Asymptomatic Summertime Shedding of Respiratory Viruses

Common cold viruses circulating in children threaten wild chimpanzees through asymptomatic adult carriers

Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory disease outbreaks as "common cold" paediatric human pathogens, but reverse zoonotic transmission pathways have remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study of 234 children aged 3-11 years in communities bordering Kibale National Park, Uganda, and 30 adults who were forest workers and regularly entered the park. We collected 2047 respiratory symptoms surveys to quantify clinical severity and simultaneously collected 1989 nasopharyngeal swabs approximately monthly for multiplex viral diagnostics. Throughout the course of the study, we also collected 445 faecal samples from 55 wild chimpanzees living nearby in Kibale in social groups that have experienced repeated, and sometimes lethal, epidemics of human-origin respiratory viral disease. We characterized respiratory pathogens in each cohort and examined statistical associations between PCR positivity for detected pathogens and potential risk factors. Children exhibited high incidence rates of respiratory infections, whereas incidence rates in adults were far lower. COVID-19 lockdown in 2020-2021 significantly decreased respiratory disease incidence in both people and chimpanzees. Human respiratory infections peaked in June and September, corresponding to when children returned to school. Rhinovirus, which caused a 2013 outbreak that killed 10% of chimpanzees in a Kibale community, was the most prevalent human pathogen throughout the study and the only pathogen present at each monthly sampling, even during COVID-19 lockdown. Rhinovirus was also most likely to be carried asymptomatically by adults. Although we did not detect human respiratory pathogens in the chimpanzees during the cohort study, we detected human metapneumovirus in two chimpanzees from a February 2023 outbreak that were genetically similar to viruses detected in study participants in 2019. Our data suggest that respiratory pathogens circulate in children and that adults become asymptomatically infected during high-transmission times of year. These asymptomatic adults may then unknowingly carry the pathogens into forest and infect chimpanzees. This conclusion, in turn, implies that intervention strategies based on respiratory symptoms in adults are unlikely to be effective for reducing reverse zoonotic transmission of respiratory viruses to chimpanzees.

Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal

BACKGROUND

The surveillance of respiratory pathogens in rural areas of West Africa has, to date, largely been focussed on symptoms. In this prospective study conducted prior to the COVID-19 pandemic, we aimed to assess the asymptomatic prevalence of respiratory pathogen carriage in a group of individuals living in a rural area of Senegalese.

METHODS

Longitudinal follow up was performed through monthly nasopharyngeal swabbing during the dry season and weekly swabbing during the rainy season. We enrolled 15 individuals from the village of Ndiop. A total of 368 nasopharyngeal swabs were collected over a one-year period. We investigated the prevalence of 18 respiratory viruses and eight respiratory bacteria in different age groups using singleplex and multiplex PCR.

RESULTS

In total, 19.56% of the samples (72/368) were positive for respiratory viruses and 13.60% of the samples (50/368) were positive for respiratory bacteria. Coronaviruses (19/72, 26.39%), adenoviruses (17/72, 23.61%), rhinoviruses (14/72, 19.44%), Streptococcus pneumoniae (17/50, 34%), and Moraxella catarrhalis (15/50, 30%) were the most frequently detected viruses. Interestingly, the carriage of respiratory pathogens was shown to be more frequent during the rainy season, as pluviometry was shown to be positively associated with the occurrence of respiratory viruses such as influenza (P = .0078, r2 =.523) and RSV (P = .0055, r2 =.554).

CONCLUSIONS

Our results show a non-negligible circulation of respiratory pathogens in a rural area in Senegal (West Africa) with an underestimated proportion of asymptomatic individuals. This study highlights the fact that the circulation of viruses and bacteria in the community has been overlooked.

Respiratory disease patterns in rural Western Uganda, 2019-2022

Introduction

Respiratory disease is a major cause of morbidity and mortality in the developing world, but prospective studies of temporal patterns and risk factors are rare.

Methods

We studied people in rural Western Uganda, where respiratory disease is pervasive. We followed 30 adults (ages 22-51 years; 534 observations) and 234 children (ages 3-11 years; 1,513 observations) between May 2019 and July 2022 and collected monthly data on their respiratory symptoms, for a total of 2,047 case records. We examined associations between demographic and temporal factors and respiratory symptoms severity.

Results

The timing of our study (before, during, and after the emergence of COVID-19) allowed us to document the effects of public health measures instituted in the region. Incidence rates of respiratory symptoms before COVID-19 lockdown were 568.4 cases per 1,000 person-months in children and 254.2 cases per 1,000 person-months in adults. These rates were 2.6 times higher than the 2019 global average for children but comparable for adults. Younger children (ages 3-6 years) had the highest frequencies and severities of respiratory symptoms. Study participants were most likely to experience symptoms in February, which is a seasonal pattern not previously documented. Incidence and severity of symptoms in children decreased markedly during COVID-19 lockdown, illustrating the broad effects of public health measures on the incidence of respiratory disease.

Discussion

Our results demonstrate that patterns of respiratory disease in settings such as Western Uganda resemble patterns in developed economies in some ways (age-related factors) but not in others (increased incidence in children and seasonal pattern). Factors such as indoor air quality, health care access, timing of school trimesters, and seasonal effects (rainy/dry seasons) likely contribute to the differences observed.

Diagnostic Stewardship for Multiplex Respiratory Testing: What We Know and What Needs to Be Done

Syndromic respiratory panels are now widely available in clinical microbiology laboratories and health care institutions. These panels can rapidly diagnose infections and detect antimicrobial resistance genes allowing for more rapid therapeutic optimization compared to standard microbiology approaches. However, given reimbursement concerns and limitations of multiplex molecular testing and results interpretation, maximum clinical utility and positive clinical outcomes depend on active diagnostic stewardship. Here, the authors review clinical outcomes of both upper and lower respiratory panels and present diagnostic stewardship strategies for optimal use of respiratory panels.

Susceptibility to the Common Cold Virus is Associated with Day Length

Seasonal rhythms are endogenous timing mechanisms that allow animals living at temperate latitudes to synchronize their physiology to the seasons. Human viral respiratory disease is prevalent in the winter at temperate latitudes, but the role of endogenous mechanisms in these recurring annual patterns is unclear. The Common Cold Project is a repository of data describing the experimental viral challenge of 1,337 participants across the seasons of the year. We report a secondary analysis of these data to investigate if susceptibility to the common cold is associated with day length. The majority of the participants (78%) showed signs of infection but only 32% developed clinical signs of disease, and the probability of infection was significantly higher in longer day lengths (summer), but the disease was more likely in short (winter) day lengths. The persistence of winter disease patterns in experimental conditions supports the role of endogenous seasonality in human susceptibility to viral infection.

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Outbreaks of viral respiratory disease recur in winter in the northern hemisphere

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In controlled experiments, common cold infection was more likely in summer

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Infection was more likely to progress to the development of cold in winter

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Innate seasonality of human immunity could affect the prevalence of the common cold

Why does viral RNA sometimes persist after recovery from acute infections?

DNA viruses often persist in the body of their host, becoming latent and recurring many months or years later. By contrast, most RNA viruses cause acute infections that are cleared from the host as they lack the mechanisms to persist. However, it is becoming clear that viral RNA can persist after clinical recovery and elimination of detectable infectious virus. This persistence can either be asymptomatic or associated with late progressive disease or nonspecific lingering symptoms, such as may be the case following infection with Ebola or Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Why does viral RNA sometimes persist after recovery from an acute infection? Where does the RNA come from? And what are the consequences?

Prospective Validation of a Rapid Host Gene Expression Test to Discriminate Bacterial From Viral Respiratory Infection

Importance

Bacterial and viral causes of acute respiratory illness (ARI) are difficult to clinically distinguish, resulting in the inappropriate use of antibacterial therapy. The use of a host gene expression-based test that is able to discriminate bacterial from viral infection in less than 1 hour may improve care and antimicrobial stewardship.

Objective

To validate the host response bacterial/viral (HR-B/V) test and assess its ability to accurately differentiate bacterial from viral infection among patients with ARI.

Design, Setting, and Participants

This prospective multicenter diagnostic study enrolled 755 children and adults with febrile ARI of 7 or fewer days' duration from 10 US emergency departments. Participants were enrolled from October 3, 2014, to September 1, 2019, followed by additional enrollment of patients with COVID-19 from March 20 to December 3, 2020. Clinical adjudication of enrolled participants identified 616 individuals as having bacterial or viral infection. The primary analysis cohort included 334 participants with high-confidence reference adjudications (based on adjudicator concordance and the presence of an identified pathogen confirmed by microbiological testing). A secondary analysis of the entire cohort of 616 participants included cases with low-confidence reference adjudications (based on adjudicator discordance or the absence of an identified pathogen in microbiological testing). Thirty-three participants with COVID-19 were included post hoc.

Interventions

The HR-B/V test quantified the expression of 45 host messenger RNAs in approximately 45 minutes to derive a probability of bacterial infection.

Main Outcomes and Measures

Performance characteristics for the HR-B/V test compared with clinical adjudication were reported as either bacterial or viral infection or categorized into 4 likelihood groups (viral very likely [probability score <0.19], viral likely [probability score of 0.19-0.40], bacterial likely [probability score of 0.41-0.73], and bacterial very likely [probability score >0.73]) and compared with procalcitonin measurement.

Results

Among 755 enrolled participants, the median age was 26 years (IQR, 16-52 years); 360 participants (47.7%) were female, and 395 (52.3%) were male. A total of 13 participants (1.7%) were American Indian, 13 (1.7%) were Asian, 368 (48.7%) were Black, 131 (17.4%) were Hispanic, 3 (0.4%) were Native Hawaiian or Pacific Islander, 297 (39.3%) were White, and 60 (7.9%) were of unspecified race and/or ethnicity. In the primary analysis involving 334 participants, the HR-B/V test had sensitivity of 89.8% (95% CI, 77.8%-96.2%), specificity of 82.1% (95% CI, 77.4%-86.6%), and a negative predictive value (NPV) of 97.9% (95% CI, 95.3%-99.1%) for bacterial infection. In comparison, the sensitivity of procalcitonin measurement was 28.6% (95% CI, 16.2%-40.9%; P < .001), the specificity was 87.0% (95% CI, 82.7%-90.7%; P = .006), and the NPV was 87.6% (95% CI, 85.5%-89.5%; P < .001). When stratified into likelihood groups, the HR-B/V test had an NPV of 98.9% (95% CI, 96.1%-100%) for bacterial infection in the viral very likely group and a positive predictive value of 63.4% (95% CI, 47.2%-77.9%) for bacterial infection in the bacterial very likely group. The HR-B/V test correctly identified 30 of 33 participants (90.9%) with acute COVID-19 as having a viral infection.

Conclusions and Relevance

In this study, the HR-B/V test accurately discriminated bacterial from viral infection among patients with febrile ARI and was superior to procalcitonin measurement. The findings suggest that an accurate point-of-need host response test with high NPV may offer an opportunity to improve antibiotic stewardship and patient outcomes.

Comparison of Severe Viral Pneumonia Caused by SARS-CoV-2 and Other Respiratory Viruses Among Malaysian Children During the COVID-19 Pandemic

OBJECTIVES

We described the etiology of severe pneumonia in children during the height of the COVID-19 pandemic in Malaysia and compared the clinical features of severe SARS-CoV-2 to other respiratory viruses.

METHODS

This retrospective study included all children aged 12 years and below hospitalized with severe pneumonia in Negeri Sembilan, Malaysia, between 1 April 2021 and 31 October 2021. We extracted demographic and clinical data and used logistic regression to examine risk factors associated with severe SARS-CoV-2 or other viral pneumonia.

RESULTS

A total of 111 children were included. The median age was 15 months. Human rhinovirus/enterovirus, SARS-CoV-2 and respiratory syncytial virus were the most common etiology of severe pneumonia. Codetection of >1 viral pathogen was present in 14 (12.6%) patients. Children with severe COVID-19 presented early in the course of illness and had lower rates of pediatric intensive care admission. The presence of sick contact with an adult was a predictor for SARS-CoV-2, whereas adventitious breath sounds were predictive of other respiratory viruses.

CONCLUSIONS

The etiology of severe pneumonia in children evolved with the epidemic curve of COVID-19 and school closures. Children with severe pneumonia due to SARS-CoV-2 experienced a milder clinical course when compared to other respiratory viruses.

Impact of multiplexed respiratory viral panels on infection control measures and antimicrobial stewardship: a review of the literature

Multiplexed respiratory viral panels (MRVP) have recently been added to the diagnostic work-up of respiratory infections. This review provides a summary of the main literature of MRVP for patients with regard to 3 different topics. Can the results of MRVP reduce the inappropriate use of antibiotics, can they guide the use of appropriate antiviral therapy and do they have an added value with respect to infection control measures? Literature was searched for based on a defined search string using both the PubMed and Embase database. Twenty-five articles report on the impact of MRVP on antibiotic therapy. In all the articles where active antimicrobial stewardship was performed (e.g., education/advice on interpreting results of MRVP) (N = 9), a reduction in antibiotic therapy was shown (with exception of 2 studies). Three studies evaluating the effect of MRVP on antimicrobial use in a population that is not suspected of having bacterial pneumonia (e.g., absence of radiology suggestive for bacterial infection or low PCT) found a positive impact on antibiotic therapy. Eight studies with a short TAT (< 7 h) had a positive impact on use of antibiotic therapy. Eleven studies focused on the impact of MRVP on antiviral use. In contrast to antibiotic reduction, all studies systematically objectified improved antiviral use as a consequence of MRVP results. With regard to the impact of MRVP on infection control, eleven articles were withheld. All these studies led to a more accurate use of infection control measures by detecting unidentified pathogens or stopping isolation precautions in case of a negative MRVP result. MRVP don’t reduce antibiotic therapy in all populations. Reduction seems more likely if the following factors are present: active antimicrobial stewardship, low likelihood of a bacterial infection, and a short turnaround time to result. With respect to antiviral therapy, all studies have an impact but the targeted use of antivirals is so far not that evidence based for all viral respiratory pathogens. Regarding infection control measures, the potential impact of MRVP is high because of the need of additional isolation precautions for many respiratory viruses, although logistical problems can occur.

Rhinovirus spread in children during the COVID-19 pandemic despite social restrictions-A nationwide register study in Finland

Social restrictions during the coronavirus disease 2019 pandemic strongly affected the epidemiology of influenza and respiratory syncytial virus (RSV). As rhinovirus seemed to spread despite the restrictions, we aimed to analyze rhinovirus epidemiology in children during the pandemic. This register‐based study used data from the Finnish Infectious Disease Register. Nationwide rhinovirus findings from July 2015 to March 2021 were included and stratified by age (0–4, 5–9, and 10–14). Cumulative 14‐day incidence per 100000 children was calculated. Four thousand five hundred and seventy six positive rhinovirus findings were included, of which 3788 (82.8%) were among children aged 0–4. The highest recorded incidence was 36.2 among children aged 0–4 in October 2017. The highest recorded incidence during the pandemic period was 13.6 in November 2020. The impact of the restrictions was mostly seen among children aged 0–4 years of age in weeks 14–22 in 2020. The incidence has since remained near reference levels in all age groups. Strict restrictions temporarily interrupted the circulation of rhinovirus in spring 2020. Rhinovirus incidence returned to normal levels soon after the harsh restrictions were lifted. These looser social restrictions prevented RSV and influenza seasons but failed to prevent the spread of rhinovirus.

Viral RNA in City Wastewater as a Key Indicator of COVID-19 Recrudescence and Containment Measures Effectiveness

In recent years, and more specifically at the beginning of the COVID-19 crisis, wastewater surveillance has been proposed as a tool to monitor the epidemiology of human viral infections. In the present work, from July to December 2020, the number of copies of SARS-CoV-2 RNA in Marseille's wastewater was correlated with the number of new positive cases diagnosed in our Institute of Infectious Disease, which tested about 20% of the city's population. Number of positive cases and number of copies of SARS-CoV-2 RNA in wastewater were significantly correlated (p = 0.013). During the great epidemic peak, from October to December 2020, the curves of virus in the sewers and the curves of positive diagnoses were perfectly superposed. During the summer period, the superposition of curves was less evident as subject to many confounding factors that were discussed. We also tried to correlate the effect of viral circulation in wastewater with containment measures, probably the most unbiased correlation on their potential inflection effect of epidemic curves. Not only is this correlation not obvious, but it also clearly appears that the drop in cases as well as the drop in the viral load in the sewers occur before the containment measures. In fact, this suggests that there are factors that initiate the end of the epidemic peak independently of the containment measure. These factors will therefore need to be explored more deeply in the future.

Direct Observation of Repeated Infections With Endemic Coronaviruses

BACKGROUND

Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk.

METHODS

Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses.

RESULTS

During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the betacoronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity, but found strong association between symptom severity and belonging to the same family.

CONCLUSIONS

This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection.

[Virological diagnosis of lower respiratory tract infections]

INTRODUCTION

The etiological diagnosis of bronchopulmonary infections cannot be assessed with clinical, radiological and epidemiological data alone. Viruses have been demonstrated to cause a large proportion of these infections, both in children and adults.

BACKGROUND

The diagnosis of viral bronchopulmonary infections is based on the analysis of secretions, collected from the lower respiratory tract when possible, by techniques that detect either influenza and respiratory syncytial viruses, or a large panel of viruses that can be responsible for respiratory disease. The latter, called multiplex PCR assays, allow a syndromic approach to respiratory infection. Their high cost for the laboratory raises the question of their place in the management of patients in terms of antibiotic economy and isolation. In the absence of clear recommendations, the strategy and equipment are very unevenly distributed in France.

OUTLOOK

Medico-economic analyses need to be performed in France to evaluate the place of these tests in the management of patients. The evaluation of the role of the different viruses often detected in co-infection, especially in children, also deserves the attention of virologists and clinicians.

CONCLUSIONS

The availability of new diagnostic technologies, the recent emergence of SARS-CoV-2, together with the availability of new antiviral drugs are likely to impact future recommendations for the management of viral bronchopulmonary infections.

Can Comprehensive Respiratory Pathogen Panels be Used to Exclude Pertussis Infection?

BACKGROUND

Pertussis is a serious public health concern and accurate diagnosis is imperative. Comprehensive, multiplex respiratory pathogen polymerase chain reaction (PCR) panels (RPPs) have recently become popular, but their utility in excluding pertussis infection has not been fully explored.

OBJECTIVES

To determine RPP testing results for pertussis using frozen banked samples that previously tested positive on dedicated Bordetella pertussis PCR testing, and to describe positive test rates for other respiratory pathogens on these samples via RPP.

METHODS

Our microbiology laboratory retrieved banked nasopharyngeal samples from inpatient, ambulatory, and emergency department sources that were positive for pertussis using B. pertussis PCR testing from March 2015 to October 2017. RPP was performed on thawed, archived samples. Rate of pertussis identification on RPP was determined, and positive tests for other pathogens were tabulated.

RESULTS

A total of 3482 specimens were submitted for pertussis PCR testing during the study period. Of those, 138 (4%) were positive for B. pertussis, and 102 (74%) samples were banked and available for RPP testing. Fifty-seven of 102 (56%) of the banked samples had positive RPP testing for pertussis. Of the 45 samples negative for pertussis on RPP testing, 20 (44%) tested positive for other respiratory pathogens.

CONCLUSION

Negative testing for B. pertussis and positive testing for other respiratory pathogens on RPP was common in samples that previously tested positive on dedicated B. pertussis PCR testing, both of which could lead to missed diagnoses of pertussis infection. Clinicians should consider using dedicated pertussis PCR testing if pertussis infection is suspected.

Asymptomatic infection by SARS-CoV-2 in healthcare workers: A study in a large teaching hospital in Wuhan, China

OBJECTIVES

To investigate the proportion and characteristics of asymptomatic infection among healthcare workers (HCWs).

METHODS

This study retrospectively investigated 1407 HCWs who were screened for COVID-19 by chest computed tomography (CT) scans and nasopharyngeal swabs for SARS-CoV-2 nucleic acid. Demographics, CT features, nasopharyngeal swabs, baseline symptoms, and laboratory data were collected.

RESULTS

Of 1407 HCWs, 235 had symptoms and 1172 were asymptomatic close contacts, of which, 107 were symptomatic cases and 84 were close contacts who had abnormal CT findings. Of 152 symptomatic individuals and 908 close contacts tested for SARS-CoV-2 nucleic acid, 122 symptomatic cases and 38 close contacts had positive reverse-transcriptase real-time polymerase chain (RT-PCR) test results. The rate of confirmed asymptomatic infections was 4.2% (38/908). Both symptomatic and asymptomatic infected cases had high titrations of specific IgG or had ≥four-fold increase in IgG during convalescence compared with the acute phase. Combining the RT-PCR tests and serological findings, the rate of asymptomatic infections was 9.7% (88/908). In terms of the duration of viral shedding, there was no significant difference between symptomatic mild/moderate participants and asymptomatic infections.

CONCLUSIONS

The findings demonstrated that a high rate of asymptomatic SARS-CoV-2 carriers existed among healthcare worker close contacts during the outbreak of COVID-19.

Rates of asymptomatic respiratory virus infection across age groups

Respiratory viral infections are a leading cause of disease worldwide. A variety of respiratory viruses produce infections in humans with effects ranging from asymptomatic to life-treathening. Standard surveillance systems typically only target severe infections (ED outpatients, hospitalisations, deaths) and fail to track asymptomatic or mild infections. Here we performed a large-scale community study across multiple age groups to assess the pathogenicity of 18 respiratory viruses. We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. We combined these test results with participant-provided daily records of cold and flu symptoms and used this information to characterise symptom severity by virus and age category. Asymptomatic infection rates exceeded 70% for most viruses, excepting influenza and human metapneumovirus, which produced significantly more severe outcomes. Symptoms were negatively associated with infection frequency, with children displaying the lowest score among age groups. Upper respiratory manifestations were most common for all viruses, whereas systemic effects were less typical. These findings indicate a high burden of asymptomatic respiratory virus infection exists in the general population.

Detection of Influenza and Other Respiratory Viruses in Air Sampled From a University Campus: A Longitudinal Study

BACKGROUND

Respiratory virus-laden particles are commonly detected in the exhaled breath of symptomatic patients or in air sampled from healthcare settings. However, the temporal relationship of detecting virus-laden particles at nonhealthcare locations vs surveillance data obtained by conventional means has not been fully assessed.

METHODS

From October 2016 to June 2018, air was sampled weekly from a university campus in Hong Kong. Viral genomes were detected and quantified by real-time reverse-transcription polymerase chain reaction. Logistic regression models were fitted to examine the adjusted odds ratios (aORs) of ecological and environmental factors associated with the detection of virus-laden airborne particles.

RESULTS

Influenza A (16.9% [117/694]) and influenza B (4.5% [31/694]) viruses were detected at higher frequencies in air than rhinovirus (2.2% [6/270]), respiratory syncytial virus (0.4% [1/270]), or human coronaviruses (0% [0/270]). Multivariate analyses showed that increased crowdedness (aOR, 2.3 [95% confidence interval {CI}, 1.5-3.8]; P < .001) and higher indoor temperature (aOR, 1.2 [95% CI, 1.1-1.3]; P < .001) were associated with detection of influenza airborne particles, but absolute humidity was not (aOR, 0.9 [95% CI, .7-1.1]; P = .213). Higher copies of influenza viral genome were detected from airborne particles >4 μm in spring and <1 μm in autumn. Influenza A(H3N2) and influenza B viruses that caused epidemics during the study period were detected in air prior to observing increased influenza activities in the community.

CONCLUSIONS

Air sampling as a surveillance tool for monitoring influenza activity at public locations may provide early detection signals on influenza viruses that circulate in the community.

Association of persistent wild-type measles virus RNA with long-term humoral immunity in rhesus macaques

Recovery from measles results in life-long protective immunity. To understand induction of long-term immunity, rhesus macaques were studied for 6 months after infection with wild-type measles virus (MeV). Infection caused viremia and rash, with clearance of infectious virus by day 14. MeV RNA persisted in PBMCs for 30-90 days and in lymphoid tissue for 6 months most often in B cells but was rarely detected in BM. Antibody with neutralizing activity and binding specificity for MeV nucleocapsid (N), hemagglutinin (H), and fusion proteins appeared with the rash and avidity matured over 3-4 months. Lymph nodes had increasing numbers of MeV-specific antibody-secreting cells (ASCs) and germinal centers with late hyalinization. ASCs appeared in circulation with the rash and continued to appear along with peripheral T follicular helper cells for the study duration. ASCs in lymph nodes and PBMCs produced antibody against both H and N, with more H-specific ASCs in BM. During days 14-21, 20- to 100-fold more total ASCs than MeV-specific ASCs appeared in circulation, suggesting mobilization of preexisting ASCs. Therefore, persistence of MeV RNA in lymphoid tissue was accompanied by continued germinal center formation, ASC production, avidity maturation, and accumulation of H-specific ASCs in BM to sustain neutralizing antibody and protective immunity.

[Coronaviruses as the cause of respiratory infections]

Hintergrund

Es gibt sechs humanpathogene Coronaviren (CoV), die vornehmlich respiratorische Infektionen auslösen. Im klinischen Alltag ist es hilfreich, Relevanz und Besonderheiten dieser Erreger zu kennen.

Fragestellung

Praxisnahe Darstellung der Epidemiologie, Klinik und Unterschiede humanpathogener CoV. Hinweise zu Diagnostik und Umgang mit Patienten bei Verdacht auf eine CoV-Infektion.

Material und Methoden

Selektive Literaturrecherche, Darstellung und Diskussion von Grundlagenarbeiten und Expertenempfehlungen einschließlich der Veröffentlichungen der Weltgesundheitsorganisation (WHO), des Europäischen Zentrums für die Prävention und die Kontrolle von Krankheiten (ECDC) und des Robert Koch-Instituts.

Ergebnisse

Die weltweit endemischen CoV (HCoV-NL63, -229E, -OC43 und -HKU1) sind häufige Ursache von leichteren respiratorischen Infektionen. Zwei epidemische, zoonotische Coronaviren (SARS- und MERS-CoV, MERS „Middle East respiratory syndrome“, SARS „severe acute respiratory syndrome“ [schweres akutes Atemwegssyndrom]) können schwere Pneumonien hervorrufen. SARS-CoV ist seit 15 Jahren nicht mehr im Menschen nachgewiesen worden. MERS-CoV zirkuliert seit 2012 hauptsächlich auf der Arabischen Halbinsel. Eine spezifische Therapie oder zugelassene Impfung existiert noch für keines der sechs humanpathogenen Coronaviren.

Schlussfolgerung

Eine Erregerdiagnostik mittels Polymerase-Kettenreaktion aus respiratorischem Material ist für alle CoV möglich, für die vier endemischen allerdings selten notwendig. SARS-CoV hat aktuell keine Relevanz in der Klinik, da es seit 15 Jahren nicht mehr im Menschen nachgewiesen wurde. Der Verdacht auf eine MERS-Infektion sollte hingegen bei entsprechender Symptomatik und Reiseanamnese differenzialdiagnostisch in Betracht gezogen werden. Hier sind eine schnelle Diagnosesicherung und allgemeine Hygienemaßnahmen zur Verhinderung der Verbreitung entscheidend.

Rapid, Sample-to-Answer Host Gene Expression Test to Diagnose Viral Infection

Objective

Distinguishing bacterial, viral, or other etiologies of acute illness is diagnostically challenging with significant implications for appropriate antimicrobial use. Host gene expression offers a promising approach, although no clinically useful test has been developed yet to accomplish this. Here, Qvella's FAST HR (Richmond Hill, Ontario, Canada) process was developed to quantify previously identified host gene expression signatures in whole blood in <45 minutes.

Method

Whole blood was collected from 128 human subjects (mean age 47, range 18-88) with clinically adjudicated, microbiologically confirmed viral infection, bacterial infection, noninfectious illness, or healthy controls. Stabilized mRNA was released from cleaned and stabilized RNA-surfactant complexes using e-lysis, an electrical process providing a quantitative real-time reverse transcription polymerase chain reaction-ready sample. Threshold cycle values (C_T) for 10 host response targets were normalized to hypoxanthine phosphoribosyltransferase 1 expression, a control mRNA. The transcripts in the signature were specifically chosen to discriminate viral from nonviral infection (bacterial, noninfectious illness, or healthy). Classification accuracy was determined using cross-validated sparse logistic regression.

Results

Reproducibility of mRNA quantification was within 1 cycle as compared to the difference seen between subjects with viral versus nonviral infection (up to 5.0 normalized C_T difference). Classification of 128 subjects into viral or nonviral etiologies demonstrated 90.6% overall accuracy compared to 82.0% for procalcitonin (P = .06). FAST HR achieved rapid and accurate measurement of the host response to viral infection in less than 45 minutes.

Conclusions

These results demonstrate the ability to translate host gene expression signatures to clinical platforms for use in patients with suspected infection.

Clinical Trials Registration

NCT00258869.

Validation of a host response test to distinguish bacterial and viral respiratory infection

BACKGROUND

Distinguishing bacterial and viral respiratory infections is challenging. Novel diagnostics based on differential host gene expression patterns are promising but have not been translated to a clinical platform nor extensively tested. Here, we validate a microarray-derived host response signature and explore performance in microbiology-negative and coinfection cases.

METHODS

Subjects with acute respiratory illness were enrolled in participating emergency departments. Reference standard was an adjudicated diagnosis of bacterial infection, viral infection, both, or neither. An 87-transcript signature for distinguishing bacterial, viral, and noninfectious illness was measured from peripheral blood using RT-PCR. Performance characteristics were evaluated in subjects with confirmed bacterial, viral, or noninfectious illness. Subjects with bacterial-viral coinfection and microbiologically-negative suspected bacterial infection were also evaluated. Performance was compared to procalcitonin.

FINDINGS

151 subjects with microbiologically confirmed, single-etiology illness were tested, yielding AUROCs 0•85-0•89 for bacterial, viral, and noninfectious illness. Accuracy was similar to procalcitonin (88% vs 83%, p = 0•23) for bacterial vs. non-bacterial infection. Whereas procalcitonin cannot distinguish viral from non-infectious illness, the RT-PCR test had 81% accuracy in making this determination. Bacterial-viral coinfection was subdivided. Among 19 subjects with bacterial superinfection, the RT-PCR test identified 95% as bacterial, compared to 68% with procalcitonin (p = 0•13). Among 12 subjects with bacterial infection superimposed on chronic viral infection, the RT-PCR test identified 83% as bacterial, identical to procalcitonin. 39 subjects had suspected bacterial infection; the RT-PCR test identified bacterial infection more frequently than procalcitonin (82% vs 64%, p = 0•02).

INTERPRETATION

The RT-PCR test offered similar diagnostic performance to procalcitonin in some subgroups but offered better discrimination in others such as viral vs. non-infectious illness and bacterial/viral coinfection. Gene expression-based tests could impact decision-making for acute respiratory illness as well as a growing number of other infectious and non-infectious diseases.

Hospital Influenza Admissions as a Harbinger for Nursing Home Influenza Cases

OBJECTIVES

To determine temporal associations of local measures of influenza morbidity and mortality by the Centers for Disease Control and Prevention (CDC) with influenza hospitalizations in nursing home residents.

DESIGN

Retrospective, longitudinal panel study.

SETTING AND PARTICIPANTS

Long-stay nursing home residents, aged 65 years or older in 823 nursing homes from 2011 to 2015.

MEASURES

CDC-reported rates of influenza and pneumonia mortality and laboratory-confirmed influenza hospitalizations. We compared the CDC measures to nursing home resident hospitalizations due to (1) all-cause, (2) a primary diagnosis of respiratory or circulatory illness, and (3) a primary diagnosis of pneumonia or influenza based on Medicare Part A Claims data.

RESULTS

Our final sample included 273,743 unique residents in 819 nursing homes in 108 cities. National laboratory-confirmed influenza-associated hospitalizations for the group aged 65 and older occurred 0 to 1 week prior to nursing home resident influenza-related hospitalizations (Spearman ρ = 0.54). CDC-reported influenza hospitalizations occurred 3 weeks prior to CDC-reported influenza deaths (ρ = 0.59). Nursing home resident influenza hospitalizations occurred 2 weeks before local CDC-reported pneumonia and influenza deaths occurred (ρ = 0.44).

CONCLUSIONS/IMPLICATIONS

Publicly reported CDC measures correlate well with nursing home hospitalizations for pneumonia and influenza. Rates of laboratory-confirmed influenza hospitalizations (as reported by the CDC) may be a useful surrogate for nursing home influenza outbreaks but should be considered along with local indicators of disease outbreaks. Early community signals could be clinically leveraged as a trigger for increased infection control measures in nursing homes.

Host-Based Diagnostics for Acute Respiratory Infections

PURPOSE

The inappropriate use of antimicrobials, especially in acute respiratory infections (ARIs), is largely driven by difficulty distinguishing bacterial, viral, and noninfectious etiologies of illness. A new frontier in infectious disease diagnostics looks to the host response for disease classification. This article examines how host response-based diagnostics for ARIs are being used in clinical practice, as well as new developments in the research pipeline.

METHODS

A limited search was conducted of the relevant literature, with emphasis placed on literature published in the last 5 years (2014-2019).

FINDINGS

Advances are being made in all areas of host response-based diagnostics for ARIs. Specifically, there has been significant progress made in single protein biomarkers, as well as in various "omics" fields (including proteomics, metabolomics, and transcriptomics) and wearable technologies. There are many potential applications of a host response-based approach; a few key examples include the ability to discriminate bacterial and viral disease, presymptomatic diagnosis of infection, and pathogen-specific host response diagnostics, including modeling disease progression.

IMPLICATIONS

As biomarker measurement technologies continue to improve, host response-based diagnostics will increasingly be translated to clinically available platforms that can generate a holistic characterization of an individual's health. This knowledge, in the hands of both patient and provider, can improve care for the individual patient and help fight rising rates of antibiotic resistance.

Respiratory virus associated with surgery in children patients

Background

Viral respiratory infection (VRI) is a common contraindication to elective surgery. Asymptomatic shedding among pediatric surgery patients (PSPs) could potentially lead to progression of symptomatic diseases and cause outbreaks of respiratory diseases. The aim of this study is to investigate the incidence of infection among mild symptomatic PSP group and asymptomatic PSP group after surgical procedure.

Methods

We collected the induced sputum from enrolled 1629 children (under 18 years of age) with no respiratory symptom prior to pediatric surgery between March 2017 and February 2019. We tested 16 different respiratory virus infections in post-surgery mild symptomatic PSP group and asymptomatic PSP group using a quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) assay panel. We analyzed symptom data and quantitative viral load to investigate the association between viruses, symptoms and viral quantity in qRT-PCR-positive PSPs.

Results

Out of 1629 children enrolled, a total of 204 respiratory viruses were present in 171 (10.50%) PSPs including 47 patients with mild symptoms and 124 with no symptoms after surgery. Commonly detected viruses were human rhino/enterovirus (HRV/EV, 42.19%), parainfluenza virus 3 (PIV3, 24.48%), coronavirus (CoV NL63, OC43, HKU1, 11.46%), and respiratory syncytial virus (RSV, 9.9%). PIV3 infection with a higher viral load was frequently found in PSPs presenting with mild symptoms, progressing to pneumonia with radiographic evidence after surgery. HRV/EV were the most commonly detected pathogens in both asymptomatic and mild symptomatic PSPs. CoV (OC43, HKU1) infections with a higher viral load were mostly observed in asymptomatic PSPs progressing to alveolar or interstitial infiltration.

Conclusions

Our study suggested that PIV3 is a new risk factor for VRI in PSPs. Employing a more comprehensive, sensitive and quantitative method should be considered for preoperative testing of respiratory viruses in order to guide optimal surgical timing.

Respiratory virus infection among hospitalized adult patients with or without clinically apparent respiratory infection: a prospective cohort study

Objectives

To determine the viral epidemiology and clinical characteristics of patients with and without clinically apparent respiratory tract infection.

Methods

This prospective cohort study was conducted during the 2018 winter influenza season. Adult patients with fever/respiratory symptoms (fever/RS group) were age- and sex-matched with patients without fever/RS (non-fever/RS group) in a 1:1 ratio. Respiratory viruses were tested using NxTAG™ Respiratory Pathogen Panel IVD, a commercially-available multiplex PCR panel.

Results

A total of 214 acutely hospitalized patients were included in the final analysis, consisting of 107 with fever/RS (fever/RS group), and 107 age- and sex-matched patients without fever/RS (non-fever/RS group). Respiratory viruses were detected in 34.1% (73/214) of patients, and co-infection occurred in 7.9% (17/214) of patients. The incidence of respiratory virus was higher in the fever/RS group than in the non-fever/RS group (44.9% (48/107) versus 23.4% (25/107), p 0.001). Influenza B virus, enterovirus/rhinovirus and coronaviruses were detected more frequently in the fever/RS group, whereas parainfluenza virus 4B and adenovirus were detected more frequently in the non-fever/RS group. Among the non-fever/RS group, chest discomfort was more common among patients tested positive for respiratory viruses than those without respiratory virus detected (44% (11/25) versus 22% (18/82), p 0.04).

Conclusions

Respiratory viruses can be frequently detected among hospitalized patients without typical features of respiratory tract infection. These patients may be a source of nosocomial outbreaks.

Uncertainty analysis in source apportionment of heavy metals in road dust based on positive matrix factorization model and geographic information system

Based on 36 road dust samples from an urbanized area of Beijing in September 2016, the information about sources (types, proportions, and intensity in spatial) of heavy metals and uncertainties were analyzed using positive matrix factorization (PMF) model, bootstrap (BS), geographic information system (GIS) and Kriging. The mean concentration of most heavy metals was higher than the corresponding background, and mean concentration of Cd was six times of its background value. Types and proportions of four sources were identified: fuel combustion (33.64%), vehicle emission (25.46%), manufacture and use of metallic substances (22.63%), and use of pesticides, fertilizers, and medical devices (18.26%). The intensity of vehicle emission and the use of pesticides, fertilizers, and medical devices were more homogeneous in spatial (extents were 1.285 and 0.955), while intensity of fuel combustion and the manufacture and use of metallic substances varied largely (extents were 4.172 and 5.518). Uncertainty analysis contained three aspects: goodness of fit, bias and variability in the PMF solution, and impact of input data size. Goodness of fit was assessed by coefficient of determination (R²) of predicted and measured values, and R² of most species were higher than 0.56. Influenced by an outlier, R² of Ni decreased from 0.59 to 0.11. Result of bootstrap (BS) showed good robust of this four-factor configuration in PMF model, and contributions of base run of factors to most species were contained in the small interquartile range and close to median values of bootstrap. Size of input data also had influence on results of PMF model. Residuals changed largely with the increase of number of site, it varied at first and then kept stable after number of site reached 70.

Asymptomatic Shedding of Respiratory Virus among an Ambulatory Population across Seasons

Most observation of human respiratory virus carriage is derived from medical surveillance; however, the infections documented by this surveillance represent only a symptomatic fraction of the total infected population. As the role of asymptomatic infection in respiratory virus transmission is still largely unknown and rates of asymptomatic shedding are not well constrained, it is important to obtain more-precise estimates through alternative sampling methods. We actively recruited participants from among visitors to a New York City tourist attraction. Nasopharyngeal swabs, demographics, and survey information on symptoms, medical history, and recent travel were obtained from 2,685 adults over two seasonal arms. We used multiplex PCR to test swab specimens for a selection of common respiratory viruses. A total of 6.2% of samples (168 individuals) tested positive for at least one virus, with 5.6% testing positive in the summer arm and 7.0% testing positive in the winter arm. Of these, 85 (50.6%) were positive for human rhinovirus (HRV), 65 (38.7%) for coronavirus (CoV), and 18 (10.2%) for other viruses (including adenovirus, human metapneumovirus, influenza virus, and parainfluenza virus). Depending on the definition of symptomatic infection, 65% to 97% of infections were classified as asymptomatic. The best-fit model for prediction of positivity across all viruses included a symptom severity score, Hispanic ethnicity data, and age category, though there were slight differences across the seasonal arms. Though having symptoms is predictive of virus positivity, there are high levels of asymptomatic respiratory virus shedding among the members of an ambulatory population in New York City.IMPORTANCE Respiratory viruses are common in human populations, causing significant levels of morbidity. Understanding the distribution of these viruses is critical for designing control methods. However, most data available are from medical records and thus predominantly represent symptomatic infections. Estimates for asymptomatic prevalence are sparse and span a broad range. In this study, we aimed to measure more precisely the proportion of infections that are asymptomatic in a general, ambulatory adult population. We recruited participants from a New York City tourist attraction and administered nasal swabs, testing them for adenovirus, coronavirus, human metapneumovirus, rhinovirus, influenza virus, respiratory syncytial virus, and parainfluenza virus. At recruitment, participants completed surveys on demographics and symptomology. Analysis of these data indicated that over 6% of participants tested positive for shedding of respiratory virus. While participants who tested positive were more likely to report symptoms than those who did not, over half of participants who tested positive were asymptomatic.