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2.
J Infect Public Health ; 15(4): 412-424, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1796484

ABSTRACT

Over the past two decades, diabetes mellitus (DM) has been receiving increasing attention among autoimmune diseases. The prevalence of type 1 and type 2 diabetes has increased rapidly and has become one of the leading causes of death worldwide. Therefore, a better understanding of the genetic and environmental risk factors that trigger the onset of DM would help develop more efficient therapeutics and preventive measures. The role and mechanism of respiratory viruses in inducing autoimmunity have been frequently reported. On the other hand, the association of DM with respiratory infections might result in severe complications or even death. Since influenza is the most common respiratory infection, DM patients experience disease severity and increased hospitalization during influenza season. Vaccinating diabetic patients against influenza would significantly reduce hospitalization due to disease severity. However, recent studies also report the role of viral vaccines in inducing autoimmunity, specifically diabetes. This review reports causes of diabetes, including genetic and viral factors, with a special focus on respiratory viruses. We further brief the burden of influenza-associated complications and the effectiveness of the influenza vaccine in DM patients.


Subject(s)
Diabetes Mellitus, Type 2 , Influenza Vaccines , Influenza, Human , Respiratory Tract Infections , Viruses , Hospitalization , Humans , Influenza, Human/complications , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Respiratory Tract Infections/complications , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control
3.
Microbiome ; 10(1): 60, 2022 Apr 12.
Article in English | MEDLINE | ID: covidwho-1789144

ABSTRACT

BACKGROUND: Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. RESULTS: Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident). CONCLUSIONS: The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.


Subject(s)
RNA Viruses , Viruses , Animals , Animals, Wild , Birds , Cloaca , Phylogeny , RNA Viruses/genetics , Virome/genetics , Viruses/genetics
4.
BMJ ; 377: o976, 2022 Apr 13.
Article in English | MEDLINE | ID: covidwho-1788946
5.
J Appl Microbiol ; 132(4): 2625-2632, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1788869

ABSTRACT

AIMS: Viral pathogens are the primary agents in bovine respiratory disease cases, and there is no direct effective antiviral drug application. Thymbra is a genus of oregano commonly found in Turkey. The primary component (34.9%) of the extract obtained from Thymbra spicata L. is the carvacrol which is used in traditional medicine. This study evaluates the potential antiviral activity and inactivation efficiency of T. spicata L. extract against bovine respiratory viruses, including BCoV, BPIV-3, BRSV, BVDV and BoHV-1. METHODS AND RESULTS: To evaluate its effect on viral replication, viral titres were taken from infected cells treated with non-cytotoxic T. spicata L. extract concentrations (0.75% and 1.5%, 1.32 and 2.64 µg/ml of carvacrol as active ingredient, respectively) and compared to non-treated infected cells. The viruses were treated directly with 1.5% T. spicata L. extract, and the viral titres were evaluated at certain time points to determine the efficiency of direct inactivation. The number of infectious virions for BCoV, BPIV-3, BRSV, BVDV and BoHV-1 treated with 1.5% T. spicata L. extract were decreased by 99.44%, 100.0%, 94.38%, 99.97% and 99.87%, respectively.T. spicata L. extract strongly inhibits the replication of mentioned viruses in a dose-dependent manner in vitro. In addition, T. spicata L. extract shared direct inactivation efficiency on the mentioned viruses in a time-dependent manner. CONCLUSION: This study shows the antiviral efficiency of T. spicata L. on BRD-related viral agents for the first time. The oregano species T. spicata and its main component, carvacrol, may have a potential for antiviral activity in the alternative treatment of respiratory viral diseases in cattle. SIGNIFICANCE AND IMPACT OF THE STUDY: Given the similarity of replication strategies, obtained data suggest the possible efficiency of T. spicata L. on human respiratory viruses.


Subject(s)
Cattle Diseases , Lamiaceae , Viruses , Animals , Antiviral Agents/pharmacology , Cattle , Plant Extracts/pharmacology
7.
Adv Exp Med Biol ; 1366: 137-153, 2022.
Article in English | MEDLINE | ID: covidwho-1782744

ABSTRACT

With the increasing global human population, travel, and socioeconomic activities, more and more novel pathogenic viruses will emerge or re-emerge. While more than 260 viruses are known to infect humans, only a small minority of these viral diseases are treatable by clinically approved antiviral drugs. Apart from these identified viruses, new emerging viruses and drug-resistant viruses are also important challenges to our public health and healthcare systems. The COVID-19 and influenza pandemics remind us the importance of getting broad-spectrum antivirals against emerging and re-emerging respiratory viruses. Broad-spectrum antivirals against different viral families for fighting the currently known viruses and novel emerging viruses are urgently needed. Viral entry is the universal first step for viral infection, and therefore is a promising target for identifying broad-spectrum antivirals. In this chapter, we mainly focus on discussing the risks of respiratory viruses, the challenge of finding broad-spectrum antivirals, the entry processes of respiratory viruses, the current studies on broad-spectrum entry inhibitors for respiratory viruses, and the directions for discovering broad-spectrum antivirals in the future.


Subject(s)
COVID-19 , Virus Diseases , Viruses , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Humans , Virus Diseases/drug therapy , Virus Internalization
8.
Sci Rep ; 12(1): 5869, 2022 Apr 07.
Article in English | MEDLINE | ID: covidwho-1778639

ABSTRACT

The ongoing COVID-19 global pandemic has necessitated evaluating various disinfection technologies for reducing viral transmission in public settings. Ultraviolet (UV) radiation can inactivate pathogens and viruses but more insight is needed into the performance of different UV wavelengths and their applications. We observed greater than a 3-log reduction of SARS-CoV-2 infectivity with a dose of 12.5 mJ/cm2 of 254 nm UV light when the viruses were suspended in PBS, while a dose of 25 mJ/cm2 was necessary to achieve a similar reduction when they were in an EMEM culture medium containing 2%(v/v) FBS, highlighting the critical effect of media in which the virus is suspended, given that SARS-CoV-2 is always aerosolized when airborne or deposited on a surface. It was found that SARS-CoV-2 susceptibility (a measure of the effectiveness of the UV light) in a buffer such as PBS was 4.4-fold greater than that in a cell culture medium. Furthermore, we discovered the attenuation of UVC disinfection by amino acids, vitamins, and niacinamide, highlighting the importance of determining UVC dosages under a condition close to aerosols that wrap the viruses. We developed a disinfection model to determine the effect of the environment on UVC effectiveness with three different wavelengths, 222 nm, 254 nm, and 265 nm. An inverse correlation between the liquid absorbance and the viral susceptibility was observed. We found that 222 nm light was most effective at reducing viral infectivity in low absorbing liquids such as PBS, whereas 265 nm light was most effective in high absorbing liquids such as cell culture medium. Viral susceptibility was further decreased in N95 masks with 222 nm light being the most effective. The safety of 222 nm was also studied. We detected changes to the mechanical properties of the stratum corneum of human skins when the 222 nm accumulative exposure exceeded 50 J/cm2.The findings highlight the need to evaluate each UV for a given application, as well as limiting the dose to the lowest dose necessary to avoid unnecessary exposure to the public.


Subject(s)
COVID-19 , Viruses , COVID-19/prevention & control , Disinfection , Humans , SARS-CoV-2 , Ultraviolet Rays , Virus Inactivation/radiation effects
9.
Nature ; 604(7904): 21, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1766964
10.
Crit Rev Immunol ; 41(5): 19-35, 2021.
Article in English | MEDLINE | ID: covidwho-1775506

ABSTRACT

Mucosal associated invariant T (MAIT) cells were first identified as specific for bacterial, mycobacterial, and fungal organisms, which detect microbially-derived biosynthetic ligands presented by MHC-related protein 1 (MR1). More recently two unexpected, additional roles have been identified for these ancient and abundant cells: a TCR-depen-dent role in tissue repair and a TCR-independent role in antiviral host defence. Data from several classes of viral disease shows their capability for activation by the cytokines interleukin (IL)-12, IL-15, IL-18, and type I interferon. MAIT cells are abundant at mucosal surfaces, particularly in the lung, and it seems likely a primary reason for their striking evolutionary conservation is an important role in early innate defence against respiratory infections, including both bacteria and viruses. Here we review evidence for their TCR-independent activation, observational human data for their activation in influenza A virus, and in vivo murine evidence of their protection against severe influenza A infection, mediated at least partially via IFN-gamma. We then survey evidence emerging from other respiratory viral infections including recent evidence for an important adjuvant role in adenovirus infection, specifically chimpanzee adenoviruses used in recent coronavirus vaccines, and data for strong associations between MAIT cell responses and adverse outcomes from coronavirus-19 (COVID-19) disease. We speculate on potential translational implications of these findings, either using corticosteroids or inhibitory ligands to suppress deleterious MAIT cell responses, or the potential utility of stimulatory MR1 ligands to boost MAIT cell frequencies to enhance innate viral defences.


Subject(s)
COVID-19 , Mucosal-Associated Invariant T Cells , Virus Diseases , Viruses , Animals , Humans , Lymphocyte Activation , Mice
11.
Nat Microbiol ; 7(4): 486-496, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1773980

ABSTRACT

Lessons learnt from the COVID-19 pandemic include increased awareness of the potential for zoonoses and emerging infectious diseases that can adversely affect human health. Although emergent viruses are currently in the spotlight, we must not forget the ongoing toll of morbidity and mortality owing to antimicrobial resistance in bacterial pathogens and to vector-borne, foodborne and waterborne diseases. Population growth, planetary change, international travel and medical tourism all contribute to the increasing frequency of infectious disease outbreaks. Surveillance is therefore of crucial importance, but the diversity of microbial pathogens, coupled with resource-intensive methods, compromises our ability to scale-up such efforts. Innovative technologies that are both easy to use and able to simultaneously identify diverse microorganisms (viral, bacterial or fungal) with precision are necessary to enable informed public health decisions. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.


Subject(s)
COVID-19 , Viruses , Animals , Humans , Metagenomics/methods , Pandemics , Viruses/genetics , Zoonoses
12.
Chin Med J (Engl) ; 134(13): 1522-1534, 2021 Mar 01.
Article in English | MEDLINE | ID: covidwho-1769417

ABSTRACT

ABSTRACT: Respiratory viruses are major human pathogens that cause approximately 200 million pneumonia cases annually and induce various comorbidities with chronic obstructive pulmonary disease (COPD), resulting in significant health concerns and economic burdens. Clinical manifestations in respiratory viral infections and inflammations vary from asymptomatic, mild, to severe, depending on host immune cell responses to pathogens and interactions with airway epithelia. We critically review the activation, effector, and regulation of T cells in respiratory virus infections and chronic inflammations associated with COPD. Crosstalk among T cells, innate immune cells, and airway epithelial cells is discussed as essential parts of pathogenesis and protection in viral infections and COPD. We emphasize the specificity of peptide antigens and the functional heterogeneity of conventional CD4+ and CD8+ T cells to shed some light on potential cellular and molecular candidates for the future development of therapeutics and intervention against respiratory viral infections and inflammations.


Subject(s)
Pneumonia , Pulmonary Disease, Chronic Obstructive , Respiratory Tract Infections , Virus Diseases , Viruses , CD8-Positive T-Lymphocytes , Humans
13.
Arch Argent Pediatr ; 120(2): 99-105, 2022 04.
Article in English, Spanish | MEDLINE | ID: covidwho-1766098

ABSTRACT

INTRODUCTION: Respiratory viruses are the main cause of acute lower respiratory tract infection (ALRTI) in the pediatric population. In March 2020, the World Health Organization declared that the new coronavirus disease 2019 (COVID-19) had reached the pandemic status. Our objective was to describe the impact of COVID-19 pandemic on hospitalizations due to ALRTI at Hospital de Niños Ricardo Gutiérrez (HNRG) and virus circulation. METHODS: Observational, retrospective, and descriptive study of patients hospitalized due to ALRTI comparing 2019 and 2020. RESULTS: In 2020, the rate of hospitalization due to ALRTI decreased by 73%. In 2019, 517 patients with ALRTI were hospitalized; the following viruses were identified in 174: respiratory syncytial virus (RSV) (71.2%), adenovirus (AV) (10.3%), parainfluenza virus (PIV) (9.7%), and influenza virus (FLU) (8.6%). In 2020, 94 patients with ALRTI were hospitalized. Until epidemiological week (EW) 13, cases of ALRTI due to PIV and AV were recorded; in EW 29, there was 1 case of bronchiolitis due to AV and rhinovirus (RV), followed by isolated cases of RV; no ALRTI due to RSV or FLU was recorded. In total, 9 cases of ALRTI due to COVID-19 were recorded: 2 moderate bronchiolitis and 7 focal pneumonia; 1 adolescent with comorbidities died due to COVID-19 pneumonia. In 2020, patients were older and had more comorbidities and prior hospitalizations compared to 2019. Focal pneumonia prevailed. CONCLUSIONS: In 2020, the rate of hospitalization due to ALRTI decreased significantly compared to 2019, with the absence of seasonal respiratory virus circulation in the pediatric population.


Introducción. Los virus respiratorios son la principal causa de infección respiratoria aguda baja (IRAB) en la población pediátrica. En marzo de 2020, la Organización Mundial de la Salud declaró el estado de pandemia de la enfermedad por el nuevo coronavirus 2019 (COVID-19) con un impacto global elevado. El objetivo de este estudio fue describir el impacto de la pandemia de COVID-19 en las internaciones por IRAB en el Hospital de Niños Ricardo Gutiérrez (HNRG) y la circulación viral. Métodos. Estudio observacional, retrospectivo y descriptivo de pacientes internados por IRAB, comparando los años 2019 y 2020. Resultados. En 2020, la tasa de hospitalización por IRAB se redujo un 73 % en el HNRG (575,1/10 000 en 2019 y 155,3/10 000 en 2020). En 2019 se internaron 517 pacientes con IRAB; en 174 se identificaron los virus: sincicial respiratorio (71,2%), adenovirus (AV) (10,3%), parainfluenza (PIF) (9,7 %) e influenza (FLU) (8,6 %). En 2020, se hospitalizaron 94 pacientes con IRAB. Hasta la semana epidemiológica (SE) 13 se registraron casos de IRAB por PIF y AV; en la SE 29 un caso de bronquiolitis por AV y rinovirus (RV), seguido de casos aislados de RV; no hubo IRAB por VSR ni por FLU. Se registraron 9 casos de IRAB por COVID-19: 2 bronquiolitis moderadas y 7 neumonías focales; con un adolescente fallecido por neumonía por COVID-19 con comorbilidades. En 2020, los casos presentaron mayor edad, más comorbilidades e internaciones previas en comparación con el 2019. La neumonía focal fue la presentación clínica predominante. Conclusión. En 2020, la tasa de hospitalización por IRAB se redujo significativamente en comparación con el año anterior, con ausencia de circulación de virus respiratorios estacionales en la población asistida en nuestro centro.


Subject(s)
COVID-19 , Viruses , Adolescent , COVID-19/epidemiology , Child , Hospitals, Pediatric , Humans , Pandemics , Retrospective Studies
14.
Viruses ; 14(3)2022 03 14.
Article in English | MEDLINE | ID: covidwho-1765953

ABSTRACT

Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.


Subject(s)
Hepatitis C, Chronic , Viruses , Animals , Antiviral Agents , High-Throughput Nucleotide Sequencing , Pandemics
15.
Viruses ; 14(3)2022 03 14.
Article in English | MEDLINE | ID: covidwho-1763118

ABSTRACT

Metabolic reprogramming is a hallmark of cancer and has proven to be critical in viral infections. Metabolic reprogramming provides the cell with energy and biomass for large-scale biosynthesis. Based on studies of the cellular changes that contribute to metabolic reprogramming, seven main hallmarks can be identified: (1) increased glycolysis and lactic acid, (2) increased glutaminolysis, (3) increased pentose phosphate pathway, (4) mitochondrial changes, (5) increased lipid metabolism, (6) changes in amino acid metabolism, and (7) changes in other biosynthetic and bioenergetic pathways. Viruses depend on metabolic reprogramming to increase biomass to fuel viral genome replication and production of new virions. Viruses take advantage of the non-metabolic effects of metabolic reprogramming, creating an anti-apoptotic environment and evading the immune system. Other non-metabolic effects can negatively affect cellular function. Understanding the role metabolic reprogramming plays in viral pathogenesis may provide better therapeutic targets for antivirals.


Subject(s)
Neoplasms , Viruses , Energy Metabolism , Glycolysis , Humans , Mitochondria/metabolism , Neoplasms/metabolism , Virus Replication , Viruses/genetics
17.
PLoS One ; 17(3): e0262373, 2022.
Article in English | MEDLINE | ID: covidwho-1753184

ABSTRACT

Human genetics has been proposed to play an essential role in inter-individual differences in respiratory virus infection occurrence and outcomes. To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and severity studies of respiratory viruses scattered over literatures in PubMed. At present, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. Users can access the records by quick searching, batch searching, advanced searching and browsing. Reference information, infection status, population information, mutation information and disease relationship are provided for each record, as well as hyperlinks to public databases in convenient of users accessing more information. In addition, a visual overview of the topological network relationship between respiratory viruses and associated genes is provided. Therefore, dbGSRV offers a convenient resource for researchers to browse and retrieve genetic associations with respiratory viruses, which may inspire future studies and provide new insights in our understanding and treatment of respiratory virus infection. Database URL: http://www.ehbio.com/dbGSRV/front/.


Subject(s)
Virus Diseases , Viruses , Databases, Factual , Databases, Genetic , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Virus Diseases/genetics , Viruses/genetics
18.
PLoS Genet ; 18(2): e1010030, 2022 02.
Article in English | MEDLINE | ID: covidwho-1753176

ABSTRACT

Viruses are highly evolvable, but what traits endow this property? The high mutation rates of viruses certainly play a role, but factors that act above the genetic code, like protein thermostability, are also expected to contribute. We studied how the thermostability of a model virus, bacteriophage λ, affects its ability to evolve to use a new receptor, a key evolutionary transition that can cause host-range evolution. Using directed evolution and synthetic biology techniques we generated a library of host-recognition protein variants with altered stabilities and then tested their capacity to evolve to use a new receptor. Variants fell within three stability classes: stable, unstable, and catastrophically unstable. The most evolvable were the two unstable variants, whereas seven of eight stable variants were significantly less evolvable, and the two catastrophically unstable variants could not grow. The slowly evolving stable variants were delayed because they required an additional destabilizing mutation. These results are particularly noteworthy because they contradict a widely supported contention that thermostabilizing mutations enhance evolvability of proteins by increasing mutational robustness. Our work suggests that the relationship between thermostability and evolvability is more complex than previously thought, provides evidence for a new molecular model of host-range expansion evolution, and identifies instability as a potential predictor of viral host-range evolution.


Subject(s)
Viral Proteins , Viruses , Host Specificity , Mutation , Phenotype , Viral Proteins/genetics
19.
STAR Protoc ; 3(2): 101188, 2022 06 17.
Article in English | MEDLINE | ID: covidwho-1747493

ABSTRACT

Transmission via fomites poses a major dissemination route for many human pathogens, particularly because of transfer via fingertips. Here, we present a protocol to investigate direct transfer of infectious agents from fomites to humans via naked fingertips. The protocol is suitable for pathogens requiring highest biosafety levels (e.g., SARS-CoV-2). We used an artificial skin to touch a defined volume of virus suspension and subsequent quantification of infectious entities allows quantitative measurement of transfer efficiency and risk assessment. For complete information on the generation and use of this manuscript, please refer to Todt et al. (2021).


Subject(s)
COVID-19 , Viruses , Fomites , Humans , SARS-CoV-2 , Touch
20.
Sci Rep ; 12(1): 4517, 2022 03 16.
Article in English | MEDLINE | ID: covidwho-1747180

ABSTRACT

This study aimed to qualitatively and quantitatively assess the prevalence of the most common respiratory and gastrointestinal viruses in the air, surface swab, and influent/effluent samples collected in wastewater treatment plants (WWTPs). Application of qPCR/RT-qPCR (quantitative polymerase chain reaction/reverse-transcription quantitative polymerase chain reaction) assays combined with PMA (propidium monoazide) dye pretreatment allowed detecting the potentially infectious and disintegrated viral particles in collected samples. In the air at workplaces in WWTPs, the most frequent isolation with the highest concentrations (reaching up to 103 gc/m3 of potentially infectious intact viral particles) were observed in case of adenoviruses (AdVs) and rotaviruses (RoVs), followed by noroviruses (NoVs). Viruses were significantly more often detected in the air samples collected with Coriolis µ impinger, than with MAS-100NT impactor. The temperature negatively (Spearman correlation: -1 < R < 0; p < 0.05), while RH (relative humidity) positively (0 < R < 1; p < 0.05) affected airborne concentrations of potentially infectious viral particles. In turn, the predominant viruses on studied surfaces were RoVs and noroviruses GII (NoV GII) with concentrations of potentially infectious virions up to 104 gc/100 cm2. In the cases of SARS-CoV-2 and presumptive SARS-CoV-2 or other coronaviruses, their concentrations reached up to 103 gc/100 cm2. The contamination level of steel surfaces in WWTPs was similar to this on plastic ones. This study revealed that the qualitative and quantitative characteristics of respiratory and gastrointestinal viruses at workplaces in WWTPs is important for proper exposure assessment and needs to be included in risk management in occupational environment with high abundance of microbial pollutants derived from wastewater.


Subject(s)
COVID-19 , Viruses , Water Purification , Humans , SARS-CoV-2 , Viruses/genetics , Workplace
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