ABSTRACT
Older people are more prone to viral infections, and often have worse outcomes. This was well demonstrated during the COVID-19 pandemic, where a disproportionate number of deaths occurred in the oldest and frailest people. The assessment of the older person with a viral infection is complicated by the high prevalence of multiple comorbidities and sensory or cognitive impairment. They often present with common geriatric syndromes such as falls or delirium, rather than the more typical features of a viral illness in younger people. Comprehensive geriatric assessment by a specialist multidisciplinary team is the gold standard of management, as viral illness is unlikely to present in isolation of other healthcare needs. We discuss the presentation, diagnosis, prevention, and management of common viral infections-respiratory syncytial virus, coronavirus, norovirus, influenza, hepatitis, herpes, and dengue viruses-with special consideration of infections in the older patient.
Subject(s)
COVID-19 , Influenza, Human , Respiratory Syncytial Virus, Human , Virus Diseases , Humans , Aged , Pandemics , COVID-19/epidemiology , Virus Diseases/epidemiology , Influenza, Human/epidemiologyABSTRACT
INTRODUCTION: Childcare centre is considered a high-risk setting for transmission of respiratory viruses. Further evidence is needed to understand the risk of transmission in childcare centres. To this end, we established the DISeases TrANsmission in ChildcarE (DISTANCE) study to understand the interaction among contact patterns, detection of respiratory viruses from environment samples and transmission of viral infections in childcare centres. METHODS AND ANALYSIS: The DISTANCE study is a prospective cohort study in multiple childcare centres of Jiangsu Province, China. Study subjects will be childcare attendees and teaching staff of different grades. A range of information will be collected from the study subjects and participating childcare centres, including attendance, contact behaviours (collected by onsite observers), respiratory viral infection (weekly respiratory throat swabs tested by multiplex PCR), presence of respiratory viruses on touch surfaces of childcare centres and weekly follow-up survey on respiratory symptoms and healthcare seeking among subjects tested positive for any respiratory viruses. Detection patterns of respiratory viruses from study subjects and environment samples, contact patterns, and transmission risk will be analysed by developing statistical and mathematical models as appropriate. The study has been initiated in September 2022 in 1 childcare centre in Wuxi City, with a total of 104 children and 12 teaching staff included in the cohort; data collection and follow-up is ongoing. One more childcare centre in Nanjing City (anticipated to include 100 children and 10 teaching staff) will start recruitment in 2023. ETHICS AND DISSEMINATION: The study has received ethics approval from Nanjing Medical University Ethics Committee (No. 2022-936) and ethics approval from Wuxi Center for Disease Control and Prevention Ethics Committee (No. 2022-011). We plan to disseminate the study findings mainly through publications in peer-reviewed journals and presentations in academic conferences. Aggregated research data will be shared freely to researchers.
Subject(s)
Virus Diseases , Viruses , Child , Humans , Child Care , Prospective Studies , Virus Diseases/diagnosis , Virus Diseases/epidemiology , Child Day Care Centers , Multicenter Studies as TopicABSTRACT
Viral skin infections are some of the most common skin diseases in medical dermatology [...].
Subject(s)
Dermatology , Virus Diseases , Humans , Virus Diseases/epidemiologyABSTRACT
OBJECTIVE OF THE WORK: The article reviews the main problems of the epidemiology of infectious diseases in Poland in 2020. It summarizes relevant findings from the national infectious disease surveillance system. MATERIAL AND METHODS: The data contained in this article come from the reports collected by the State Sanitary Inspection on cases of notifiable infectious diseases notified by clinicians and/or laboratories. These are supplemented by mortality data published by the Statistics Poland. RESULTS AND THEIR DISCUSSION: The epidemiology of infectious diseases was highly impacted by the COVID-19 pandemic. There were 1,306,983 cases notified in 2020 and 41,451 deaths attributed to COVID-19 (according to Statistics Poland). The reported incidence of other infections decreased by 10-98%. We noted especially high decreases in the incidence of viral gastrointestinal infections (by over 70%). The incidence of influenza and influenza-like infections decreased by 34% and tuberculosis by 36% as compared to 2019. However, important decreases were also noted for other diseases under surveillance, which could point to disruption of diagnosis services and reporting due to lockdowns and high workload on the public health services.
Subject(s)
COVID-19 , Communicable Diseases , Influenza, Human , Virus Diseases , Humans , Infant , Influenza, Human/epidemiology , Poland/epidemiology , Pandemics , COVID-19/epidemiology , Communicable Disease Control , Communicable Diseases/epidemiology , Virus Diseases/epidemiology , Incidence , Age Distribution , Disease Outbreaks , Registries , Urban PopulationABSTRACT
BACKGROUND: Acute lower respiratory tract infections (ALRIs) are one one of the leading causes of morbidity and mortality among people of all ages worldwide, particularly in low- and middle-income countries (LMICs). The purpose of this study was to determine epidemiological characteristics of respiratory viruses in acute respiratory infection (ARI) patients during the COVID-19 pandemic in Yaoundé, Cameroon. METHODS: Patients were monitored for respiratory symptoms as part of the surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viral infections. Patients of all ages with respiratory symptoms less than 5 days were considered. Sociodemographic and clinical data as well as nasopharyngeal samples was collected from patients. Nasopharyngeal samples were tested for SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) using real-time reverse-transcription polymerase chain reaction methods. Virus distribution and demographic data were analyzed with R version 2.15.1. RESULTS: From July 2020 to October 2021, 1120 patients were included. The overall viral detection rate was 32.5%, including 9.5% for RSV, 12.6% for influenza virus and 12.8% for SARS-CoV-2. Co-infections were detected in 6.9% of positive cases. While RSV and influenza virus showed seasonal trends, SARS-CoV-2 was detected throughout the study period. CONCLUSION: We found that during COVID-19 pandemic, respiratory viruses play an important role in etiology of influenza-like illness in Cameroon, and this observation was true for patients of all ages.
Subject(s)
COVID-19 , Coinfection , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Virus Diseases , Viruses , Humans , Infant, Newborn , COVID-19/epidemiology , Respiratory Syncytial Virus, Human/genetics , Influenza, Human/epidemiology , Pandemics , Coinfection/epidemiology , Cameroon/epidemiology , SARS-CoV-2 , Virus Diseases/epidemiology , Respiratory Tract Infections/epidemiology , Respiratory Syncytial Virus Infections/epidemiologyABSTRACT
Zoonoses are diseases and infections naturally transmitted between humans and vertebrate animals. Over the years, zoonoses have become increasingly significant threats to global health. They form the dominant group of diseases among the emerging infectious diseases (EID) and currently account for 73% of EID. Approximately 25% of zoonoses originate in domestic animals. The etiological agents of zoonoses include different pathogens, with viruses accounting for approximately 30% of all zoonotic infections. Zoonotic diseases can be transmitted directly or indirectly, by contact, via aerosols, through a vector, or vertically in utero. Zoonotic diseases are found in every continent except Antarctica. Numerous factors associated with the pathogen, human activities, and the environment play significant roles in the transmission and emergence of zoonotic diseases. Effective response and control of zoonotic diseases call for multiple-sector involvement and collaboration according to the One Health concept.
Subject(s)
Communicable Diseases, Emerging , Virus Diseases , Animals , Humans , Animals, Domestic , Disease Reservoirs/veterinary , Zoonoses , Communicable Diseases, Emerging/epidemiology , Communicable Diseases, Emerging/prevention & control , Communicable Diseases, Emerging/veterinary , Virus Diseases/epidemiology , Virus Diseases/veterinaryABSTRACT
Autoimmune diseases (AIDs) are the consequence of a breach in immune tolerance, leading to the inability to sufficiently differentiate between self and non-self. Immune reactions that are targeted towards self-antigens can ultimately lead to the destruction of the host's cells and the development of autoimmune diseases. Although autoimmune disorders are comparatively rare, the worldwide incidence and prevalence is increasing, and they have major adverse implications for mortality and morbidity. Genetic and environmental factors are thought to be the major factors contributing to the development of autoimmunity. Viral infections are one of the environmental triggers that can lead to autoimmunity. Current research suggests that several mechanisms, such as molecular mimicry, epitope spreading, and bystander activation, can cause viral-induced autoimmunity. Here we describe the latest insights into the pathomechanisms of viral-induced autoimmune diseases and discuss recent findings on COVID-19 infections and the development of AIDs.
Subject(s)
Autoimmune Diseases , COVID-19 , Virus Diseases , Humans , COVID-19/complications , Autoimmune Diseases/epidemiology , Autoimmune Diseases/genetics , Virus Diseases/complications , Virus Diseases/epidemiology , Autoimmunity , AutoantigensABSTRACT
The threat of respiratory virus infection to human health and well-being has been clearly highlighted by the coronavirus disease 2019 (COVID-19) pandemic. For people with cystic fibrosis (CF), the clinical significance of viral infections long predated the emergence of severe acute respiratory syndrome coronavirus 2. This article reviews the epidemiology, diagnosis, and treatment of respiratory virus infection in the context of CF as well as the current understanding of interactions between viruses and other microorganisms in the CF lung. The incidence of respiratory virus infection in CF varies by age with young children typically experiencing more frequent episodes than adolescents and adults. At all ages, respiratory viruses are very common in CF and are associated with pulmonary exacerbations. Respiratory viruses are identified at up to 69% of exacerbations, while viruses are also frequently detected during clinical stability. The full impact of COVID-19 in CF is yet to be established. Early studies found that rates of COVID-19 were lower in CF cohorts than in the general population. The reasons for this are unclear but may be related to the effects of shielding, infection control practices, maintenance CF therapies, or the inflammatory milieu in the CF lung. Observational studies have consistently identified that prior solid organ transplantation is a key risk factor for poor outcomes from COVID-19 in CF. Several key priorities for future research are highlighted. First, the impact of highly effective CFTR modulator therapy on the epidemiology and pathophysiology of viral infections in CF requires investigation. Second, the impact of respiratory viruses on the development and dynamics of the CF lung microbiota is poorly understood and viral infection may have important interactions with bacteria and fungi in the airway. Finally, bacteriophages represent a key focus of future investigation both for their role in transmission of antimicrobial resistance and as a promising treatment modality for multiresistant pathogens.
Subject(s)
COVID-19 , Cystic Fibrosis , Virus Diseases , Viruses , Child , Adult , Humans , Child, Preschool , Adolescent , Cystic Fibrosis/therapy , Cystic Fibrosis/drug therapy , COVID-19/complications , Virus Diseases/epidemiology , LungABSTRACT
BACKGROUND: Respiratory disease is a major cause of morbidity and mortality; however, surveillance for circulating respiratory viruses is passive and biased. Wastewater-based epidemiology has been used to understand SARS-CoV-2, influenza A, and respiratory syncytial virus (RSV) infection rates at a community level but has not been used to investigate other respiratory viruses. We aimed to use wastewater-based epidemiology to understand community viral respiratory infection occurrence. METHODS: A retrospective wastewater-based epidemiology surveillance study was carried out at a large wastewater treatment plant located in California, USA. Using droplet digital RT-PCR, we measured RNA concentrations of influenza A and influenza B viruses, RSV A and RSV B, parainfluenza (1-4) viruses, rhinovirus, seasonal coronaviruses, and metapneumovirus in wastewater solids three times per week for 17 months (216 samples) between Feb 1, 2021, and June 21, 2022. Novel probe-based RT-PCR assays for non-influenza viral targets were developed and validated. We compared viral RNA concentrations to positivity rates for viral infections from clinical specimens submitted to California Sentinel Clinical Laboratories (sentinel laboratories) to assess concordance between the two datasets. FINDINGS: We detected RNA from all tested viruses in wastewater solids. Human rhinovirus (median concentration 4300 [0-9500] copies per gram dry weight) and seasonal human coronaviruses (35 000 [17 000-56 000]) were found at the highest concentrations. Concentrations of viral RNA correlated significantly and positively with positivity rates of associated viral diseases from sentinel laboratories (tau 0·32-0·57, p<0·0009); the only exceptions were influenza B and RSV A, which were rarely detected in wastewater solids. Measurements from wastewater indicated coronavirus OC43 dominated the seasonal human coronavirus infections whereas parainfluenza 3 dominated among parainfluenza infections during the study period. Concentrations of all tested viral RNA decreased noticeably after the omicron BA.1 surge suggesting a connection between changes in human behaviour during the surge and transmission of all respiratory viruses. INTERPRETATION: Wastewater-based epidemiology can be used to obtain information on circulation of respiratory viruses at a localised, community level without the need to test many individuals because a single sample of wastewater represents the entire contributing community. Results from wastewater can be available within 24 h of sample collection, generating real time information to inform public health responses, clinical decision making, and individual behaviour modifications. FUNDING: CDC Foundation.
Subject(s)
COVID-19 , Influenza, Human , Metapneumovirus , Nucleic Acids , Paramyxoviridae Infections , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Virus Diseases , Humans , Influenza, Human/epidemiology , Metapneumovirus/genetics , Rhinovirus/genetics , Wastewater , Seasons , Pandemics , Retrospective Studies , Respiratory Tract Infections/epidemiology , COVID-19/epidemiology , SARS-CoV-2/genetics , Respiratory Syncytial Virus, Human/genetics , Paramyxoviridae Infections/epidemiology , Virus Diseases/epidemiology , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Influenza B virus/genetics , RNA, Viral/genetics , RNA, Viral/analysisSubject(s)
COVID-19 , Virus Diseases , Child , Humans , Finland/epidemiology , COVID-19/epidemiology , Virus Diseases/epidemiology , EpidemicsABSTRACT
The emergence of the COVID-19 pandemic has led to significant progress in the field of wastewater-based surveillance (WBS) of respiratory pathogens and highlighted its potential for a wider application in public health surveillance. This study aimed to evaluate whether monitoring of respiratory syncytial virus (RSV) in wastewater can provide a comprehensive picture of disease transmission at the community level. The study was conducted in Larissa (Central Greece) between October 2022 and January 2023. Forty-six wastewater samples were collected from the inlet of the wastewater treatment plant of Larissa and analyzed with a real-time reverse transcription polymerase chain reaction (RT-PCR) based method. RSV and SARS-CoV-2 wastewater viral loads (genome copies/100,000 inhabitants) were analyzed against sentinel surveillance data on influenza-like illness (ILI) to identify potential associations. Univariate linear regression analysis revealed that RSV wastewater viral load (lagged by one week) and ILI notification rates in children up to 14 years old were strongly associated (std. Beta: 0.73 (95% CI: 0.31-1.14), p = 0.002, R2 = 0.308). A weaker association was found between SARS-CoV-2 viral load and ILI rates in the 15+ age group (std. Beta: 0.56 (95% CI: 0.06-1.05), p = 0.032, R2 = 0.527). The results support the incorporation of RSV monitoring into existing wastewater-based surveillance systems.
Subject(s)
COVID-19 , Influenza, Human , Respiratory Syncytial Virus Infections , Sexually Transmitted Diseases , Virus Diseases , Humans , Child , Respiratory Syncytial Viruses/genetics , Wastewater , Influenza, Human/epidemiology , Respiratory Syncytial Virus Infections/epidemiology , Greece/epidemiology , Pandemics , COVID-19/epidemiology , SARS-CoV-2 , Virus Diseases/epidemiology , Sexually Transmitted Diseases/epidemiologyABSTRACT
Molecular biology amplification enables sensitive detection of most respiratory viruses through nasopharyngeal swabbing. We developed an innovative approach to detect viral genomes on used facial tissues. In 2 communities of children, used tissues were collected once weekly for 1 year. Pooled analysis of tissues enabled detection of successive virus circulation in 4 age groups over time and forecasted by several weeks the circulation of influenza in the general population. At the individual level, in a proof-of-concept study of 30 volunteers with influenza-like signs/symptoms, we identified common respiratory viruses. The signals for SARS-CoV-2 obtained in parallel from 15 facial tissues and swab samples were similar and often higher for the tissues (11/15). Individual analysis of tissues offers a noninvasive, sensitive, and affordable alternative to self-sampling without a medical care requirement. Pooled analyses may be used to detect virus spread in specific communities, predict seasonal epidemics, and alert the population to viral infections.
Subject(s)
COVID-19 , Influenza, Human , Respiratory Tract Infections , Virus Diseases , Viruses , Child , Humans , Influenza, Human/epidemiology , Respiratory Tract Infections/epidemiology , SARS-CoV-2 , Virus Diseases/epidemiologyABSTRACT
Southeast Asia is considered a global hotspot of emerging zoonotic diseases. There, wildlife is commonly traded under poor sanitary conditions in open markets; these markets have been considered 'the perfect storm' for zoonotic disease transmission. We assessed the potential of wildlife trade in spreading viral diseases by quantifying the number of wild animals of four mammalian orders (Rodentia, Chiroptera, Carnivora and Primates) on sale in 14 Indonesian wildlife markets and identifying zoonotic viruses potentially hosted by these animals. We constructed a network analysis to visualize the animals that are traded alongside each other that may carry similar viruses. We recorded 6725 wild animals of at least 15 species on sale. Cities and markets with larger human population and number of stalls, respectively, offered more individuals for sale. Eight out of 15 animal taxa recorded are hosts of 17 zoonotic virus species, nine of which can infect more than one species as a host. The network analysis showed that long-tailed macaque has the greatest potential for spreading viral diseases, since it is simultaneously the most traded species, sold in 13/14 markets, and a potential host for nine viruses. It is traded alongside pig-tailed macaques in three markets, with which it shares six viruses in common (Cowpox, Dengue, Hepatitis E, Herpes B, Simian foamy, and Simian retrovirus type D). Short-nosed fruit bats and large flying foxes are potential hosts of Nipah virus and are also sold in large quantities in 10/14 markets. This study highlights the need for better surveillance and sanitary conditions to avoid the negative health impacts of unregulated wildlife markets.
Subject(s)
Carnivora , Chiroptera , Communicable Diseases , Virus Diseases , Viruses , Animals , Humans , Animals, Wild , Rodentia , Indonesia/epidemiology , Primates , Zoonoses , Virus Diseases/epidemiology , Virus Diseases/veterinaryABSTRACT
OBJECTIVE: To evaluate the behavior of the viruses responsible for acute respiratory infections before (2016-2019) and after (2020-2021) the start of the circulation of the SARS-CoV-2 virus in pediatric patients treated at a reference center from Barranquilla, Colombia. MATERIALS AND METHODS: A descriptive observational study was carried out, and data were obtained by reviewing the influenza-like illness and severe acute respiratory infection database in the pediatric population of the sentinel surveillance reference center in the district of Barranquilla during the years 2016-2021, applying inclusion and exclusion criteria. RESULTS: During 2016-2019, the average age of individuals was 1.3 (±1.7) years, during 2021, it was 2.3 (±3.5) years. The distribution by sex was similar, predominantly male. August and February were the months with the highest record of symptoms for 2016-2019 and 2021, respectively, the most frequent being cough, fever, shortness of breath, and diarrhea. By 2021 there was a higher use of antibiotics and antivirals reported than in 2016-2019. Most patients tested negative for viral detection. When comparing the percentage of viruses detected by age group and years of detection, positivity was lower in 2021 by every age group, and respiratory syncytial virus (RSV) was the most frequently detected. CONCLUSIONS: There was less virus positivity in viral detection tests in the pediatric population in 2021. RSV persists as the main etiology affecting this population, especially infants. The use of antibiotic therapy in viral infections continues to be a problematic practice in their management. Sentinel surveillance can be strengthened throughout the country.
Subject(s)
COVID-19 , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Virus Diseases , Viruses , Infant , Child , Humans , Male , Child, Preschool , Female , SARS-CoV-2 , Colombia/epidemiology , COVID-19/epidemiology , Virus Diseases/epidemiology , Respiratory Syncytial Virus Infections/epidemiologyABSTRACT
We evaluated clinical and socioeconomic burdens of respiratory disease in banana farm workers in Guatemala. We offered all eligible workers enrollment during June 15-December 30, 2020, and annually, then tracked them for influenza-like illnesses (ILI) through self-reporting to study nurses, sentinel surveillance at health posts, and absenteeism. Workers who had ILI submitted nasopharyngeal swab specimens for testing for influenza virus, respiratory syncytial virus, and SARS-CoV-2, then completed surveys at days 0, 7, and 28. Through October 10, 2021, a total of 1,833 workers reported 169 ILIs (12.0 cases/100 person-years), and 43 (25.4%) were laboratory-confirmed infections with SARS-CoV-2 (3.1 cases/100 person-years). Workers who had SARS-CoV-2âpositive ILIs reported more frequent anosmia, dysgeusia, difficulty concentrating, and irritability and worse clinical and well-being severity scores than workers who had test resultânegative ILIs. Workers who had positive results also had greater absenteeism and lost income. These results support prioritization of farm workers in Guatemala for COVID-19 vaccination.
Subject(s)
COVID-19 , Influenza, Human , Virus Diseases , Humans , COVID-19/epidemiology , SARS-CoV-2 , Influenza, Human/epidemiology , COVID-19 Vaccines , COVID-19 Testing , Virus Diseases/epidemiologyABSTRACT
BACKGROUND: Lower respiratory tract infections are among the main causes of death. Although there are many respiratory viruses, diagnostic efforts are focused mainly on influenza. The Respiratory Viruses Network (RespVir) collects infection data, primarily from German university hospitals, for a high diversity of infections by respiratory pathogens. In this study, we computationally analysed a subset of the RespVir database, covering 217,150 samples tested for 17 different viral pathogens in the time span from 2010 to 2019. METHODS: We calculated the prevalence of 17 respiratory viruses, analysed their seasonality patterns using information-theoretic measures and agglomerative clustering, and analysed their propensity for dual infection using a new metric dubbed average coinfection exclusion score (ACES). RESULTS: After initial data pre-processing, we retained 206,814 samples, corresponding to 1,408,657 performed tests. We found that Influenza viruses were reported for almost the half of all infections and that they exhibited the highest degree of seasonality. Coinfections of viruses are frequent; the most prevalent coinfection was rhinovirus/bocavirus and most of the virus pairs had a positive ACES indicating a tendency to exclude each other regarding infection. CONCLUSIONS: The analysis of respiratory viruses dynamics in monoinfection and coinfection contributes to the prevention, diagnostic, treatment, and development of new therapeutics. Data obtained from multiplex testing is fundamental for this analysis and should be prioritized over single pathogen testing.
Subject(s)
Coinfection , Respiratory Tract Infections , Virus Diseases , Viruses , Coinfection/epidemiology , Humans , Infant , Rhinovirus , Virus Diseases/epidemiologySubject(s)
Veterinary Medicine , Virus Diseases , Animals , Virus Diseases/epidemiology , Virus Diseases/veterinaryABSTRACT
Acute respiratory tract infections pose a serious threat to the health of children worldwide, with viral infections representing a major etiology of this type of disease. Protective measures such as mask-wearing, social distancing, and hand hygiene can be effective in curbing the spread of severe acute respiratory syndrome coronavirus 2. These precautions may also have an impact on the spread of other respiratory viruses. In this study, we retrospectively compared the respiratory virus infections of children in Southwest China before and after the outbreak of COVID-19. Nasopharyngeal swabs were collected from 1578 patients under 14 years old with acute respiratory tract infection symptoms before and after COVID-19 pandemic. Nine common respiratory viruses including human bocavirus, human rhinoviruses, human coronaviruses, human adenoviruses, human metapneumovirus, respiratory syncytial virus, influenza A virus, influenza B virus, and parainfluenza virus were measured by advanced fragment analysis. The respiratory virus infection rates among children of all ages and genders in Southwest China under the precautions against COVID-19 pandemic were significantly lower than that of the same period before the pandemic. Our findings indicate that public health measures implemented during the COVID-19 pandemic, including strict mask-wearing, social distancing, and hand hygiene, may be effective in preventing the transmission of other respiratory viruses in children, thereby controlling the spread of infections.
Subject(s)
COVID-19 , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Virus Diseases , Adolescent , COVID-19/epidemiology , COVID-19/prevention & control , Child , Female , Humans , Influenza B virus , Male , Pandemics/prevention & control , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control , Retrospective Studies , Virus Diseases/epidemiologyABSTRACT
BACKGROUND: Measuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. However, there is little information to indicate how the performance of various published signatures compare to one another. METHODS: This systematic comparison of host gene expression signatures evaluated the performance of 28 signatures, validating them in 4589 subjects from 51 publicly available datasets. Thirteen COVID-specific datasets with 1416 subjects were included in a separate analysis. Individual signature performance was evaluated using the area under the receiving operating characteristic curve (AUC) value. Overall signature performance was evaluated using median AUCs and accuracies. RESULTS: Signature performance varied widely, with median AUCs ranging from 0.55 to 0.96 for bacterial classification and 0.69-0.97 for viral classification. Signature size varied (1-398 genes), with smaller signatures generally performing more poorly (P < 0.04). Viral infection was easier to diagnose than bacterial infection (84% vs. 79% overall accuracy, respectively; P < .001). Host gene expression classifiers performed more poorly in some pediatric populations (3 months-1 year and 2-11 years) compared to the adult population for both bacterial infection (73% and 70% vs. 82%, respectively; P < .001) and viral infection (80% and 79% vs. 88%, respectively; P < .001). We did not observe classification differences based on illness severity as defined by ICU admission for bacterial or viral infections. The median AUC across all signatures for COVID-19 classification was 0.80 compared to 0.83 for viral classification in the same datasets. CONCLUSIONS: In this systematic comparison of 28 host gene expression signatures, we observed differences based on a signature's size and characteristics of the validation population, including age and infection type. However, populations used for signature discovery did not impact performance, underscoring the redundancy among many of these signatures. Furthermore, differential performance in specific populations may only be observable through this type of large-scale validation.
Subject(s)
Bacterial Infections/diagnosis , Datasets as Topic/statistics & numerical data , Host-Pathogen Interactions/genetics , Transcriptome , Virus Diseases/diagnosis , Adult , Bacterial Infections/epidemiology , Bacterial Infections/genetics , Biomarkers/analysis , COVID-19/diagnosis , COVID-19/genetics , Child , Cohort Studies , Diagnosis, Differential , Gene Expression Profiling/statistics & numerical data , Genetic Association Studies/statistics & numerical data , Humans , Publications/statistics & numerical data , SARS-CoV-2/pathogenicity , Validation Studies as Topic , Virus Diseases/epidemiology , Virus Diseases/geneticsABSTRACT
In a viral epidemic, the emergence of a novel strain with increased transmissibility (larger value of basic reproduction number R0) sparks the fear that the increase in transmissibility is likely to lead to an increase in disease severity. It is required to investigate if a new, more contagious strain will be necessarily dominant in the population and resulting in more disease severity. In this paper, the impact of the asymptomatic transmission and the emergence time of a more transmissible variant of a multi-strain viral disease on the disease prevalence, disease severity, and the dominant variant in an epidemic was investigated by a proposed 2-strain epidemic model. The simulation results showed that considering only R0, is insufficient to predict the outcome of a new, more contagious strain in the population. A more transmissible strain with a high fraction of asymptomatic cases can substantially reduce the mortality rate. If the emergence time of the new strain is closer to the start of the epidemic, the new, more contagious variant has more chance to win the viral competition and be the dominant strain; otherwise, despite being more contagious, it cannot dominate previous strains. In conclusion, three factors of R0, the fraction of asymptomatic transmission, and the emergence time of the new strain are required to correctly determine the prevalence, disease severity, and the winner of the viral competition.