Emerging viruses, emerging threat.
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Acquired Immunodeficiency Syndrome↗
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West Nile virus: an emerging virus in North America.
West Nile virus is an emerging virus that first appeared in North America during the summer of 1999 in New York City. There were seven deaths associated with this event. Surveillance reports indicate that the virus had been spreading south and west and in 2002, had been reported in 42 states and the District of Columbia. As of September 2002, there were 2121 total human cases reported, induding 104 deaths. The fatality rate for the West Nile virus is very low and the majority of individuals will have no clinical symptoms; however, individuals at most risk for more serious form of the disease are the elderly, the immunocompromised, and young individuals. The virus is spread by certain mosquito species and certain populations of birds serve as the reservoir hosts. Because person-to-person transmission does not occur, humans are therefore considered dead-end hosts. Confirmation of cases West Nile virus infections in humans are determined based on clinical and laboratory findings.
Animals↗
Sugarcane yellow leaf virus: an emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors.
We have derived the genomic nucleotide sequence of an emerging virus, the Sugarcane yellow leaf virus (ScYLV), and shown that it produces one to two subgenomic RNAs. The family Luteoviridae currently includes the Luteovirus, Polerovirus, and Enamovirus genera. With the new ScYLV nucleotide sequence and existing Luteoviridae sequence information, we have utilized new phylogenetic and evolutionary methodologies to identify homologous regions of Luteoviridae genomes, which have statistically significant altered nucleotide substitution ratios and have produced a reconstructed phylogeny of the Luteoviridae. The data indicate that Pea enation mosaic virus-1 (PEMV-1), Soybean dwarf virus (SbDV), and ScYLV exhibit spatial phylogenetic variation (SPV) consistent with recombination events that have occurred between poleroviral and luteoviral ancestors, after the divergence of these two progenitor groups. The reconstructed phylogeny confirms a contention that a continuum in the derived sequence evolution of the Luteoviridae has been established by intrafamilial as well as extrafamilial RNA recombination and expands the database of recombinant Luteoviridae genomes that are currently needed to resolve better defined means for generic discrimination in the Luteoviridae (D'Arcy, C. J. and Mayo, M. 1997. Arch. Virol. 142, 1285-1287). The analyses of the nucleotide substitution ratios from a nucleotide alignment of Luteoviridae genomes substantiates the hypothesis that hot spots for RNA recombination in this virus family are associated with the known sites for the transcription of subgenomic RNAs (Miller et al. 1995. Crit. Rev. Plant Sci. 14, 179-211), and provides new information that might be utilized to better design more effective means to generate transgene-mediated host resistance.
Amino Acid Sequence↗
Japanese encephalitis as an emerging virus: the emergence and spread of Japanese encephalitis virus in Australasia.
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Animals↗
Tomato yellow leaf curl virus, an emerging virus complex causing epidemics worldwide.
Tomato yellow leaf curl (TYLC) is one of the most devastating viral diseases of cultivated tomato (Lycopersicon esculentum) in tropical and subtropical regions worldwide, and losses of up to 100% are frequent. In many regions, TYLC is the main limiting factor in tomato production. The causal agents are a group of geminivirus species belonging to the genus Begomovirus of the family Geminiviridae, all of them named Tomato yellow leaf curl virus (TYLCV) (sensu lato). There has been almost 40 years of research on TYLCV epidemics and intensive research programmes have been conducted to find solutions to the severe problem caused by these viruses. This paper provides an overview of the most outstanding achievements in the research on the TYLCV complex that could lead to more effective control strategies.
Animals↗
Emerging viruses.
An emerging virus is a term applied to a newly discovered virus, one that is increasing in incidence or with the potential to increase in incidence. Many viruses fit into this definition. HIV is the clearest example of a previously unknown virus that has now produced one of the largest pandemics in history. Recent advances have occurred in the identification and understanding of new hantaviruses in the Americas, causing an acute respiratory disease. The possible causal role of human herpesvirus 8 in Kaposi's sarcoma has gained support, whereas that of a newly discovered flavivirus in causing hepatitis has not been confirmed. A major advance has been evidence showing that the bovine spongiform encephalopathy agent is almost certainly the cause of a new variant of Creutzfeldt-Jakob disease. Although new viruses are discovered almost yearly (e.g., Australian bat lyssavirus), other "older" viruses (e.g., dengue) are reemerging, infecting millions of people every year with significant mortality.
Animals↗
Design of microarray probes for virus identification and detection of emerging viruses at the genus level.
BACKGROUND: Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral genomes available in GenBank, and established a virus probe library. The virus probes are used not only to identify known viruses but also for discerning the genera of emerging or uncharacterized ones. RESULTS: Using the microarray approach, the identity of the virus in a test sample is determined by the signals of both genus and species-specific probes. The genera of emerging and uncharacterized viruses are determined based on hybridization of the viral sequences to the conserved probes for the existing viral genera. A detection and classification procedure to determine the identity of a virus directly from detection signals results in the rapid identification of the virus. CONCLUSION: We have demonstrated the validity and feasibility of the above strategy with a small number of viral samples. The probe design algorithm can be applied to any publicly available viral sequence database. The strategy of using separate genus and species probe sets enables the use of a straightforward virus identity calculation directly based on the hybridization signals. Our virus identification strategy has great potential in the diagnosis of viral infections. The virus genus and specific probe database and the associated summary tables are available at http://genestamp.sinica.edu.tw/virus/index.htm.
Animals↗
Molecular epidemiology of infectious bursal disease viruses: distribution and genetic analysis of newly emerging viruses in the United States.
Genetic mutations in the genome of infectious bursal disease virus (IBDV) have resulted in antigenic and pathogenic variants that continue to cause disease in commercially reared chickens. The extent of the genetic diversity among IBDV strains circulating in the United States is unknown. This study was designed to identify newly emerging viruses infecting chickens on poultry farms experiencing immune suppression-related problems. Fifty IBDV-positive samples were identified from 273 bursa samples using a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. Mutation probes were designed to the hydrophilic B coding region of the VP2 gene. Six mutation probes used in this study were based on the nucleotide sequences of the Del-E, Bursine 2, D-78, STC, G6, and T1 IBDV strains. Following real-time RT-PCR, these mutation probes identified 11 of the 50 viruses in the melting temperature (Tm) analysis. The results indicated that the remaining 39 viruses had one or more nucleotide mutations compared with the six mutation probes in this region of the VP2 gene. Thirty-eight viruses were chosen for nucleotide sequence analysis across the hypervariable region of the VP2 gene. Within this group of 38 viruses, four were identified by the mutation probes and their nucleotide sequences confirmed that real-time RT-PCR data. In the remaining 34 viruses, nucleotide mutations were observed in as many as 8 of 23 nucleotides across the hydrophilic B epitope coding region. Furthermore, every amino acid position except one between 316 and 324 had at least one substitution mutation. Phylogenic analysis placed two of the 38 viruses sequenced on branches with classic viruses and the remaining 36 viruses were placed on four distinct branches. Branches 1 and 2 contained a majority of the viruses, which were distributed across most of the major poultry-producing states in the United States. These branches contained previously characterized variant IBDV strains. Viruses in branches 3 and 4 were confined to three states and did not contain any previously characterized IBDV strains.
Animals↗
North American and French caprine arthritis-encephalitis viruses emerge from ovine maedi-visna viruses.
The full extent of genetic diversity among small ruminant lentiviruses (SRLVs), i.e., caprine arthritis encephalitis viruses (CAEVs) and maedi-visna viruses (MVVs), remains unknown. This is due in part to the fact that few sequences of CAEV are available. To contribute to this knowledge, gag, pol, and env nucleotide sequences from an SRLV named CA680 originating from a goat from western France were determined. This analysis revealed that this virus is closely related to the Cork and 63 CAEV American isolates. Mismatched amino acids between the CA680 virus and prototype CAEVs ranged from 6.7, 0. 7, and 17.5% for gag, pol, and SU sequences, respectively. The differences between the CA680 virus and MVV prototypes ranged from 16.5, 12.5, and 32.3% for the protein sequences, respectively. A screening using a heteroduplex mobility assay (HMA) adapted to SRLVs revealed that 6 of 10 caprine virus field isolates were closely related to CA680, indicating that this latter isolate was a prototype of CAEVs common in the west of France. Phylogenetic trees drawn using CA, RT, or SU sequences of numerous SRLVs and rooted with EIAV sequences revealed that CA680 and CAEV prototypes, all infectious for goat, clustered in one group. From these HMA and phylogenetic analyses, it appears that U.S. and French caprine SRLVs form a clade that had emerged from a much more diverse group containing all SRLVs infectious for sheep. These ovine SRLVs form a more ancient group in which the EIAV is rooted.
Amino Acid Sequence↗
The potential impacts of human genetics on virus emergence.
Human monogenic traits can confer resistance to viral infection in exposed individuals or predisposition to severe disease in infected individuals. Enhanced susceptibility can be driven directly by mutations in genes essential for control of the virus or indirectly via the production of autoantibodies against components of host defense. While the impact of viruses on individuals carrying these genotypes permitted their identification and has been amply studied, little is known about the impact of these human genotypes on the natural history of viruses, including not only persisting but also emerging viruses. We envisage several scenarios, including the possibility that genetically susceptible individuals serve as patient zeros, superspreaders, or mutation incubators, or that genetically resistant individuals even permit the selection of new viral mutants. Viruses are continually shared between individuals and even host species, where they can benefit from adaption to new environments. Current human viruses, as well as novel viruses from animal reservoirs, will continue to threaten the human population. Improvements in the scale of human genomic sequencing and analysis will permit testing hypotheses about the impact of human genetics on the origin and trajectory of viral infections, including future pandemics, which may ultimately help to prevent or curtail impending outbreaks.
Humans↗
Influenza--a model of an emerging virus disease.
Influenza A viruses continue to emerge from the aquatic avian reservoir and cause pandemics. Phylogenetic analysis of the nucleotide sequence of all eight influenza A virus RNA segments indicate that all of the influenza viruses in mammalian hosts originate from the avian gene pool. In contrast to the rapid progressive changes in both the nucleotide and amino acid sequences of mammalian virus gene lineages, avian virus genes show far less variation and, in most cases, appear to be in evolutionary stasis. There are periodic exchanges of influenza virus genes or whole viruses between species giving rise to pandemics of diseases in humans, lower animals and birds. The periodic emergence of influenza viruses in mammalian species has been illustrated by the appearance of a new influenza virus in horses in northern China in 1989. Phylogenetic analysis of classical H1N1, avian-like H1N1 and human H3N2 viruses circulating in Italian pigs reveals that genetic reassortment is taking place between avian- and human-like viruses in the European pig population. These studies provide evidence supporting the possibility that pigs serve as a mixing vessel for reassortment between influenza viruses in mammalian and avian hosts and raise the question of whether the next pandemic of influenza will emerge in Europe!
Animals↗
Emerging viruses set to soar.
The emergence rate of novel viruses, such as the coronavirus that sparked SARS, could well be on the rise. Researchers now think that the SARS virus split from group 2 coronaviruses, and that this happened relatively recently on the scale of coronavirus evolution.
Coronaviridae Infections↗
High recombination and mutation rates in mouse hepatitis virus suggest that coronaviruses may be potentially important emerging viruses.
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Alleles↗
Lymphocytic choriomeningitis virus: emerging fetal teratogen.
Lymphocytic choriomeningitis virus (LCMV), a rodent-borne arenavirus, is an often undiagnosed human fetal teratogen. We describe a neonate born with hydrocephalus and chorioretinitis after maternal second-trimester symptomatic LCMV infection. Previously reported affected infants are reviewed. We strongly suggest that obstetricians counsel their pregnant patients regarding the potential hazard that contact with infected pet, laboratory, and household mice and hamsters poses to pregnant women and their unborn children.
Animals↗
Emerging viruses in blood transfusion.
BACKGROUND AND OBJECTIVES: The development of new technologies leads to the discovery of new viruses. For each of these new infectious agents relevance to transfusion needs to be assessed. MATERIALS AND METHODS: The questions to be answered are transmissibility by transfusion, pathogenicity, prevalence in blood donors, persistence and the availability of screening assays. RESULTS: Since 1995, four new viruses have been identified and for three of them extensive studies have been carried out. GBV-C/HGV and TTV were both initially thought to be related to post-transfusion hepatitis but neither were proven to be in any way related to hepatitis and are still in search of a disease. HHV-8 is a major factor in the pathogenesis of Kaposi's sarcoma and other tumours related to immunodeficiency. HHV-8 transmission by organ transplantation but not by transfusion has been demonstrated. SEN-V has been claimed as a potential cause of non-A-E hepatitis but no data has been published. CONCLUSION: To date, none of the emerging viruses have been proven relevant to transfusion.
Blood Donors↗
Viral surveillance beyond detection: JMTV and the need for ensemble approaches in emerging virus discovery.
The recent report by T. Murillo, L. E. Enrique Chaves-González, S. Temmam, S. Bermúdez, et al. (Microbiol Spectr 14:e04078-25, 2026, https://doi.org/10.1128/spectrum.04078-25) expands the known geographic and ecological range of Jingmen tick virus (JMTV) by detecting the virus in Amblyomma mixtum ticks collected from horses in Costa Rica. This is an important finding because A. mixtum can feed on wildlife, domestic animals, and humans, creating a possible interface for virus movement across various hosts. The study also places the Costa Rican virus in a wider phylogenetic context, linking it to JMTV diversity reported from other regions. However, the detection of viral RNA in ticks should not be interpreted as proof of local disease, human infection, or active transmission, especially in the absence of supporting results. Instead, it reflects an important signal for careful viral surveillance. Here, I discuss how JMTV illustrates the need for ensemble approaches that combine field sampling, phylogeny, segment-level genome analysis, serology, experimental validation, and data-driven virus discovery tools.
emerging viruses↗
[Emergent viruses: SARS-associate coronavirus and H5N1 influenza virus].
Two viral agents with RNA genome are responsible for emerging illnesses: influenza virus A/H5N1 and Severe Acute Respiratory Syndrome virus (SARS). For the diagnosis of SARS virus infection, an epidemiological investigation is necessary to know whether the patient has been exposed to a risk in a country where the SARS virus is circulating or whether the patient had worked in a laboratory handling SARS virus. The detection of SARS virus is possible in various clinical samples (including urine) by viral culture or RT-PCR. The handling of those samples and RNA extraction must be performed in a BSL3 laboratory. The SARS virus RT-PCR is poorly sensitive, therefore the test should be performed on samples collected consecutively for several days. In front of a suspicion of A/H5N1, similar procedures are recommended. An epidemiologic investigation is necessary to specify whether the patient stayed in a country where A/H5N1 virus was circulating. Clinical samples needed for a specific diagnosis are: nasopharyngeal, throat-swab or fecal samples, cerebrospinal fluid and blood. The presence of A/H5N1 virus is confirmed by viral isolation or RNA detection by RT-PCR. RNA extraction must be performed in a BSL3 laboratory. For diagnosis of A/H5N1 virus infection, RT-PCR test amplifies specifically a fragment of H5 gene (Hemagglutinin). In french laboratories of medical virology, procedures are ready to diagnose the first case of A/H5N1 virus infection and cases of reemerging SARS virus infection.
Communicable Diseases, Emerging↗
[Development of influenza vaccines against newly emerging A/H5N1 virus].
Emergence of highly virulent influenza A/H5N1 viruses in Hong Kong in 1997 posed a threat of pandemic and brought an urgent need to develop a suitable seed virus for vaccine production. The virulence of the H5N1 viruses to chicken embryos should hamper the efficient production of the vaccine. In addition, potential virulence to humans raised safety issue in manufacturing vaccine. Toward vaccine development, one approach is to use an avirulent avian influenza virus antigenically similar to the virulent ones as a surrogate vaccine strain. The other approach is based on the attenuation of pathogenicity of virulent H5N1 virus by genetic engineering of the hemagglutinin gene and selection of a gene constellation. The reverse genetics technique can make the latter approach possible. Candidate strains suitable for vaccine production could be prepared by using either approach.
Animals↗