ICTV Virus Taxonomy Profile: Nairoviridae 2024.

Nairoviridae is a family for negative-sense RNA viruses with genomes of about 17.2-21.1 kb. These viruses are maintained in and/or transmitted by arthropods among birds, reptiles and mammals. Norwaviruses and orthonairoviruses can cause febrile illness in humans. Several orthonairoviruses can infect mammals, causing mild, severe and sometimes, fatal diseases. Nairovirids produce enveloped virions containing two or three single-stranded RNA segments with open reading frames that encode a nucleoprotein (N), sometimes a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Nairoviridae, which is available at www.ictv.global/report/nairoviridae.

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota).

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

History and classification of Aigai virus (formerly Crimean-Congo haemorrhagic fever virus genotype VI).

Crimean-Congo haemorrhagic fever virus (CCHFV) is the medically most important member of the rapidly expanding bunyaviral family Nairoviridae. Traditionally, CCHFV isolates have been assigned to six distinct genotypes. Here, the International Committee on Taxonomy of Viruses (ICTV) Nairoviridae Study Group outlines the reasons for the recent decision to re-classify genogroup VI (aka Europe-2 or AP-92-like) as a distinct virus, Aigai virus (AIGV).

ICTV Virus Taxonomy Profile: Nairoviridae.

Members of the family Nairoviridae produce enveloped virions with three single-stranded RNA segments comprising 17.1 to 22.8 kb in total. These viruses are maintained in arthropods and transmitted by ticks to mammals or birds. Crimean-Congo hemorrhagic fever virus is tick-borne and is endemic in most of Asia, Africa, Southern and Eastern Europe whereas Nairobi sheep disease virus, which is also tick-borne, causes lethal haemorrhagic gastroenteritis in small ruminants in Africa and India. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Nairoviridae, which is available at ictv.global/report/nairoviridae.

Low prevalence of hypervirulent Klebsiella pneumoniae in Anatolia, screened via phenotypic and genotypic testing.

Hypervirulent Klebsiella pneumoniae (hvKP) strains are associated with vigorous clinical presentation and relapses. Initially reported from Asia, these variants have spread globally and become an emerging agent of significant health threat. This study was carried out to identify hvKP strains in a previously uninvestigated region and to evaluate the impact of commonly-employed phenotypic and genotypic markers as diagnostic assays. A total of 111 blood culture isolates, collected at a tertiary care center was investigated. The hvKP strains were sought by a string test and the amplification of partial magA, rmpA, iucA and peg344. All products were characterized via sequencing. Evidence for hvKP was observed in 10.8% via iucA amplification (7.2%), string test (2.7%) and magA amplification (0.9%). Specific products were not produced by assays targeting rmpA and peg344 genes. Antibiotic susceptibility patterns compatible with possible extensive or pan-antimicrobial resistance was noted in 66.7% of the hvKP candidate strains. Capsule type in the magA positive strain was characterized as K5. We have detected hvKP in low prevalence at a region with no prior documentation. Targetting the aerobactin gene via iucA amplification provided the most accurate detection in this setting. The epidemiology of hvKP in Anatolia requires elucidation for effective control and management.

Taxonomy of the order Bunyavirales: second update 2018.

In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Taxonomy of the order Bunyavirales: update 2019.

In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Novel and emergent sandfly-borne phleboviruses in Asia Minor: a systematic review.

Sandfly-transmitted phleboviruses are globally spread agents causing febrile diseases and central nervous system infections. The activity of pathogenic phleboviruses, as well as several novel strains, has been reported from Turkey, a transboundary country connecting Asia, Europe, and Africa with suitable habitats for sandflies. This study overviews all published data on phleboviruses from Turkey and evaluates the impact from the virological, epidemiological, and public health perspectives. A systematic review of Web-based global and local resources was performed. Comparison and phylogenetic analyses of particular phlebovirus sequences were also undertaken. Through the evaluation of 1693 international and regional entries, 31 manuscripts providing data on case reports or outbreaks, serological surveillance, animal infections and exposure, virus characterization, vector surveillance, and/or diagnostics were accessed. Detailed information on 5 novel phleboviruses completely or partially characterized during 2008-2015 as well as on clinical and epidemiological features of major phleboviruses established as human pathogens such as Toscana virus and sandfly fever Sicilian virus has been compiled. The ongoing activity of these agents, as indicated by consistently reported symptomatic cases and confirmed exposure in vertebrates including humans, was noted. The circulation in the Anatolian peninsula of phleboviruses with surprising diversity as well as distinct virus species is documented. Specific phlebovirus strains constitute a public health threat for local populations and travelers and must be considered in the diagnostic workup of clinically compatible cases. Human health impact and epidemiological aspects of certain viruses require further investigation via intensive surveillance.

MicroRNA expression profiles in patients with acute Crimean Congo hemorrhagic fever reveal possible adjustments to cellular pathways.

Several viral diseases are associated with altered microRNA (miRNA) expression, which can provide vital information about how cellular pathways respond to infection. However, the miRNA profile of Crimean Congo Hemorrhagic Fever (CCHFV) infections are not known. To address this gap, we performed real-time PCR-based miRNA analysis in individuals with acute Crimean Congo Hemorrhagic Fever (CCHFV) infections, with the goal of identifying pathways that might be associated with this disease. Peripheral blood mononuclear cells were analysed in eight individuals with detectable viral RNA and compared to five healthy subjects. A total of 106 differentially expressed miRNAs were identified, of which 19 miRNAs were either fivefold prominently up- or down-regulation. Several miRNAs associated with cytokine expression, some of which were previously associated with Dengue and Hantavirus infections were revealed. Moreover, possible mechanisms related to secretion of adhesion molecules and viral escape from innate immunity were identified. Pathway enrichment analyses further revealed the putative involvement of TNF-alfa, TGF-beta, MAPK, WNT, and neurotrophin signaling pathways in disease pathogenesis. J. Med. Virol. 89:417-422, 2017. © 2016 Wiley Periodicals, Inc.

A novel rhabdovirus, related to Merida virus, in field-collected mosquitoes from Anatolia and Thrace.

Next-generation sequencing technologies have significantly facilitated the discovery of novel viruses, and metagenomic surveillance of arthropods has enabled exploration of the diversity of novel or known viral agents. We have identified a novel rhabdovirus that is genetically related to the recently described Merida virus via next-generation sequencing in a mosquito pool from Thrace. The complete viral genome contains 11,798 nucleotides with 83% genome-wide nucleotide sequence similarity to Merida virus. Five major putative open reading frames that follow the canonical rhabdovirus genome organization were identified. A total of 1380 mosquitoes comprising 13 species, collected from Thrace and the Mediterranean and Aegean regions of Anatolia were screened for the novel virus using primers based on the N and L genes of the prototype genome. Eight positive pools (6.2%) exclusively comprised Culex pipiens sensu lato specimens originating from all study regions. Infections were observed in pools with female as well as male or mixed-sex individuals. The overall and Cx. pipiens-specific minimal infection rates were calculated to be 5.7 and 14.8, respectively. Sequencing of the PCR products revealed marked diversity within a portion of the N gene, with up to 4% divergence and distinct amino acid substitutions that were unrelated to the collection site. Phylogenetic analysis of the complete and partial viral polymerase (L gene) amino acid sequences placed the novel virus and Merida virus in a distinct group, indicating that these strains are closely related. The strain is tentatively named "Merida-like virus Turkey". Studies are underway to isolate and further explore the host range and distribution of this new strain.

[Multicenter investigation of bufavirus in the etiology of viral central nervous system infections of adults and children]. / Bufavirusun çocuklar ve eriskinlerdeki viral santral sinir sistemi enfeksiyonlarinin etiyolojisi açisindan çok Mmerkezli olarak arastirilmasi.

Bufavirus (BuV) is a newly-identified parvovirus in the family of Parvoviridae. Metagenomic analysis of fecal samples from children in Burkina Faso with acute diarrhea showed a highly divergent parvovirus, which was named bufavirus (BuV). The global distribution, epidemiology and genetic characteristics of BuVs infections are obscure. It was first discovered as an agent causing gastroenteritis but the association of BuV infections with various clinical presentations mostly remain to be explored. The aims of this study were to investigate probable impact of BuV in central nervous system infections in a region where it was previously reported to cause human infections and to detect enteroviruses (EV) which are reported as a cause of central nervous system infections in our country. The study was undertaken in three institutions in Ankara province, Central Anatolia, Turkey. Patients, clinically diagnosed with febrile disease and/or central nervous system infections of presumed viral etiology, were enrolled in the study with informed consent. Cerebrospinal fluid specimens were collected from 93 children attended to Gazi University Hospital and Diskapi Yildirim Beyazit Hospital from October 2011-April 2015 and 33 adult patients, attended to Hacettepe University Hospital from June 2012 to March 2013. Clinical history and follow-up, physical examination and standard laboratory findings of the patients were recorded. Nucleic acid extraction was performed via commercially available spin-column assays and complementery DNA (cDNA) synthesis was performed by using commercially available cDNA synthesis kit with randomised hexamer primers. BuV detection was carried out by in house nested-polymerase chain reaction (PCR) utilized with previously-described primers. EV detection was carried out by in house PCR with pan-enterovirus primers. Seventy-four percent (93/126) and 26% (33/126) of the patients were children (0-18) and adults (19-86), respectively. In all patients, bacterial, mycobacterial and fungal cultures were negative, as well as PCR for herpes simplex virus (HSV) types 1 and 2. PCR results of all samples were negative for BuV and EV. This is the first study that evaluates a probable association of BuV and central nervous system infections. Although Parvovirus B19, a well-characterized human pathogen can rarely cause encephalitis, our findings did not confirm such an association for BuV in this preliminary investigation. However, long-term evaluation of individual cases with unknown etiology is required to reveal the relationship of the virus with specific environments.

Isolation, genetic characterization, and seroprevalence of Adana virus, a novel phlebovirus belonging to the Salehabad virus complex, in Turkey.

UNLABELLED: A new phlebovirus, Adana virus, was isolated from a pool of Phlebotomus spp. (Diptera; Psychodidae) in the province of Adana, in the Mediterranean region of Turkey. Genetic analysis based on complete coding of genomic sequences indicated that Adana virus belongs to the Salehabad virus species of the genus Phlebovirus in the family Bunyaviridae. Adana virus is the third virus of the Salehabad virus species for which the complete sequence has been determined. To understand the epidemiology of Adana virus, a seroprevalence study using microneutralization assay was performed to detect the presence of specific antibodies in human and domestic animal sera collected in Adana as well as Mersin province, located 147 km west of Adana. The results demonstrate that the virus is present in both provinces. High seroprevalence rates in goats, sheep, and dogs support intensive exposure to Adana virus in the region, which has not been previously reported for any virus included in the Salehabad serocomplex; however, low seroprevalence rates in humans suggest that Adana virus is not likely to constitute an important public health problem in exposed human populations, but this deserves further studies. IMPORTANCE: Until recently, in the genus Phlebovirus, the Salehabad virus species consisted of two viruses: Salehabad virus, isolated from sand flies in Iran, and Arbia virus, isolated from sand flies in Italy. Here we present the isolation and complete genome characterization of the Adana virus, which we propose to be included in the Salehabad virus species. To our knowledge, this is the first report of the isolation and complete genome characterization, from sand flies in Turkey, of a Salehabad virus-related phlebovirus with supporting seropositivity in the Mediterranean, Aegean, and Central Anatolia regions, where phleboviruses have been circulating and causing outbreaks. Salehabad species viruses have generally been considered to be a group of viruses with little medical or veterinary interest. This view deserves to be revisited according to our results, which indicate a high animal infection rate of Adana virus and recent evidence of human infection with Adria virus in Greece.

Close relationship between West Nile virus from Turkey and lineage 1 strain from Central African Republic.

We sequenced West Nile viruses (WNVs) from Turkey and found close relationships to WNV lineage 1 strain ArB310/67 from the Central African Republic, distinct from other WNVs circulating in the Mediterranean Basin, eastern Europe, and the Middle East. These findings suggest independent introductions of WNV strains from Africa to the Middle East.

Prospective investigation of the impact of West Nile Virus infections in renal diseases.

An increased incidence of chronic kidney disease (CKD) after West Nile Virus (WNV) infections has been suggested but the association of WNV infections with renal damage remain inconclusive. This study was undertaken to characterize WNV infections in individuals with acute kidney injury (AKI) and CKD, and to evaluate hemodialysis as a probable transmission route. A total of 463 plasma and urine samples were collected from 45 AKI and 77 CKD patients. Nested and real-time polymerase chain reaction (PCR) assays were employed for viral RNA detection. Specific immunoglobulins were investigated via immunofluorescence and plaque reduction neutralization assays. Consecutive pre and post-dialysis samples were evaluated in CKD cases. WNV RNA and specific immunoglobulins were detected in 7 (5.7%) and 5 (4.1%) individuals, respectively. The AKI patients with WNV RNA in blood and urine had underlying diseases requiring immunosuppressive therapy and demonstrated moderate to high viral loads. No clinical symptom related to WNV infection were observed in CKD cases with detectable viral nucleic acids. All WNV sequences were characterized as lineage 1 clade 1a and several amino acid substitutions with unknown impact were noted. Detailed epidemiologic investigation of WNV RNA positive CKD cases revealed probable vector-borne virus exposure, without the evidence for transmission via hemodialysis.

[Clinical impact of hepatitis C virus genomic variations]. / Hepatit C virusu genomik varyasyonlari ve klinige etkileri.

Hepatitis C virus (HCV) is a globally-dispersed agent of chronic hepatitis with a significant public health threat, affecting over 110 million individuals throughout the world. The increased risk for chronicity after exposure and the lack of a protective vaccine make HCV is a leading infectious cause of cirrhosis, liver failure requiring transplantation and hepatocellular carcinoma. The replicative process and infection dynamics in the host enable HCV to generate an array of closely-related but non-identical genetic variants known as quasispecies in the infected individuals. Pathogenesis and outcome in HCV infections are directly affected by the virus genetic heterogeneity, reflected as the emergence of quasispecies in infected individuals. The evolution of these highly-diverse viral populations in the host directly influences the disease course, via providing a pool of variants capable of resuming viral replication under extrinsic and/or intrinsic selective pressures. Viral quasispecies go through several alterations during the course of the infection, and provide a background for the selection of escape mutants from the host humoral and cell-mediated immune responses and antiviral treatment. Supported by the robust next generation sequencing techniques, recent studies have provided significant insights on the genomic diversity and progression as well as on the origin and the epidemiology of HCV. This review provides an overview of the mechanisms of HCV genetic variability, and the interactions with the host, that affects clinical disease, covering viral and host determinants of humoral and cell-mediated immune responses, alterations during the early and late stages of the infection and disease progression leading to chronicity. In addition, current findings in virus evolution and epidemiology were briefly interpreted from the inter-species and population perspectives. The impact of viral genomic heterogeneity on antiviral treatment in the era of direct-acting agents is also discussed, along with an overview of current methods employed for the characterization of viral diversity.

[Investigation of the hepatitis E virus seroprevalence in cases admitted to Hacettepe University Medical Faculty Hospital]. / Hacettepe Üniversitesi Tip Fakültesi Hastanesine basvuran olgularda hepatit E virusu seroprevalansinin arastirilmasi.

Hepatitis E virus (HEV), classified in Hepeviridae family, Hepevirus genus, is a non-enveloped virus with icosahedral capsid containing single-stranded positive sense RNA genome. HEV infections may be asymptomatic especially in children, however it may present as fulminant hepatitis in pregnant women, as well as chronic hepatitis in immunocompromised patients. There are four well-known genotypes of HEV that infect humans and many mammalian species. Genotype 1 and 2 are frequently responsible for water-borne infections transmitted by fecal-oral way in developing countries, while genotype 3 and 4 cause zoonotic infections in developed countries. Turkey is considered as an endemic country with a total seroprevalence rate of 6.3% for normal population, showing significant variation (0-73%) according to the regions and study groups. The aims of this study were to investigate the HEV seropositivity in cases admitted to Hacettepe University Medical Faculty Hospital (HUMFH), to evaluate the results according to the demographic features of patients, and to determine the current HEV seroprevalence in our region, contributing seroepidemiological data in Turkey. A total of 1043 serum samples (514 female, 529 male; age range: 1-90 years, mean age: 38.03) obtained from 327 blood donors (32 female, 295 male; age range: 19-59 years, mean age: 31.1) who were admitted to HUMFH Blood Center, and 716 sera (482 female, 234 male; age range: 1-90 years, mean age: 41.7) that were sent to HUMFH Central Laboratory from various outpatient/inpatient clinics, between November 2012 to November 2013, were included in the study. The presence of HEV-IgG antibodies in serum samples was detected by a commercial ELISA method (Euroimmun, Germany), and the presence of HEV-IgM antibodies was also investigated in the sera with IgG-positive results. The overall HEV-IgG seropositivity rate was determined as 4.4% (46/1043), and the seropositivity rates for blood donors and in/outpatients were as 0.92% (3/327) and 6.0% (43/716), respectively. HEV-IgM antibody was not detected in any of the cases. The HEV-IgG seropositivity was 3.2% among male, and 5.6% among female, yielding no statistically significant difference between the gender (p= 0.056). HEV-IgG antibodies were detected in none (0/118) of the pediatric age group (0-18 years), while the seropositivity rates were 1.9% (14/731) and 16.5% (32/194) in 19-55 and ≥ 56 years-old groups, respectively. The difference between the age groups was statistically significant (p< 0.001), indicating the age-related pattern of HEV exposure. In conclusion, the total HEV seroprevalence rate found as 4.4% in our study, is comparable to the average results reported from Turkey. Our data is also in agreement with the result of a previous report (3.8%) that performed from Ankara province in 2002 with similar study groups, emphasizing that there was no significant changes for HEV exposure have occured over more than the last decade in Ankara, Cental Anatolia, Turkey.

[Serological investigation of phlebovirus exposure in blood donors from the Mediterranean Province of Mersin, Turkey]. / Mersin bölgesi kan donörlerinde fl ebovirus maruziyetinin serolojik olarak arastirilmasi.

Phleboviruses are enveloped segmented RNA viruses, capable of inducing febrile disease and/or meningoencephalitis in exposed individuals, according to the infecting strain, following transmission via arthropods. Prototype medically-important phlebovirus strains responsible for sandfly fever are sandfly fever Sicilian virus (SFSV) and sandfly fever Naples virus (SFNV), where the SFSV variant sandfly fever Cyprus virus (SFCV) is also detected in individuals with febrile disease. Toscana virus (TOSV) is unique among phleboviruses as the cause of infections involving central nervous system. In this seroepidemiological study, human exposure to selected medically-important phleboviruses was investigated in healthy adult residents of the Mersin province, Mediterranean Anatolia, Turkey, where the current data on phlebovirus epidemiology is scarce. A total of 1784 healthy individuals (mean age: 34.7±9.6 years; 97.3% were male), accepted as blood donors at the Mersin University Center for Health Research and Application Blood Bank were included in the study after informed consent during a seventeen month period between July 2011 to November 2012. All participants were requested to fill out a questionnaire to reveal risk factors for vector exposure. SFSV, SFNV, SFCV and TOSV IgG antibodies in serum were investigated via a commercial indirect immunofluorescence test (IIFT) (Sandfly Fever Virus IgG Mosaic I; Euroimmun, Germany). Sera interpreted as positive or strong positive for TOSV or SFNV+TOSV in IIFT were evaluated via TOSV virus neutralization test (VNT) for specificity confirmation. IIFT seroreactivity for at least one of the tested phleboviruses was present in 66.8% (1192/1784) of the samples. The most frequently-detected phlebovirus strain was SFSV (51.6%; 920/1784), followed by SFNV (46.4%; 827/1784), TOSV (43.7%; 779/1784) and SFCV (47.3%; 843/1784). Among the reactive sera, 6.6% (79/1192) were positive for a single virus serotype, whereas in 39.8% (475/1192) antibodies reacting with all tested virus serotypes were revealed. A total of 187 sera was included in the TOSV VNT and neutralizing antibodies were detected in 13.9%. According to the IIFT reactivity, residing in rural areas was observed as a statistically significant risk factor for exposure in all phleboviruses tested (p values for SFSV, SFNV, TOSV and SFCV were 0.002, 0.001, <0.001 and 0.003, respectively). TOSV exposure is more frequently detected via IIFT in individuals having pets or domestic farm animals around the living quarters (p=0.005). As a result, frequent exposure to SFSV/SFCV or antigenically similar phlebovirus strains and viruses of the SFNV species were determined in healthy blood donors in Mersin province, located in the Mediterranean region of Turkey. Furthermore, TOSV neutralizing antibodies were detected in selected samples with IIFT reactivity, confirming previous reports suggesting TOSV activity in the region. TOSV and other phleboviruses must be included in the diagnostic work-up in cases with febrile diseases and viral central nervous system infections during the sandfly-active months.

[Flavivirus seroepidemiology in blood donors in Mersin province, Turkey]. / Mersin ili kan donörlerinde flavivirus seroepidemiyolojisi.

Among the vector-borne flaviviruses, West Nile virus (WNV), tick-borne encephalitis virus (TBEV) and Dengue virus (DENV) constitute the most frequently-observed pathogens with significant public health impact in endemic regions throughout the globe. This seroepidemiological study was undertaken to investigate human exposure to DENV, WNV and TBEV, as well as other flaviviruses via various serological assays in the Mediterranean province of Mersin, Turkey, where scarce data is currently present for the circulation of these agent. A total of 920 sera were collected after informed consent from asymptomatic blood donors (all were male; age range: 18-63 yrs, mean age: 35.17 ± 9.56 yrs) were taken between August 2010 and April 2011. All samples were initially screened via a commercial ELISA kit for DENV IgM and IgG. Reactive samples were further evaluated via commercial indirect immunofluorescence tests (IIFTs) for yellow fever virus (YFV) IgG, TBEV IgG and via ELISA for WNV IgG. Moreover, presence of neutralizing antibodies were investigated in all reactive samples via plaque reduction neutralization (PRNT) assay for WNV, whose activity has been detected previously in the region. Samples interpreted as positive for TBEV IgG were further evaluated for specificity by TBEV PRNT assay. DENV IgM reactive samples were also assessed for NS1 antigens and IgM/IgG antibodies via a commercial immunochromatographic assay (ICA). DENV IgM and IgG antibodies were detected in 0.9% (8/920) and 16.6% (153/920) of the samples, respectively. One sample was simultaneously positive for IgM and IgG. WNV PRNT revealed positive results in 85.6% (137/160) of the reactive samples, which indicated frequent WNV exposure and frequent development of cross-reactions in the screening assay. Positive or borderline DENV IgM reactivity was identified in 0.43% (4/920) of the samples, which remained negative for NS1 antigen and antibodies in the ICA. Antibody specificity in two samples, positive for DENV and TBEV IgG in IIFT could not be confirmed by TBEV PRNT. A total of 19 reactive samples (19/920, 2.1%), that comprise seven borderline and six positive DENV IgG positivities as well as six samples with IgG positivity for different virus combinations remained negative after DENV confirmatory and WNV/TBEV PRNT assays. When the samples with borderline results were omitted from the evaluation, 12 samples (12/920, 1.3%) were considered to represent exposure to DENV or an antigenically-similar flavivirus. These findings indicated the activity of and frequent exposure (137/920, 14.9%) to WNV, as previously suggested in the study region. In 1.3% of the samples, probable exposure to DENV or other flaviviruses was revealed and this requires further serosurveillance efforts. WNV must be considered in the etiology of febrile diseases or viral neuroinvasive infections of unexplained etiology in the study area.

Comprehensive evaluation of nucleic acid amplification methods widely used for generic detection of sandfly-borne phleboviruses.

Sandfly-borne phleboviruses (SBPs), which cause sandfly fever, aseptic meningitis, encephalitis, and meningoencephalitis, are emerging pathogens of major public health concern. Virus nucleic acid testing is essential for SBP diagnosis, especially in the early stages of infection, and for the discovery of novel SBPs. The efficacy of utilizing generic primers that target conserved nucleotide sequences for the detection of both known and novel SBPs has not been extensively evaluated. We aimed to compare and evaluate the performance of five generic primer sets, widely used to detect S- and L-segments of arthropod-borne phleboviruses and designed as singleplex (n = 3) and nested (n = 2) formats, including both well-known and recently characterized 15 Old World virus strains. Furthermore, we performed in silico analysis to assess the detection capabilities of these generic primer sets. The initial evaluation of previously published generic primer sets for SBP detection yielded two singleplex primer sets with the potential to be adapted for use in real-time or high-throughput detection settings. Studies are ongoing to develop and further optimize a preliminary assay and test various hosts and vectors to assess their capacity to detect known and novel viruses. IMPORTANCE: Virus nucleic acid testing is the primary diagnostic method, particularly in the early stages of illness. Virus-specific or syndromic tests are widely used for this purpose. The use of generic primers has had a considerable impact on the discovery, identification, and detection of Old World sandfly-borne phleboviruses (OWSBP). The study is significant because it is the first to carry out a comparative evaluation of all published OWSBP generic primer sets.

Viral pathogen detection in U.S. game-farm mallard (Anas platyrhynchos) flags spillover risk to wild birds.

The threat posed by emerging infectious diseases is a major concern for global public health, animal health and food security, and the role of birds in transmission is increasingly under scrutiny. Each year, millions of mass-reared game-farm birds are released into the wild, presenting a unique and a poorly understood risk to wild and susceptible bird populations, and to human health. In particular, the shedding of enteric pathogens through excrement into bodies of water at shared migratory stop-over sites, and breeding and wintering grounds, could facilitate multi-species long-distance pathogen dispersal and infection of high numbers of naive endemic birds annually. The Mallard (Anas platyrhynchos) is the most abundant of all duck species, migratory across much of its range, and an important game species for pen-rearing and release. Major recent population declines along the US Atlantic coast has been attributed to game-farm and wild mallard interbreeding and the introduction maladaptive traits into wild populations. However, pathogen transmission and zoonosis among game-farms Mallard may also impact these populations, as well as wildlife and human health. Here, we screened 16 game-farm Mallard from Wisconsin, United States, for enteric viral pathogens using metatranscriptomic data. Four families of viral pathogens were identified - Picobirnaviridae (Genogroup I), Caliciviridae (Duck Nacovirus), Picornaviridae (Duck Aalivirus) and Sedoreoviridae (Duck Rotavirus G). To our knowledge, this is the first report of Aalivirus in the Americas, and the first report of Calicivirus outside domestic chicken and turkey flocks in the United States. Our findings highlight the risk of viral pathogen spillover from peri-domestically reared game birds to naive wild bird populations.