scholarly journals An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses

2021 ◽  
Author(s):  
Sifan Ye ◽  
Congyu Lu ◽  
Ye Qiu ◽  
Heping Zheng ◽  
Xingyi Ge ◽  
...  
Keyword(s):  
Gc Content ◽  
Tissue Tropism ◽  
Virus Species ◽  
Interacting Proteins ◽  
Random Forest Algorithm ◽  
Dna Viruses ◽  
Human Virus ◽  
Age Dependent ◽  
Human Viruses ◽  
Viral Receptors

Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. This study curated an atlas of human viruses from public databases and literatures, and built the Human Virus Database (HVD) available at http://computationalbiology.cn/humanVirusBase/#/. The HVD contains 1,131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue range of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue range of DNA viruses was predicted using a random-forest algorithm with a medium performance. Overall, the study not only provides a valuable resource for further studies of human viruses, but also deepens our understanding towards the diversity and tissue tropism of human viruses.

scholarly journals Human viruses: discovery and emergence

2012 ◽  
Vol 367 (1604) ◽  
pp. 2864-2871 ◽  
Author(s):  
Mark Woolhouse ◽  
Fiona Scott ◽  
Zoe Hudson ◽  
Richard Howey ◽  
Margo Chase-Topping
Keyword(s):  
New Species ◽  
Yellow Fever ◽  
Surveillance System ◽  
Yellow Fever Virus ◽  
Potential Range ◽  
Virus Species ◽  
Foreseeable Future ◽  
Species Barrier ◽  
Human Virus ◽  
Human Viruses

There are 219 virus species that are known to be able to infect humans. The first of these to be discovered was yellow fever virus in 1901, and three to four new species are still being found every year. Extrapolation of the discovery curve suggests that there is still a substantial pool of undiscovered human virus species, although an apparent slow-down in the rate of discovery of species from different families may indicate bounds to the potential range of diversity. More than two-thirds of human viruses can also infect non-human hosts, mainly mammals, and sometimes birds. Many specialist human viruses also have mammalian or avian origins. Indeed, a substantial proportion of mammalian viruses may be capable of crossing the species barrier into humans, although only around half of these are capable of being transmitted by humans and around half again of transmitting well enough to cause major outbreaks. A few possible predictors of species jumps can be identified, including the use of phylogenetically conserved cell receptors. It seems almost inevitable that new human viruses will continue to emerge, mainly from other mammals and birds, for the foreseeable future. For this reason, an effective global surveillance system for novel viruses is needed.

scholarly journals Factors Determining Transmission of Persistent Viruses by Bemisia tabaci and Emergence of New Virus–Vector Relationships

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1808
Author(s):  
Saptarshi Ghosh ◽  
Murad Ghanim
Keyword(s):  
Bemisia Tabaci ◽  
Plant Viruses ◽  
Tomato Yellow Leaf ◽  
Tissue Tropism ◽  
Insect Vectors ◽  
Virus Species ◽  
Yellow Leaf ◽  
Virus Diseases ◽  
Persistent Viruses ◽  
Leaf Curl Virus

Many plant viruses depend on insect vectors for their transmission and dissemination. The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is one of the most important virus vectors, transmitting more than four hundred virus species, the majority belonging to begomoviruses (Geminiviridae), with their ssDNA genomes. Begomoviruses are transmitted by B. tabaci in a persistent, circulative manner, during which the virus breaches barriers in the digestive, hemolymph, and salivary systems, and interacts with insect proteins along the transmission pathway. These interactions and the tissue tropism in the vector body determine the efficiency and specificity of the transmission. This review describes the mechanisms involved in circulative begomovirus transmission by B. tabaci, focusing on the most studied virus in this regard, namely the tomato yellow leaf curl virus (TYLCV) and its closely related isolates. Additionally, the review aims at drawing attention to the recent knowhow of unorthodox virus—B. tabaci interactions. The recent knowledge of whitefly-mediated transmission of two recombinant poleroviruses (Luteoviridae), a virus group with an ssRNA genome and known to be strictly transmitted with aphids, is discussed with its broader context in the emergence of new whitefly-driven virus diseases.

scholarly journals Link of a ubiquitous human coronavirus to dromedary camels

2016 ◽  
Vol 113 (35) ◽  
pp. 9864-9869 ◽  
Author(s):  
Victor M. Corman ◽  
Isabella Eckerle ◽  
Ziad A. Memish ◽  
Anne M. Liljander ◽  
Ronald Dijkman ◽  
...  
Keyword(s):  
Human Infection ◽  
Interferon Response ◽  
Type I ◽  
Respiratory Pathogens ◽  
Airway Epithelial ◽  
Dromedary Camels ◽  
Human Hepatoma Cells ◽  
Human Virus ◽  
Epithelial Cultures ◽  
Human Viruses

The four human coronaviruses (HCoVs) are globally endemic respiratory pathogens. The Middle East respiratory syndrome (MERS) coronavirus (CoV) is an emerging CoV with a known zoonotic source in dromedary camels. Little is known about the origins of endemic HCoVs. Studying these viruses’ evolutionary history could provide important insight into CoV emergence. In tests of MERS-CoV–infected dromedaries, we found viruses related to an HCoV, known as HCoV-229E, in 5.6% of 1,033 animals. Human- and dromedary-derived viruses are each monophyletic, suggesting ecological isolation. One gene of dromedary viruses exists in two versions in camels, full length and deleted, whereas only the deleted version exists in humans. The deletion increased in size over a succession starting from camelid viruses via old human viruses to contemporary human viruses. Live isolates of dromedary 229E viruses were obtained and studied to assess human infection risks. The viruses used the human entry receptor aminopeptidase N and replicated in human hepatoma cells, suggesting a principal ability to cause human infections. However, inefficient replication in several mucosa-derived cell lines and airway epithelial cultures suggested lack of adaptation to the human host. Dromedary viruses were as sensitive to the human type I interferon response as HCoV-229E. Antibodies in human sera neutralized dromedary-derived viruses, suggesting population immunity against dromedary viruses. Although no current epidemic risk seems to emanate from these viruses, evolutionary inference suggests that the endemic human virus HCoV-229E may constitute a descendant of camelid-associated viruses. HCoV-229E evolution provides a scenario for MERS-CoV emergence.

scholarly journals Effect of Geographic Isolation on the Nasal Virome of Indigenous Children

2019 ◽  
Vol 93 (17) ◽  
Author(s):  
Eda Altan ◽  
Juan Carlos Dib ◽  
Andres Rojas Gulloso ◽  
Duamaco Escribano Juandigua ◽  
Xutao Deng ◽  
...  
Keyword(s):  
Young Children ◽  
Viral Infections ◽  
Small Population ◽  
Multiple Infections ◽  
Geographic Isolation ◽  
Human Virus ◽  
Cultural Isolation ◽  
Nasal Swabs ◽  
Nasal Passages ◽  
Human Viruses

ABSTRACT The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses. IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.

scholarly journals Human viruses and viral indicators in marine water at two recreational beaches in Southern California, USA

2013 ◽  
Vol 12 (1) ◽  
pp. 136-150 ◽  
Author(s):  
David C. Love ◽  
Roberto A. Rodriguez ◽  
Christopher D. Gibbons ◽  
John F. Griffith ◽  
Qilu Yu ◽  
...  
Keyword(s):  
Southern California ◽  
Enteric Viruses ◽  
Water Quality Monitoring ◽  
Fecal Coliforms ◽  
Detection Methods ◽  
Potential Health ◽  
Human Virus ◽  
Recreational Beaches ◽  
Viral Indicators ◽  
Human Viruses

Waterborne enteric viruses may pose disease risks to bather health but occurrence of these viruses has been difficult to characterize at recreational beaches. The aim of this study was to evaluate water for human virus occurrence at two Southern California recreational beaches with a history of beach closures. Human enteric viruses (adenovirus and norovirus) and viral indicators (F+ and somatic coliphages) were measured in water samples over a 4-month period from Avalon Beach, Catalina Island (n = 324) and Doheny Beach, Orange County (n = 112). Human viruses were concentrated from 40 L samples and detected by nested reverse transcriptase polymerase chain reaction (PCR). Detection frequencies at Doheny Beach were 25.5% (adenovirus) and 22.3% (norovirus), and at Avalon Beach were 9.3% (adenovirus) and 0.7% (norovirus). Positive associations between adenoviruses and fecal coliforms were observed at Doheny (p = 0.02) and Avalon (p = 0.01) Beaches. Human viruses were present at both beaches at higher frequencies than previously detected in the region, suggesting that the virus detection methods presented here may better measure potential health risks to bathers. These virus recovery, concentration, and molecular detection methods are advancing practices so that analysis of enteric viruses can become more effective and routine for recreational water quality monitoring.

scholarly journals Why genes overlap in viruses

2010 ◽  
Vol 277 (1701) ◽  
pp. 3809-3817 ◽  
Author(s):  
Nicola Chirico ◽  
Alberto Vianelli ◽  
Robert Belshaw
Keyword(s):  
Rna Viruses ◽  
Harmful Effect ◽  
Negative Relationship ◽  
Mutation Rates ◽  
Virus Species ◽  
Overlapping Genes ◽  
Genome Length ◽  
Dna Viruses ◽  
The Relationship ◽  
Gene Overlap

The genomes of most virus species have overlapping genes—two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length.

scholarly journals A multi-task CNN learning model for taxonomic assignment of human viruses

2021 ◽  
Vol 22 (S6) ◽  
Author(s):  
Haoran Ma ◽  
Tin Wee Tan ◽  
Kenneth Hon Kim Ban
Keyword(s):  
Sequence Data ◽  
Learning Model ◽  
Genomic Region ◽  
Taxonomic Assignment ◽  
Viral Pathogens ◽  
Human Virus ◽  
Bayesian Ranking ◽  
Taxonomic Assignments ◽  
Human Viruses ◽  
Hiv 1

Abstract Background Taxonomic assignment is a key step in the identification of human viral pathogens. Current tools for taxonomic assignment from sequencing reads based on alignment or alignment-free k-mer approaches may not perform optimally in cases where the sequences diverge significantly from the reference sequences. Furthermore, many tools may not incorporate the genomic coverage of assigned reads as part of overall likelihood of a correct taxonomic assignment for a sample. Results In this paper, we describe the development of a pipeline that incorporates a multi-task learning model based on convolutional neural network (MT-CNN) and a Bayesian ranking approach to identify and rank the most likely human virus from sequence reads. For taxonomic assignment of reads, the MT-CNN model outperformed Kraken 2, Centrifuge, and Bowtie 2 on reads generated from simulated divergent HIV-1 genomes and was more sensitive in identifying SARS as the closest relation in four RNA sequencing datasets for SARS-CoV-2 virus. For genomic region assignment of assigned reads, the MT-CNN model performed competitively compared with Bowtie 2 and the region assignments were used for estimation of genomic coverage that was incorporated into a naïve Bayesian network together with the proportion of taxonomic assignments to rank the likelihood of candidate human viruses from sequence data. Conclusions We have developed a pipeline that combines a novel MT-CNN model that is able to identify viruses with divergent sequences together with assignment of the genomic region, with a Bayesian approach to ranking of taxonomic assignments by taking into account both the number of assigned reads and genomic coverage. The pipeline is available at GitHub via https://github.com/MaHaoran627/CNN_Virus.

scholarly journals Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

2020 ◽  
Author(s):  
Tao Zuo ◽  
Qin Liu ◽  
Fen Zhang ◽  
Yun Kit Yeoh ◽  
Yating Wan ◽  
...  
Keyword(s):  
Disease Severity ◽  
Rna Virus ◽  
Host Immunity ◽  
Virus Species ◽  
Human Gut ◽  
Dna Virus ◽  
Dna Viruses ◽  
Cell Counts ◽  
Faecal Samples ◽  
Rna And Dna

Abstract Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had faecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Results: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, Pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.Conclusions: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19.

scholarly journals Tissue Tropism and Transmission Ecology Predict Virulence of Human RNA Viruses

2019 ◽  
Author(s):  
Liam Brierley ◽  
Amy B. Pedersen ◽  
Mark E. J. Woolhouse
Keyword(s):  
Public Health ◽  
Machine Learning ◽  
Risk Factors ◽  
Random Forest ◽  
Infectious Diseases ◽  
Rna Viruses ◽  
Rna Virus ◽  
Tissue Tropism ◽  
Virus Species ◽  
Ecological Traits

AbstractNovel infectious diseases continue to emerge within human populations. Predictive studies have begun to identify pathogen traits associated with emergence. However, emerging pathogens vary widely in virulence, a key determinant of their ultimate risk to public health. Here, we use structured literature searches to review the virulence of each of the 214 known human-infective RNA virus species. We then use a machine learning framework to determine whether viral virulence can be predicted by ecological traits including human-to-human transmissibility, transmission routes, tissue tropisms and host range. Using severity of clinical disease as a measurement of virulence, we identified potential risk factors using predictive classification tree and random forest ensemble models. The random forest model predicted literature-assigned disease severity of test data with 90.3% accuracy, compared to a null accuracy of 74.2%. In addition to viral taxonomy, the ability to cause systemic infection, having renal and/or neural tropism, direct contact or respiratory transmission, and limited (0 < R0 ≤ 1) human-to-human transmissibility were the strongest predictors of severe disease. We present a novel, comparative perspective on the virulence of all currently known human RNA virus species. The risk factors identified may provide novel perspectives in understanding the evolution of virulence and elucidating molecular virulence mechanisms. These risk factors could also improve planning and preparedness in public health strategies as part of a predictive framework for novel human infections.Author SummaryNewly emerging infectious diseases present potentially serious threats to global health. Although studies have begun to identify pathogen traits associated with the emergence of new human diseases, these do not address why emerging infections vary in the severity of disease they cause, often termed ‘virulence’. We test whether ecological traits of human viruses can act as predictors of virulence, as suggested by theoretical studies. We conduct the first systematic review of virulence across all currently known human RNA virus species. We adopt a machine learning approach by constructing a random forest, a model that aims to optimally predict an outcome using a specific structure of predictors. Predictions matched literature-assigned ratings for 28 of 31 test set viruses. Our predictive model suggests that higher virulence is associated with infection of multiple organ systems, nervous systems or the renal systems. Higher virulence was also associated with contact-based or airborne transmission, and limited capability to transmit between humans. These risk factors may provide novel starting points for questioning why virulence should evolve and identifying causative mechanisms of virulence. In addition, our work could suggest priority targets for infectious disease surveillance and future public health risk strategies.BlurbComparative analysis using machine learning shows specificity of tissue tropism and transmission biology can act as predictive risk factors for virulence of human RNA viruses.

scholarly journals Temporal Landscape of Human Gut RNA and DNA Viromes in SARS-CoV-2 Infection and Severity

2020 ◽  
Author(s):  
Tao Zuo ◽  
Qin Liu ◽  
Fen Zhang ◽  
Yun Kit Yeoh ◽  
Yating Wan ◽  
...  
Keyword(s):  
Disease Severity ◽  
Rna Virus ◽  
Host Immunity ◽  
Virus Species ◽  
Disease Course ◽  
Human Gut ◽  
Dna Virus ◽  
Dna Viruses ◽  
Faecal Samples ◽  
Rna And Dna

Abstract Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as virome) that play a role in regulating host immunity and pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods:We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All study subjects had faecal specimens sampled at inclusion. Blood specimens were sampled for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serially faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome respectively. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Results: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome dysbiosis persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Human faecal baseline abundance of 10 virus species (1 RNA virus, Pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease severity of COVID-19. These viruses were also inversely associated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.Conclusions: Both enteric RNA and DNA viromes were perturbed in COVID-19, which prolonged even after disease resolution. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age partly explains that older subjects are prone to severe and unfavorable COVID-19 outcomes. Our data altogether highlight the significance of human gut virome in COVID-19 disease course and potentially therapeutics.

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