Respiratory syncytial virus: a community problem.
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Adult↗
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Results for “virus communities”
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Making sense of the virome in light of evolution and ecology.
Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.
Virome↗
Detection of Venezuelan equine encephalitis virus in rural communities of Southern Florida by exposure of sentinel hamsters.
Venezuelan equine encephalitis (VEE) virus strains were recovered from sentinel hamsters exposed in close proximity to homes in rural South Florida. Sentinel hamster surveillance methods over extended periods offer one effective way of uncovering VEE virus activity in relation to human habitation.
Animals↗
Respiratory syncytial virus and influenza. Practical community surveillance.
Concurrent and sequential outbreaks of infection with respiratory syncytial virus (RSV) and influenza A virus were studied, utilizing a local surveillance system for infectious diseases that involved weekly reports from primary care physicians. The patterns of illness in the community and in hospital admissions were relatively specific for these two viruses, and differed according to whether RSV and influenza A virus occurred together or separately. This surveillance system appeared to be a practical and accurate indicator of the activity of RSV and influenza A virus in the community. Such a system may serve as a valuable means of relatively early detection of the local arrival of these viruses, and recognition of these illness patterns might aid the physician in diagnosis.
Adolescent↗
Co-circulation of two influenza A (H3N2) antigenic variants detected by virus surveillance in individual communities.
From March through June 1977 a total of 31 influenza A (H3N2) viruses were isolated from students with respiratory disease who were seen at the student health service on the Berkeley campus of the University of California, and 32 influenza A (H3N2) viruses were isolated from persons who participated in a city-wide febrile respiratory disease surveillance program in Seattle. The antigenic specificity of the hemagglutinin was determined for each isolate by hemagglutination inhibition testing with sera from ferrets infected with prototype strains A/Victoria/3/75 and A/Texas/1/77. In each of the three months, April, May and June, A/Victoria/3/75-like and A/Texas/1/77-like viruses were identified among isolates from both communities, and the numbers of isolates of the two antigenic variants from patients seen with influenza-like illnesses were similar. The findings emphasize the need to examine multiple isolates even from within single communities to determine the antigenic specificity of current strains of influenza virus.
Adolescent↗
Aspects of infection in isolated communities.
Respiratory viruses are not generally carried by normal subjects and cannot persist in small isolated communities. When infection does occur epidemics are seen and the illness may be more severe than in the outside world. These points are illustrated by reference to studies on the island of Tristan da Cunha and stations of the British Antarctic Survey.
Antarctic Regions↗
Ecology of respiratory virus transmission: a comparison of three communities in West Bengal.
Respiratory virus transmission in children was studied comparatively in three ecologically different low-income communities in West Bengal: an isolated village, a suburban village, and a crowded urban community. Continued use of contaminated pond water for bathing, irrigation of nasal passages, post-defecation washing of the anus, and washing of food vessels was common to all, as was intense crowding of indoor sleeping quarters during cold and wet seasons. Intensity of infection was highest (26%) in the most crowded urban area, the variety of virus types least in the most isolated village. Sources of drinking water differed but seemed unrelated to virus transmission. Toxigenic diphtheria organisms were found in nonspecific skin lesions in children in each area.
Child↗
Virome metatranscriptomic profiling of birch pollen reveals a diverse viral community.
INTRODUCTION: Viruses are increasingly recognized as integral components of plant-associated biological systems. However, their occurrence and diversity in the reproductive tissues of woody plants remain poorly understood. Birch (Betula spp.) produces large quantities of wind-dispersed pollen that can travel over long distances and may harbour viruses or virus-derived nucleic acids originating from the host plant and/or its associated microbiota. METHODS: We investigated the virome of birch pollen collected from trees growing in central and suburban Berlin, Germany. Metatranscriptomic analyses were performed on pooled pollen samples collected in 2020. These analyses were complemented by RT-PCR screening of individually processed pollen samples collected in 2025 from resampled trees. Primer walking was additionally used to recover an extended genome sequence of a pollen-associated birch toti-like virus. RESULTS: Multiple virus-associated contigs were identified in both pooled metatranscriptomic datasets. These included sequences corresponding to the cherry leaf roll virus (CLRV), the birch idaeovirus (BIV) and the birch toti-like virus (BTLV), as well as additional virus-like contigs provisionally assigned to lineages related to the Orthototiviridae, Botourmiaviridae, Endornaviridae, and Chrysoviridae families. RT-PCR analysis of individually processed pollen samples confirmed the continued detection of CLRV, BIV, and BTLV within the Berlin sampling framework. A near-complete genome sequence was recovered from a pollen-derived BTLV isolate from Berlin, showing high amino acid sequence identity to a recently described leaf-derived BTLV isolate from the United States. DISCUSSION: These findings demonstrate that birch pollen harbours a diverse assemblage of plant- and/or microbiome-associated viruses and expand the known tissue distribution and geographic range of BTLV. More broadly, they establish pollen as an underexplored ecological niche for virome research and provide a foundation for future studies on the ecology, transmission dynamics, and epidemiological significance of pollen-associated and pollen-transmitted viruses.
Betula↗
Leukemia and lymphoma: infrequent manifestations of common viral infections? A review.
Horizontally transmitted viruses have been etiologically linked to leukemia and lymphoma in several higher mammals (gibbons, cows, and cats). In the best-studied example, the cat, feline leukemia virus is a common community-acquired virus that infrequently produces cancer. However, the infection and its complications (cancer) are not typical of infectious diseases. Epidemilogically, serologically, and virologically, infections with this type of virus can contradict classic infectious disease dogma. Therefore, previous studies that failed to link characteristics of infectious diseases (epidemiologic, serologic, or virologic) to human cancer must be cautiously interpreted. A link between retroviruses and/or DNA viruses and human lympho-reticular malignancies is hypothesized, and it is suggested that systematized nation-wide studies of selected cancer patients and their contacts be executed with the most sensitive and specific laboratory probes available.
Animals↗
Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.
Microbiomes influence diverse ecosystems, and viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, host identification for these viruses remains challenging due to the limitations in scaling cultivation-based approaches and the uncertain reliability and relative low resolution of in silico predictions - particularly for understudied viral taxa. Towards this, Hi-C proximity ligation uses sequenced, cross-linked virus and host genomic fragments to infer virus-host linkages and has now been applied in at least 10 studies. However, its accuracy remains unknown. Here we assess Hi-C performance in recovering virus-host interactions using synthetic communities (SynComs) composed of four marine bacterial strains and nine phages with known interactions and then apply optimized bioinformatic protocols to natural soil samples. In SynComs, standard Hi-C sample preparations and analyses showed poor normalized contact score performance (26% specificity, 100% sensitivity, incorrect matches up to class level) that could be dramatically improved by Z-score filtering (Z ≥ 0.5, 99% specificity), though at reduced sensitivity (62% down from 100%). Detection limits were established as reproducibility was poor below minimal phage abundances of 105 PFU/mL. Applying optimized bioinformatic protocols to natural soil samples, we compared virus-host linkages inferred from proximity-ligated Hi-C sequencing with predictions generated by in silico homology-based and machine learning-based bioinformatic approaches. Prior to Z-score thresholding, agreement was relatively high at the phylum to family levels (72%), but not at the genus (43%) or species (15%) levels. Z-score thresholding reduced sensitivity (only 34% of predictions were retained), with only modest improvements in congruence with bioinformatic methods (48% or 18% at genus or species levels, respectively). Regardless, this led to 79 genus-level-congruent virus-host linkages and 293 new ones revealed by Hi-C alone, i.e., providing many new virus-host interactions to explore in already well-studied climate-critical soils. Overall, these findings provide empirical benchmarks and methodological guidelines to improve the accuracy and reliability of Hi-C for virus-host linkage studies in complex microbial communities.
Benchmarking↗
Seroepidemiologic study of Epstein-Barr virus infections in a rural community.
The prevalence and titers of antibodies to capsid antigens of Epstein-Barr virus ad to the diffuse and restricted components of the Epstein-Barr virus-induced early antigen complex were determined in 109 families of a semirural community in Louisiana. Titers of antibody to the capsid antigens larger than or equal to 10 were found in 84 percent of children aged two to five years, and the prevalence increased with age to nearly 100 percent. There was a positive but variable correlation of the prevalence of anti-capsid antigen reactivity with low socioeconomic status and crowding. An overrepresentation of high titers of antibody to capsid antigens was present in individuals with a past history of pneumonia and urinary tract infections. The geometric mean titers of antibody to capsid antigens were highest in early childhood, lowest in adolescence and young adulthood, and high in the elderly. Females in all age groups and tonsillectomized children showed a higher geometric mean titer than their male and nontonsillectomized counterparts, respectively. Antibodies to the early antigen complex were found rarely (8.2 percent) and only in sera with relatively high titers of antibody to capsid antigens.
Adolescent↗
Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.
Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.
Antarctica↗
A programme for collaborative influenza surveillance. A report of a working group of the Public Health Laboratory Service.
A surveillance programme is described which is intended to assess the effects of influenza virus infections on communities at large by collating influenza virus isolations and consultations for respiratory infections from general practices with new claims for sickness benefit and deaths from all causes. Particular importance is attached to relating virus isolations to symptomatic respiratory disease seen in practices of known age and sex structure.
Acute Disease↗
Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.
Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.
Wetlands↗
Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.
Microbiomes influence diverse ecosystems, and viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, host identification for these viruses remains challenging due to the limitations in scaling cultivation-based approaches and the uncertain reliability and relative low resolution of in silico predictions - particularly for understudied viral taxa. Towards this, Hi-C proximity ligation uses sequenced, cross-linked virus and host genomic fragments to infer virus-host linkages and has now been applied in at least ten studies. However, its accuracy remains unknown. Here we assess Hi-C performance in recovering virus-host interactions using synthetic communities (SynComs) composed of four marine bacterial strains and nine phages with known interactions and then apply optimized bioinformatic protocols to natural soil samples. In SynComs, standard Hi-C sample preparations and analyses showed poor normalized contact score performance (26% specificity, 100% sensitivity, incorrect matches up to class level) that could be dramatically improved by Z-score filtering (Z ≥ 0.5, 99% specificity), though at reduced sensitivity (62% down from 100%). Detection limits were established as reproducibility was poor below minimal phage abundances of 105 PFU/mL. Applying optimized bioinformatic protocols to natural soil samples, we compared virus-host linkages inferred from proximity-ligated Hi-C sequencing with predictions generated by in silico homology-based and machine learning-based bioinformatic approaches. Prior to Z-score thresholding, agreement was relatively high at the phylum to family levels (72%), but not at the genus (43%) or species (15%) levels. Z-score thresholding reduced sensitivity (only 34% of predictions were retained), with only modest improvements in congruence with bioinformatic methods (48% or 18% at genus or species levels, respectively). Regardless, this led to 79 genus-level-congruent virus-host linkages and 293 new ones revealed by Hi-C alone - i.e., providing many new virus-host interactions to explore in already well-studied climate-critical soils. Overall, these findings provide empirical benchmarks and methodological guidelines to improve the accuracy and reliability of Hi-C for virus-host linkage studies in complex microbial communities.
Genomics↗
Stool viruses in babies in Glasgow. 3. Community studies.
Twenty-seven babies from one deprived housing area in Glasgow were followed-up regularly, for periods varying between 2 months and 11 months (mean 7 months), in a prospective study of the viruses to be found in their stools by electron microscopy. Weekly stool specimens were collected in the home together with a history of the baby's health. Additional stool specimens were obtained, up to a maximum of one per day, during admissions to hospital. Over 500 specimens were obtained at home and another 320 in hospital. A wide variety of viruses (over 200 recognizates) were detected and it has been possible to plot their temporal relation to disease episodes. It became apparent that virus excretion was frequently unaccompanied by evidence of illness and it has not been possible to describe a typical illness syndrome associated with any of the morphological types of virus observed. The results suggest that, in one area of Glasgow at least, patterns of virus excretion in young babies are complex and will need further elucidation before the need for a vaccine to prevent infantile diarrhoea could be defined.
Diarrhea, Infantile↗
In utero sensitization with influenza virus in man.
Following a community-wide epidemic of influenza A/England virus infection, 64 cord blood samples were evaluated for their fetal serum and lymphocyte responses to this virus. Cord sera were tested for HI antibody vs. A/England with and without 2-ME. A fourfold or greater reduction in titer was observed in four, indicating fetal IgM antibody responses. In addition, lymphocyte samples from three of 16 tested showed proliferative responses to influenza A suggesting fetal lymphocyte sensitization with influenza virus. These data suggest that, in some pregnancies, influenza virus is capable of transplacental sensitization of the fetus.
Female↗
Serologic profile of children in a Mexican highland community: prevalence of complement-fixing antibodies to Mycoplasma pneumoniae, respiratory syncytial virus and parainfluenza viruses.
The study investigated the prevalence of antibodies to five leading agents of childhood respiratory disease in the county of Huixquilucan, Mexico. Tests of sera from a random sample of children between 3 months and 18 years of age confirmed serologically the presence of Mycoplasma pneumoniae, respiratory syncytial (RS) virus and parainfluenza 1, 2 and 3 viruses in this relatively isolated highland community. Highest overall antibody frequency of 64.2% was seen for parainfluenza 3, and antibody to this virus was acquired early in life. Antibody to M. pneumoniae was least prevalent among children surveyed; this rate was 15.5% overall. This was only slightly below the prevalence rates for antibodies to RS virus and parainfluenza 1 and 2 viruses, which had intermediate frequency rates of 23%, 32%, and 22.9%, respectively. The relatively low prevalence of antibody to RS virus was unexpected. Differences in prevalence rates in regard to location of residence or family size were insignificant. Statistically significant differences in age-specific antibody prevalence rates in respect to sex were noted only for the 5- to 9-year-old group to M. pneumoniae and to parainfluenza 3.
Adolescent↗