was processed individually for virus screening using RT-PCR and sequencing.

RESULTS

Seven out of 60 sand fly samples (two samples of Idiophlebotomus spp., three of Phlebotomus papatasi and two of Sergentomyia khawi) were positive for the Orbivirus genus, which is closely related to Changuinola virus (CGLV). Phlebovirus genus, Flavivirus genus and family Rhabdoviridae were negative in all samples.

CONCLUSIONS

CGLV causes Changuinola virus disease or Changuinola fever, a febrile illness in Central and South America. The virus has never been reported in Thailand. This study is the first report of the detection of CGLV in sand flies from Thailand. An extensive study of sand flies from other regions of the country and the associations between sand flies, viruses and vertebrate hosts in Thailand should be undertaken.

Serological Evidence of West Nile Virus in Wild Birds in Bangladesh

West Nile Virus (WNV) is a vector-borne zoonotic disease maintained in a sylvatic cycle involving mosquito vectors and birds. To detect WNV and other flavivirus infections in wild resident and migratory birds, we tested 184 samples from 19 identified species within nine families collected during 2012–2016 from four districts in Bangladesh. We tested serum samples for the immunoglobulin G (IgG) antibody against WNV using competitive Enzyme-Linked Immunosorbent Assay (c-ELISA), whereas tracheal and cloacal swabs were subjected to consensus Polymerase Chain Reaction (c-PCR) for the detection of the flavivirus RNA. Overall, we detected 11.9% (n = 22; 95% CI: 0.07–0.16) samples were seropositive, including 15.9% in the migratory wild birds and 10.7% in the resident wild birds. The migratory wild Tufted duck showed 28.5% seropositivity, whereas the resident wild house crows showed 12.5% seropositivity. None of the swab samples was positive for flavivirus RNA infection (0%, n = 184; 95% CI: 0–0.019). These study findings recommend continued surveillance for early detection and to better understand the epidemiology of WNV and other flavivirus circulation in both birds and mosquitoes in Bangladesh.

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.

No Evidence of Coronaviruses or Other Potentially Zoonotic Viruses in Sunda pangolins (Manis javanica) Entering the Wildlife Trade via Malaysia

The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins (Manis javanica) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (> 50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families-Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In the light of recent reports of coronaviruses including a SARS-CoV-2-related virus in Sunda pangolins in China, the lack of any coronavirus detection in our 'upstream' market chain samples suggests that these detections in 'downstream' animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally.

Toscana, West Nile, Usutu and tick-borne encephalitis viruses: external quality assessment for molecular detection of emerging neurotropic viruses in Europe, 2017

BackgroundNeurotropic arboviruses are increasingly recognised as causative agents of neurological disease in Europe but underdiagnosis is still suspected. Capability for accurate diagnosis is a prerequisite for adequate clinical and public health response.AimTo improve diagnostic capability in EVD-LabNet laboratories, we organised an external quality assessment (EQA) focusing on molecular detection of Toscana (TOSV), Usutu (USUV), West Nile (WNV) and tick-borne encephalitis viruses (TBEV).MethodsSixty-nine laboratories were invited. The EQA panel included two WNV RNA-positive samples (lineages 1 and 2), two TOSV RNA-positive samples (lineages A and B), one TBEV RNA-positive sample (Western subtype), one USUV RNA-positive sample and four negative samples. The EQA focused on overall capability rather than sensitivity of the used techniques. Only detection of one, clinically relevant, concentration per virus species and lineage was assessed.ResultsThe final EQA analysis included 51 laboratories from 35 countries; 44 of these laboratories were from 28 of 31 countries in the European Union/European Economic Area (EU/EEA). USUV diagnostic capability was lowest (28 laboratories in 18 countries), WNV detection capacity was highest (48 laboratories in 32 countries). Twenty-five laboratories were able to test the whole EQA panel, of which only 11 provided completely correct results. The highest scores were observed for WNV and TOSV (92%), followed by TBEV (86%) and USUV (75%).ConclusionWe observed wide variety in extraction methods and RT-PCR tests, showing a profound absence of standardisation across European laboratories. Overall, the results were not satisfactory; capacity and capability need to be improved in 40 laboratories.

An Observational Study of Sepsis in Takeo Province Cambodia: An in-depth examination of pathogens causing severe infections

The world's most consequential pathogens occur in regions with the fewest diagnostic resources, leaving the true burden of these diseases largely under-represented. During a prospective observational study of sepsis in Takeo Province Cambodia, we enrolled 200 patients over an 18-month period. By coupling traditional diagnostic methods such as culture, serology, and PCR to Next Generation Sequencing (NGS) and advanced statistical analyses, we successfully identified a pathogenic cause in 46.5% of our cohort. In all, we detected 25 infectious agents in 93 patients, including severe threat pathogens such as Burkholderia pseudomallei and viral pathogens such as Dengue virus. Approximately half of our cohort remained undiagnosed; however, an independent panel of clinical adjudicators determined that 81% of those patients had infectious causes of their hospitalization, further underscoring the difficulty of diagnosing severe infections in resource-limited settings. We garnered greater insight as to the clinical features of severe infection in Cambodia through analysis of a robust set of clinical data.

West Nile Virus: An Update on Pathobiology, Epidemiology, Diagnostics, Control and "One Health" Implications

West Nile virus (WNV) is an important zoonotic flavivirus responsible for mild fever to severe, lethal neuroinvasive disease in humans, horses, birds, and other wildlife species. Since its discovery, WNV has caused multiple human and animal disease outbreaks in all continents, except Antarctica. Infections are associated with economic losses, mainly due to the cost of treatment of infected patients, control programmes, and loss of animals and animal products. The pathogenesis of WNV has been extensively investigated in natural hosts as well as in several animal models, including rodents, lagomorphs, birds, and reptiles. However, most of the proposed pathogenesis hypotheses remain contentious, and much remains to be elucidated. At the same time, the unavailability of specific antiviral treatment or effective and safe vaccines contribute to the perpetuation of the disease and regular occurrence of outbreaks in both endemic and non-endemic areas. Moreover, globalisation and climate change are also important drivers of the emergence and re-emergence of the virus and disease. Here, we give an update of the pathobiology, epidemiology, diagnostics, control, and “One Health” implications of WNV infection and disease.

Performance of rapid tests in the management of dengue fever imported cases in Lazio, Italy 2014-2019

BACKGROUND

In Italy, dengue virus is the most frequent agent of imported viral infections. The use of rapid diagnostic tests (RDTs) may be of help as a preliminary user-friendly quick assay to facilitate dengue diagnosis, as ordinary laboratory diagnosis of dengue fever may require special efforts in terms of tools availability, interpretation of results, and skilled personnel. The performance of RDTs, however, may vary according to different epidemiological and laboratory background.

METHODS

We reviewed five years of laboratory records of two dengue RDT results (Colorimetric SD-Bioline Dengue-Duo-RDT and Fluorimetric SD-Biosensor-STANDARD-F-Dengue-RDT), able to detect viral NS1 antigen and specific IgM and IgG. Diagnostic parameters were calculated using as reference the results of molecular (RT-PCR) and serological (immunofluorescence, IFA) tests. Overall performance, calculated considering the final case definition, was included in the accuracy assessment of RDTs.

RESULTS

The combined use of NS1 and IgM/IgG RDT for the detection of acute dengue cases resulted in an overall sensitivity and specificity of 87.2% and 97.9% for Colorimetric RDT, 96.2% and 96.2% for Fluorimetric RDT. NS1 was the most reliable marker of acute infection, while IgM resulted falsely positive in nine samples, including sera derived from 2 Zika and 4 non-arbovirus infected patients.

CONCLUSIONS

The inclusion of RDT in the diagnostic algorithm is of undeniable help in the prompt management and surveillance of dengue infection in non-endemic areas. Confirmatory tests are, however, necessary to rule in or rule out dengue fever diagnosis.

Expanding Usutu virus circulation in Italy: detection in the Lazio region, central Italy, 2017 to 2018

Blood donation screening for West Nile virus (WNV) was mandatory in the Lazio region in 2017 and 2018 (June-November) according to the national surveillance plan. In these years, all five donations reactive in WNV nucleic acid amplification tests harboured instead Usutu virus (USUV). Clade ‘Europe 2’ was identified in four blood donations and a 2018 mosquito pool. The cocirculation of WNV and USUV in Lazio warrants increased laboratory support and awareness of possible virus misidentification.

Applying a pan-flavivirus RT-qPCR assay in Brazilian public health surveillance

The aim of this study was to improve flavivirus field monitoring in Brazil using a reliable probe-based RT-qPCR assay. Standard flavivirus strains were employed to evaluate the performance of the assay, and its applicability was evaluated using 235 stored pools of Culicidae samples collected between 1993 and 1997 and in 2016. Flavivirus species were identified by sequencing. Sixteen (6.8%) samples tested positive: Ilheus virus, Iguape virus, and Saint Louis encephalitis virus were identified in historical specimens from 1993-1994, while insect-specific flaviviruses were detected in the samples from 2016. This approach was demonstrated to be accurate for flavivirus detection and characterization, and it can be successfully applied for vector surveillance and for monitoring and discovery of insect specific flaviviruses.

A Duplex Quantitative Real-Time Reverse Transcription-PCR for Simultaneous Detection and Differentiation of Flaviviruses of the Japanese Encephalitis and Ntaya Serocomplexes in Birds

High impact, mosquito-borne flaviviruses such as West Nile virus (WNV), Usutu virus (USUV), Japanese encephalitis virus (JEV), Tembusu virus (TMUV), and Bagaza/Israel turkey meningoencephalomyelitis virus (BAGV/ITV) are emerging in different areas of the world. These viruses belong to the Japanese encephalitis (JE) serocomplex (JEV, WNV, and USUV) and the Ntaya serocomplex (TMUV and BAGV/ITV). Notably, they share transmission route (mosquito bite) and reservoir host type (wild birds), and some of them co-circulate in the same areas, infecting overlapping mosquito and avian population. This may simplify epidemiological surveillance, since it allows the detection of different infections targeting the same population, but also represents a challenge, as the diagnostic tools applied need to detect the whole range of flaviviruses surveyed, and correctly differentiate between these closely related pathogens. To this aim, a duplex real-time RT-PCR (dRRT-PCR) method has been developed for the simultaneous and differential detection of JE and Ntaya flavivirus serocomplexes. The method has been standardized and evaluated by analyzing a panel of 49 flaviviral and non-flaviviral isolates, and clinical samples of different bird species obtained from experimental infections or from the field, proving its value for virus detection in apparently healthy or suspicious animals. This new dRRT-PCR technique is a reliable, specific and highly sensitive tool for rapid detection and differentiation of JE and Ntaya flavivirus groups in either domestic or wild animals. This novel method can be implemented in animal virology diagnostic laboratories as screening tool in routine surveillance and in the event of bird encephalitis emergence.

Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya

Dengue virus (DENV) has caused recent outbreaks in coastal cities of Kenya, but the epidemiological situation in other areas of Kenya is largely unknown. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. Altogether, 560 patients were sampled in 2016–2017 in rural Taita–Taveta County (n = 327) and urban slums of Kibera, Nairobi (n = 233). The samples were studied for DENV IgM, IgG, NS1 antigen and flaviviral RNA. IgG seroprevalence was found to be higher in Taita–Taveta (14%) than in Nairobi (3%). Five Taita–Taveta patients were positive for flaviviral RNA, all identified as DENV-2, cosmopolitan genotype. Local transmission in Taita–Taveta was suspected in a patient without travel history. The sequence analysis suggested that DENV-2 strains circulating in coastal and southern Kenya likely arose from a single introduction from India. The molecular clock analyses dated the most recent ancestor to the Kenyan strains a year before the large 2013 outbreak in Mombasa. After this, the virus has been detected in Kilifi in 2014, from our patients in Taita–Taveta in 2016, and in an outbreak in Malindi in 2017. The results highlight that silent transmission occurs between epidemics and also affects rural areas. More information is needed to understand the local epidemiological characteristics and future risks of dengue in Kenya.

Dengue virus (DENV) is an emerging mosquito-borne global health threat in the tropics and subtropics. The majority of the world’s population live in areas at risk of dengue that can cause a wide variety of symptoms from febrile illness to haemorrhagic fever. Information of DENV in Africa is limited and fragmented. In Kenya, dengue is a recognized disease in coastal cities that have experienced recent outbreaks. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. We found DENV-2 in five febrile patients from rural Taita–Taveta, where no dengue has been reported before. Genetic analysis of the virus suggests it to be most likely of Indian origin. This Indian origin DENV-2 was detected in the Mombasa outbreak in 2013, in Kilifi in 2014, in Taita–Taveta in 2016 (our study samples) and again in the Malindi outbreak in 2017. The results suggest that dengue is unrecognized in rural Kenya and more studies are needed for local risk assessment. Our findings of virus transmission between epidemics contribute to better understanding of the epidemiological situation and origins of DENV in Kenya.

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.

Evaluation of a novel microfluidic immuno-magnetic agglutination assay method for detection of dengue virus NS1 antigen

BACKGROUND

Dengue virus (DENV) is the most important arbovirus worldwide, causing infections in endemic countries and returning travellers from these areas. Rapid diagnostic tests are needed to improve patient management and monitor local transmission. The detection of DENV non-structural protein 1 (NS1) is a useful tool for the diagnosis, but the currently available methods can be time consuming or lack sensitivity. The objective of our study was to evaluate a new rapid and semi-quantitative microfluidic DENV NS1 immuno-magnetic agglutination assay based on aggregation of magnetic nanoparticles detected by an electronic reader (Virotrack Dengue Acute and Blubox, Blusense diagnostics, Copenhagen, Denmark).

METHODOLOGY/PRINCIPAL FINDINGS

A panel of 135 serum samples from travelers returning from dengue endemic countries was analyzed (74 DENV positive samples including the four DENV serotypes, 26 Zika virus positive samples, 25 chikungunya virus positive samples, 5 malaria positive samples and 5 negative samples). Samples were tested by three different antigen detection methods: SD Dengue NS1 Ag ELISA, SD BIOLINE Dengue Duo and ViroTrack Dengue Acute. The sensitivity observed for SD Dengue NS1 Ag ELISA, ViroTrack Dengue Acute and SD BIOLINE Dengue Duo was 97.2%, 91.1% and 68.1%, respectively. All methods showed high specificity (98.4% for ViroTrack Dengue Acute and 100% for both SD Dengue NS1 Ag ELISA and SD BIOLINE Dengue Duo). SD Dengue NS1 Ag ELISA and ViroTrack Dengue Acute only failed to detect samples positive for DENV-2.

CONCLUSIONS/SIGNIFICANCE

ViroTrack Dengue Acute is a sensitive and specific assay for DENV NS1 detection. It provides faster results than the ELISA method and a better performance than the rapid immunochromatographic tests. ViroTrack Dengue Acute could represent a valuable tool for rapid diagnosis of DENV infections in returning travellers from endemic countries.

Evidence of Low-Level Dengue Virus Circulation in the South Region of Cameroon in 2018

Dengue fever is an understudied disease in many parts of Africa and little is known about its prevalence in Cameroon. We tested blood from 629 individuals from the South Region of Cameroon, collected over the course of one year, for flavivirus RNA using conventional broad range PCR. Flavivirus RNA corresponding to dengue virus (DENV) serotype 1 was identified in two individuals who were also diagnosed with malaria. This finding confirms previous reports that indicate the presence of low-level circulation of DENV in Cameroon and supports the concern that dengue fever may be underdiagnosed due to more prevalent diseases that have similar symptomology and insufficient diagnostic capacity.

Spillover of ebolaviruses into people in eastern Democratic Republic of Congo prior to the 2018 Ebola virus disease outbreak

BACKGROUND

The second largest Ebola virus disease (EVD) outbreak began in the Democratic Republic of Congo in July 2018 in North Kivu Province. Data suggest the outbreak is not epidemiologically linked to the 2018 outbreak in Equateur Province, and that independent introduction of Ebola virus (EBOV) into humans occurred. We tested for antibodies to ebolaviruses in febrile patients seeking care in North Kivu Province prior to the EVD outbreak.

METHODS

Patients were enrolled between May 2017 and April 2018, before the declared start of the outbreak in eastern DRC. Questionnaires were administered to collect demographic and behavioural information to identify risk factors for exposure. Biological samples were evaluated for ebolavirus nucleic acid, and for antibodies to ebolaviruses. Prevalence of exposure was calculated, and demographic factors evaluated for associations with ebolavirus serostatus.

RESULTS

Samples were collected and tested from 272 people seeking care in the Rutshuru Health Zone in North Kivu Province. All patients were negative for filoviruses by PCR. Intial screening by indirect ELISA found that 30 people were reactive to EBOV-rGP. Results were supported by detection of ebolavirus reactive linear peptides using the Serochip platform. Differential screening of all reactive serum samples against the rGP of all six ebolaviruses and Marburg virus (MARV) showed that 29 people exhibited the strongest reactivity to EBOV and one to Bombali virus (BOMV), and western blotting confirmed results. Titers ranged from 1:100 to 1:12,800. Although both sexes and all ages tested positive for antibodies, women were significantly more likely to be positive and the majority of positives were in February 2018.

CONCLUSIONS

We provide the first documented evidence of exposure to Ebola virus in people in eastern DRC. We detected antibodies to EBOV in 10% of febrile patients seeking healthcare prior to the declaration of the 2018-2020 outbreak, suggesting early cases may have been missed or exposure ocurred without associated illness. We also report the first known detection of antibodies to BOMV, previously detected in bats in West and East Africa, and show that human exposure to BOMV has occurred. Our data suggest human exposure to ebolaviruses may be more frequent and geographically widespread.