Association of the CT values of real-time PCR of viral upper respiratory tract infection with clinical severity, Kenya

Antibody levels against respiratory syncytial virus fusion protein conformations and lack of association with life-threatening infection in previously healthy infants

BACKGROUND

Humoral immune response against the pre-fusion (pre-F) conformation of respiratory syncytial virus (RSV) F protein has been proposed to play a protective role against infection. An RSV pre-F maternal vaccine has been recently approved in several countries to protect young infants against RSV. We aimed to assess serum IgG titers against the pre-F and post-F conformations of RSV F protein and their association with life-threatening RSV disease (LTD) in previously healthy infants.

METHODS

A prospective cohort study including hospitalized infants <12 months with a first RSV infection was conducted during 2017-2019. Patients with LTD required intensive care and mechanical respiratory assistance. RSV pre-F exclusive and post-F antibody responses were determined by post-F competition and non-competition immunoassays, respectively, and neutralizing activity was measured by plaque reduction neutralization test.

RESULTS

Fifty-eight patients were included; the median age was 3.5 months and 41 % were females. Fifteen patients developed LTD. RSV F-specific antibody titers positively correlated with neutralizing antibody titers in acute and convalescent phases but, importantly, they did not associate with LTD. Acute RSV pre-F exclusive and post-F IgG titers negatively correlated with patient age (P = 0.0007 and P < 0.0001), while a positive correlation was observed between the fold changes in RSV F-specific antibody titers between convalescent and acute phase and patient age (P = 0.0014 and P < 0.0001). Infants ≤2 months exhibited significantly lower fold-changes in RSV F-specific and neutralizing antibody titers between convalescence and acute phase than older infants. Additionally, acute RSV antibody titers showed no correlation with nasal RSV load and, furthermore, nasal viral load was not associated with the development of LTD.

CONCLUSIONS

This study highlights that protection against life-threatening RSV disease is not necessarily antibody-dependent. Further characterization of the immune response against RSV and its role in protection against severe disease is important for the development of the safest possible preventive strategies.

Cutavirus Infection in Large-Plaque Parapsoriasis, a Premalignant Condition of Mycosis Fungoides

BACKGROUND

Cutavirus (CuV) is associated with mycosis fungoides; however, the CuV status in parapsoriasis en plaques (PP), a premalignant inflammatory condition of mycosis fungoides, has not been fully delineated.

METHODS

Fifty-five Japanese patients with chronic inflammatory skin diseases, including 13 patients with PP, were studied.

RESULTS

CuV DNA was detected significantly more frequently in biopsies of the lesional skin from patients with PP (38%; 4 of 13) than in those from patients with other inflammatory skin diseases (2%; 1 of 42; P = .009). All CuV-positive PP cases were of the large-plaque parapsoriasis (LPP) subtype. The viral loads ranged from 83 450 to 2 164 170 copies/103 cells. We recovered near-full-length CuV sequences from the CuV-positive LPP biopsies, all of which were of the Japanese/Asian genotype. The CuV genome appeared to be present within lymphoid cells infiltrating the epidermis and dermis. CuV NS1 and VP1 gene transcripts were also detected in the affected tissues.

CONCLUSIONS

The detection of high levels of CuV DNA with the expression of viral mRNA suggests a potential role for CuV in the pathogenesis of LPP, making it necessary to study further the impact of CuV, especially regarding the viral genotype, on the outcomes of patients with CuV-positive LPP.

Symptom propagation in respiratory pathogens of public health concern: a review of the evidence

Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clusters of severe disease. Conversely, it could result in chains of mild infection, generating widespread immunity with minimal cost to public health. Despite accumulating evidence that symptom propagation occurs for many respiratory pathogens, the underlying mechanisms are not well understood. Here, we conducted a scoping literature review for 14 respiratory pathogens to ascertain the extent of evidence for symptom propagation by two mechanisms: dose-severity relationships and route-severity relationships. We identify considerable heterogeneity between pathogens in the relative importance of the two mechanisms, highlighting the importance of pathogen-specific investigations. For almost all pathogens, including influenza and SARS-CoV-2, we found support for at least one of the two mechanisms. For some pathogens, including influenza, we found convincing evidence that both mechanisms contribute to symptom propagation. Furthermore, infectious disease models traditionally do not include symptom propagation. We summarize the present state of modelling advancements to address the methodological gap. We then investigate a simplified disease outbreak scenario, finding that under strong symptom propagation, isolating mildly infected individuals can have negative epidemiological implications.

Cycle threshold dynamics of non-severe acute respiratory coronavirus virus 2 (SARS-CoV-2) respiratory viruses

OBJECTIVE

Many providers use severe acute respiratory coronavirus virus 2 (SARS-CoV-2) cycle thresholds (Ct values) as approximate measures of viral burden in association with other clinical data to inform decisions about treatment and isolation. We characterized temporal changes in Ct values for non-SARS-CoV-2 respiratory viruses as a first step to determine whether cycle thresholds could play a similar role in the management of non-SARS-CoV-2 respiratory viruses.

DESIGN

Retrospective cohort study.

SETTING

Brigham and Women's Hospital, Boston.

METHODS

We retrospectively identified all adult patients with positive nasopharyngeal PCRs for influenza, respiratory syncytial virus (RSV), parainfluenza, human metapneumovirus (HMPV), rhinovirus, or adenovirus between January 2022 and March 2023. We plotted Ct distributions relative to days since symptom onset, and we assessed whether distributions varied by immunosuppression and other comorbidities.

RESULTS

We analyzed 1,863 positive samples: 506 influenza, 502 rhinovirus, 430 RSV, 219 HMPV, 180 parainfluenza, 26 adenovirus. Ct values were generally 25-30 on the day of symptom onset, lower over the ensuing 1-3 days, and progressively higher thereafter with Ct values ≥30 after 1 week for most viruses. Ct values were generally higher and more stable over time for rhinovirus. There was no association between immunocompromised status and median intervals from symptom onset until Ct values were ≥30.

CONCLUSIONS

Ct values relative to symptom onset for influenza, RSV, and other non-SARS-CoV-2 respiratory viruses generally mirror patterns seen with SARS-CoV-2. Further data on associations between Ct values and viral viability, transmissibility, host characteristics, and response to treatment for non-SARS-CoV-2 respiratory viruses are needed to determine how clinicians and infection preventionists might integrate Ct values into treatment and isolation decisions.

Asymptomatic viruses detectable in saliva in the first year of life: a narrative review

Viral infections are common in children. Many can be asymptomatic or have delayed health consequences. In view of increasing availability of point-of-care viral detection technologies, with possible application in newborn screening, this review aimed to (1) identify potentially asymptomatic viruses detectable in infants under one year old, via saliva/nasopharyngeal swab, and (2) describe associations between viruses and long-term health conditions. We systematically searched Embase(Ovid), Medline(Ovid) and PubMed, then further searched the literature in a tiered approach. From the 143 articles included, 28 potentially asymptomatic viruses were identified. Our second search revealed associations with a range of delayed health conditions, with most related to the severity of initial symptoms. Many respiratory viruses were linked with development of recurrent wheeze or asthma. Of note, some potentially asymptomatic viruses are linked with later non-communicable diseases: adenovirus serotype 36 and obesity, Enterovirus-A71 associated Hand, Foot, Mouth Disease and Attention-Deficit Hyperactivity Disorder, Ebstein Barr Virus (EBV) and malignancy, EBV and multiple sclerosis, HHV-6 and epilepsy, HBoV-1 and lung fibrosis and Norovirus and functional gastrointestinal disorders. Our review identified many potentially asymptomatic viruses, detectable in early life with potential delayed health consequences, that could be important to screen for in the future using rapid point-of-care viral detection methods. IMPACT: Novel point-of-care viral detection technologies enable rapid detection of viruses, both old and emerging. In view of increasing capability to screen for viruses, this is the first review to explore which potentially asymptomatic viruses, that are detectable using saliva and/or nasopharyngeal swabs in infants less than one year of age, are associated with delayed adverse health conditions. Further research into detecting such viruses in early life and their delayed health outcomes may pave new ways to prevent non-communicable diseases in the future.

Clinical Outcomes of Acutely Ill Children According to Cycle Threshold Values of Respiratory Viruses Detected by Multiplex PCR Testing

In this cohort study of 800 children attending a pediatric emergency department at Oulu University Hospital, Finland with fever or respiratory symptoms, the cycle threshold values of point-of-care multiplex polymerase chain reaction testing for respiratory viruses were not associated with hospitalization, respiratory support, or need for intensive care.

Involvement of cutavirus in a subset of patients with cutaneous T-cell lymphoma with an unfavorable outcome

BACKGROUND

European studies suggest an association between cutavirus (CuV) and cutaneous T-cell lymphoma (CTCL); however, the worldwide prevalence of CuV in patients with CTCL and its prognostic impact remain unknown.

METHODS

We investigated the prevalence and viral loads of CuV DNA using biopsy specimens from the lesional skins of 141 Japanese patients with cutaneous malignancies, including 55 patients with various types of CTCL.

RESULTS

CuV DNA was detected significantly more frequently in biopsies from patients with mycosis fungoides (MF) (38% [13/34]; the most common subtype of CTCL) than in those from patients with other cutaneous malignancies (6% [6/107]; P<0.001). The viral-load range in patients with CuV DNA-positive MF was 23-3922 copies/10³ cells and 8-65 copies/μg of DNA. A phylogenetic analysis using the partial sequences of the CuV viral capsid protein 1 (VP1)/VP2 genes revealed that the CuV sequences identified here were clustered in a Japanese-specific clade distinct from that comprising CuV sequences from European patients with MF. Kaplan-Meier curves and a log-rank test showed that CuV positivity was associated with a shorter disease-specific survival in patients with MF (P = 0.031), whereas no significant difference in overall survival was observed (P = 0.275). No significant correlation was observed between CuV DNA load and survival in patients with CuV-positive MF.

CONCLUSIONS

Our results suggest that CuV is associated with MF in a subset of Japanese patients. Large-scale prospective studies are warranted to clarify the role of CuV status, especially regarding the viral genotype, on adverse outcomes in patients with CuV-positive MF.

Evaluation of four laboratory-based high-throughput SARS-CoV-2 automated antigen tests compared to RT-PCR on nasal and oropharyngeal samples

BACKGROUND

The demand for RT-PCR testing has been unprecedented during the SARS-CoV-2 pandemic. Fully automated antigen tests (AAT) are less cumbersome than RT-PCR, but data on performance compared to RT-PCR are scarce.

METHODS

The study consists of two parts. A retrospective analytical part, comparing the performance of four different AAT on 100 negative and 204 RT-PCR positive deep oropharyngeal samples divided into four groups based on RT-PCR cycle of quantification levels. In the prospective clinical part, 206 individuals positive for and 199 individuals negative for SARS-CoV-2 were sampled from either the anterior nasal cavity (mid-turbinate) or by deep oropharyngeal swabs or both. The performance of AATs was compared to RT-PCR.

RESULTS

The overall analytical sensitivity of the AATs differed significantly from 42% (95% CI 35-49) to 60% (95% CI 53-67) with 100% analytical specificity. Clinical sensitivity of the AATs differed significantly from 26% (95% CI 20-32) to 88% (95% CI 84-93) with significant higher sensitivity for mid-turbinate nasal swabs compared to deep oropharyngeal swabs. Clinical specificity varied from 97% to 100%.

CONCLUSION

All AATs were highly specific for detection of SARS-CoV-2. Three of the four AATs were significantly more sensitive than the fourth AAT both in terms of analytical and clinical sensitivity. Anatomical test location significantly influenced the clinical sensitivity of AATs.

Pathogenetic and etiologic considerations of febrile seizures

Febrile seizure (FS), which occurs in febrile children without underlying health problems, is the most common type of seizure disorder in children. The suggested pathogenesis of FS derived from several animal and human studies is multifactorial and debatable. Neuronal hyperexcitability, which develops during inflammatory responses that accompany fever, provokes seizures. However, the exact role of each inflammatory mediator (e.g., cytokines) is undefined in terms of the connection between systemic or local inflammation and the central nervous system, and the mechanisms by which cytokines increase neuronal excitability remain unclear. In contrast, the cause of fever in most children with FS is usually mild respiratory virus infection (e.g., rhinovirus, influenza virus, adenovirus, and enterovirus) rather than severe bacterial infections. In temperate regions, the major causative respiratory viruses seem to mirror seasonally prevalent respiratory viruses in the community. Therefore, vigorous efforts to identify the causative pathogen of fever may not be necessary in children with FS. Genetic factors seem to play a role in neuronal hyperexcitability, and some types of genetic variation have been identified in several genes encoding ion channels of neurons that participate in neuronal excitation. Although most children with FS have benign outcomes, some characteristics such as complex FS, febrile status epilepticus, consecutive afebrile seizures, and the presence of neurodevelopmental disabilities may require further genetic and neurologic evaluations.

Molecular epidemiology of respiratory syncytial virus in children with acute respiratory illnesses in Africa: A systematic review and meta-analysis

Background

Globally, the respiratory syncytial virus (RSV) is the most common etiologic agent of acute respiratory illnesses in children. However, its burden has not been well addressed in developing countries. We aimed to estimate the molecular epidemiology of RSV in children less than 18 years of age with acute respiratory infections in Africa by conducting a systematic review and meta-analysis.

Methods

We systematically searched PubMed, Scopus, CINAHL, and Global Index Medicus databases to identify studies published from January 1, 2002, to April 27, 2022, following the PRISMA 2020 guideline. We assessed the study quality using the Joanna Brigg's Institute (JBI) critical appraisal checklists. We conducted a qualitative synthesis by describing the characteristics of included studies and performed the quantitative synthesis with random effects model using STATA-14. We checked for heterogeneity with Q statistics, quantified by I², and determined the prediction interval. We performed subgroup analyses to explain the sources of heterogeneity and assessed publication biases by funnel plots augmented with Egger's test.

Results

Eighty-eight studies with 105 139 participants were included in the review. The overall pooled prevalence of RSV in children <18 years of age was 23% (95% confidence interval (CI) = 20, 25%). Considerable heterogeneity was present across the included studies. The adjusted prediction interval was found to be 19%-27%. Heterogeneities were explained by subgroups analyses. The highest prevalence of RSV was found among inpatients, 28% (95% CI = 25, 31%) compared with inpatients/outpatients and outpatients, with statistically significant differences (P < 0.01). The RSV estimate was also highest among those with acute lower respiratory tract illnesses (ALRTIs), 28% (95% CI = 25, 31%) compared with acute upper respiratory tract illnesses (AURTIs) and both acute upper/lower respiratory manifestations, with statistically different prevalence (P < 0.01). RSV infection estimates in each sub-region of Africa were statistically different (P < 0.01). There were no statistically significant differences in RSV infections by designs, specimen types, and specimen conditions, despite them contributing to heterogeneity.

Conclusions

We found a high prevalence of RSV in pediatric populations with acute respiratory tract illnesses in Africa, highlighting that the prevention and control of RSV infections in children deserve more attention.

Registration

PROSPERO CRD42022327054.

Age-related cognitive impairments in domestic cats naturally infected with feline immunodeficiency virus

BACKGROUND

Age-related dementia has been documented in domestic cats; however, its interaction with naturally occurring feline immunodeficiency virus (FIV) infection has been investigated minimally.

METHODS

Visuospatial working memory (VSWM) and problem-solving (PS) ability were evaluated in FIV-infected (n = 37) and control cats (n = 39) using two cognitive tasks tested serially, which assessed the ability of cats to remember the location of a baited container after a set delay, then evaluated the capability of the cats to manipulate the container to obtain the food within a time limit. Cats were categorized using 7 years of age as a cut-off to determine age-related differences. The relationship between cognitive performance and FIV viral load was investigated using real-time PCR cycle threshold (C_t ) values.

RESULTS

Age significantly affected VSWM and PS ability. Younger cats had better VSWM performance and PS ability compared to older cats with the same FIV status. There was no difference between younger FIV-positive and negative cats in either part of the task. While older FIV-positive cats had significantly worse VSWM than older FIV-negative cats, no differences were found in PS ability. Additionally, C_t values predicted VSWM but not PS ability.

CONCLUSION

Age-related cognitive impairments and FIV infection appear synergetic, causing greater cognitive deficits in older FIV-infected cats.

A new dynamic deep learning noise elimination method for chip-based real-time PCR

Point-of-care (POC) real-time polymerase chain reaction (PCR) has become one of the most important technologies for many fields such as pathogen detection and water-quality monitoring. POC real-time PCR usually adopts chips with small-volume chambers for portability, which is more likely to produce complex noise that seriously affects the accuracy. Such complex noises are difficult to be eliminated by the traditional fixed area algorithm that is most commonly used at present because they usually have random shape, location, and brightness. To address this problem, we proposed a novel image analysis method, Dynamic Deep Learning Noise Elimination Method (DIPLOID), in this paper. Our new method could recognize and output the mask of the interference by Mask R-CNN, and then subtract the interference and select the maximum valid contiguous area for brightness analysis by dynamic programming. Compared with the traditional method, DIPLOID increased the accuracy, sensitivity, and specificity from 57.9 to 94.6%, 49.1 to 93.9%, and 65.9 to 95.2%, respectively. DIPLOID has great anti-interference, robustness, and sensitivity, which can reduce the impact of complex noise as much as possible from the aspect of the algorithm. As shown in the experiments of this paper, our method significantly improved the accuracy to over 94% under the complex noise situation, which could make the POC real-time PCR have greater potential in the future.

Factors associated with severe respiratory syncytial virus disease in hospitalised children: a retrospective analysis

BACKGROUND

Early recognition of children at risk of severe respiratory syncytial virus (RSV) lower respiratory tract infection is important as it informs management decisions. We aimed to evaluate factors associated with severe disease among young children hospitalised with RSV infection.

METHODS

We conducted a retrospective cohort study of all children <2 years of age hospitalised for RSV lower respiratory tract infection at a single tertiary paediatric hospital over three RSV seasons (January 2017-December 2019). We classified children as having 'moderate' or 'severe' disease based on the level of respiratory intervention and used univariable and multivariable regression models to determine factors associated with severe disease.

RESULTS

Of 970 hospitalised children, 386 (40%) were classified as having 'severe' and 584 (60%) as having 'moderate' RSV disease. On multivariable analyses, age <2 months (OR: 2.3, 95% CI 1.6 to 3.3, p<0.0001), prematurity (OR: 1.6, 95% CI 1.1 to 2.4, p=0.02) and RSV-parainfluenza virus type 3 (PIV3) codetection (OR: 2.6, 95% CI 1.05 to 6.5, p=0.04) were independently associated with severe disease.

CONCLUSION

Younger age, prematurity and PIV3 codetection were associated with severe RSV disease in children <2 years of age hospitalised with RSV infection. The association between PIV3 and severe RSV disease is a novel finding and warrants further investigation.

Evaluation of the QIAstat-Dx RP2.0 and the BioFire FilmArray RP2.1 for the Rapid Detection of Respiratory Pathogens Including SARS-CoV-2

Point-of-care syndromic panels allow for simultaneous and rapid detection of respiratory pathogens from nasopharyngeal swabs. The clinical performance of the QIAstat-Dx Respiratory SARS-CoV-2 panel RP2.0 (QIAstat-Dx RP2.0) and the BioFire FilmArray Respiratory panel RP2.1 (BioFire RP2.1) was evaluated for the detection of SARS-CoV-2 and other common respiratory pathogens. A total of 137 patient samples were retrospectively selected based on emergency department admission, along with 33 SARS-CoV-2 positive samples tested using a WHO laboratory developed test. The limit of detection for SARS-CoV-2 was initially evaluated for both platforms. The QIAstat-Dx RP2.0 detected SARS-CoV-2 at 500 copies/mL and had a positive percent agreement (PPA) of 85%. The BioFire RP2.1 detected SARS-CoV-2 at 50 copies/mL and had a PPA of 97%. Both platforms showed a negative percent agreement of 100% for SARS-CoV-2. Evaluation of analytical specificity from a range of common respiratory targets showed a similar performance between each platform. The QIAstat-Dx RP2.0 had an overall PPA of 82% (67–100%) in clinical samples, with differences in sensitivity depending on the respiratory target. Both platforms can be used to detect acute cases of SARS-CoV-2. While the QIAstat-Dx RP2.0 is suitable for detecting respiratory viruses within a clinical range, it has less analytical and clinical sensitivity for SARS-CoV-2 compared to the BioFire RP2.1.

Nitrogen Accumulation in Oyster (Crassostrea gigas) Slurry Exposed to Virucidal Cold Atmospheric Plasma Treatment

Viral contamination of edible bivalves is a major food safety issue. We studied the virucidal effect of a cold atmospheric plasma (CAP) source on two virologically different surrogate viruses [a double-stranded DNA virus (Equid alphaherpesvirus 1, EHV-1), and a single-stranded RNA virus (Bovine coronavirus, BCoV)] suspended in Dulbecco’s Modified Eagle’s Medium (DMEM). A 15 min exposure effectuated a statistically significant immediate reduction in intact BCoV viruses by 2.8 (ozone-dominated plasma, “low power”) or 2.3 log cycles (nitrate-dominated, “high power”) of the initial viral load. The immediate effect of CAP on EHV-1 was less pronounced, with “low power” CAP yielding a 1.4 and “high power” a 1.0 log reduction. We observed a decline in glucose contents in DMEM, which was most probably caused by a Maillard reaction with the amino acids in DMEM. With respect to the application of the virucidal CAP treatment in oyster production, we investigated whether salt water could be sanitized. CAP treatment entailed a significant decline in pH, below the limits acceptable for holding oysters. In oyster slurry (a surrogate for live oysters), CAP exposure resulted in an increase in total nitrogen, and, to a lower extent, in nitrate and nitrite; this was most probably caused by absorption of nitrate from the plasma gas cloud. We could not observe a change in colour, indicative for binding of NO_x to haemocyanin, although this would be a reasonable assumption. Further studies are necessary to explore in which form this additional nitrogen is deposited in oyster flesh.

Viral Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Patients with Coronavirus Disease 2019

To determine the relationship between viral kinetics and severity of disease in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, we investigated the viral kinetics and compared the viral loads of patients with coronavirus disease 2019 (COVID-19; the disease caused by SARS-CoV-2), stratified by symptoms and severity. We determined the viral kinetics of 100 patients diagnosed with COVID-19 at Chosun University Hospital between February 2020 and May 2021 and analyzed the differences between asymptomatic, symptomatic, and nonsurvivor patients and between patients who died and those who survived. Clinical samples, comprising respiratory specimens (sputum samples and nasopharynx and oropharynx swab samples), were obtained at different time points of hospitalization, at 1, 3 to 5, 7, 10, 14, and 30 days. SARS-CoV-2 was detected using real-time reverse transcription-PCR (RT-PCR). All three groups, asymptomatic, symptomatic, and deceased patients, had higher numbers of viral copies at symptom onset, and the asymptomatic group had lower numbers of viral copies than the symptomatic or nonsurvivor group. Viral RNA release was detected until 30 days after symptom onset. The virus cleared up earlier in asymptomatic patients than in symptomatic and nonsurvivor patients, and it cleared up earlier in mildly affected patients than in severely affected patients. The cycle threshold values tended to be significantly lower in the group receiving steroids than in the nonsteroid group, even in the low-risk group with a pneumonia severity index of less than 90. The viral loads in patients with COVID-19 were significantly different according to disease severity and steroid use. IMPORTANCE In our study, we analyzed the viral kinetics of COVID-19 patients. Our study reveals differences in viral shedding according to the severity of disease in COVID-19 patients. Viral shedding had a longer duration in severely affected patients, and the cyclic threshold values were lower in the group receiving steroids. This study is expected to be helpful in analyzing the trend of the disease course according to steroid use and severity of SARS-CoV-2 disease.

Systematic review on the association between respiratory virus real-time PCR cycle threshold values and clinical presentation or outcomes

Objectives

It is unclear whether real-time (rt)-PCR cycle threshold (Ct) values can be utilized to guide clinical and infection-control decisions. This systematic review assesses the association between respiratory pathogen rt-PCR Ct values and clinical presentation or outcomes.

Methods

We searched MEDLINE, EMBASE and Cochrane library databases on 14–17 January 2020 for studies reporting the presence or absence of an association between Ct values and clinical presentation or outcomes, excluding animal studies, reviews, meta-analyses, and non-English language studies.

Results

Among 33 studies identified (reporting on between 9 and 4918 participants by pathogen), influenza (n = 11 studies; 4918 participants), human rhinovirus (HRV, n = 11; 2012) and respiratory syncytial virus (RSV, n = 8; 3290) were the most-studied pathogens. Low influenza Ct values were associated with mortality in 1/3 studies, with increased disease severity/duration or ICU admission in 3/9, and with increased hospitalization or length of hospital stay (LOS) in 1/6. Low HRV Ct values were associated with increased disease severity/duration or ICU admission in 3/10 studies, and with increased hospitalization or LOS in 1/3. Low RSV Ct values were associated with increased disease severity/duration or ICU admission in 3/6 studies, and with increased hospitalization or LOS in 4/4. Contradictory associations were also identified for other respiratory pathogens.

Conclusions

Respiratory infection Ct values may inform clinical and infection-control decisions. However, the study heterogeneity observed in this review highlights the need for standardized workflows to utilize Ct values as a proxy of genomic load and confirm their value for respiratory infection management.

Estimating epidemiologic dynamics from cross-sectional viral load distributions

Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance-in the form of cycle threshold (Ct) values obtained from reverse transcription quantitative polymerase chain reaction testing-changes during an epidemic. Thus, Ct values from even limited numbers of random samples can provide improved estimates of an epidemic's trajectory. Combining data from multiple such samples improves the precision and robustness of this estimation. We apply our methods to Ct values from surveillance conducted during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in a variety of settings and offer alternative approaches for real-time estimates of epidemic trajectories for outbreak management and response.

Hospital utilization rates for influenza and RSV: a novel approach and critical assessment

BACKGROUND

Influenza and respiratory syncytial virus (RSV) contribute significantly to the burden of acute lower respiratory infection (ALRI) inpatient care, but heterogeneous coding practices and availability of inpatient data make it difficult to estimate global hospital utilization for either disease based on coded diagnoses alone.

METHODS

This study estimates rates of influenza and RSV hospitalization by calculating the proportion of ALRI due to influenza and RSV and applying this proportion to inpatient admissions with ALRI coded as primary diagnosis. Proportions of ALRI attributed to influenza and RSV were extracted from a meta-analysis of 360 total sources describing inpatient hospital admissions which were input to a Bayesian mixed effects model over age with random effects over location. Results of this model were applied to inpatient admission datasets for 44 countries to produce rates of hospital utilization for influenza and RSV respectively, and rates were compared to raw coded admissions for each disease.

RESULTS

For most age groups, these methods estimated a higher national admission rate than the rate of directly coded influenza or RSV admissions in the same inpatient sources. In many inpatient sources, International Classification of Disease (ICD) coding detail was insufficient to estimate RSV burden directly. The influenza inpatient burden estimates in older adults appear to be substantially underestimated using this method on primary diagnoses alone. Application of the mixed effects model reduced heterogeneity between countries in influenza and RSV which was biased by coding practices and between-country variation.

CONCLUSIONS

This new method presents the opportunity of estimating hospital utilization rates for influenza and RSV using a wide range of clinical databases. Estimates generally seem promising for influenza and RSV associated hospitalization, but influenza estimates from primary diagnosis seem highly underestimated among older adults. Considerable heterogeneity remains between countries in ALRI coding (i.e., primary vs non-primary cause), and in the age profile of proportion positive for influenza and RSV across studies. While this analysis is interesting because of its wide data utilization and applicability in locations without laboratory-confirmed admission data, understanding the sources of variability and data quality will be essential in future applications of these methods.

Nasopharyngeal density of respiratory viruses in childhood pneumonia in a highly vaccinated setting: findings from a case-control study

Background

Detection of pneumonia-causing respiratory viruses in the nasopharynx of asymptomatic children has made their actual contribution to pneumonia unclear. We compared nasopharyngeal viral density between children with and without pneumonia to understand if viral density could be used to diagnose pneumonia.

Methods

Nasopharyngeal swabs (NPS) were collected from hospitalised pneumonia cases at Princess Margaret Hospital (PMH) and contemporaneous age-matched controls at PMH outpatient clinics and a local immunisation clinic in Perth, Australia. The density (copies/mL) of respiratory syncytial virus (RSV), influenza A virus (InfA), human metapneumovirus (HMPV) and rhinovirus in NPS was determined using quantitative PCR. Linear regression analysis was done to assess the trend between viral density and age in months. The association between viral density and disease status was examined using logistic regression. Area under receiver operating characteristic (AUROC) curves were assessed to determine optimal discriminatory viral density cut-offs.

Results

Through May 2015 to October 2017, 230 pneumonia cases and 230 controls were enrolled. Median nasopharyngeal density for any respiratory virus was not substantially higher in cases than controls (p>0.05 for each). A decreasing density trend with increasing age was observed—the trend was statistically significant for RSV (regression coefficient −0.04, p=0.004) but not for other viruses. After adjusting for demographics and other viral densities, for every log₁₀ copies/mL density increase, the odds of being a case increased by six times for RSV, three times for HMPV and two times for InfA. The AUROC curves were <0.70 for each virus, suggesting poor case–control discrimination based on viral density.

Conclusion

The nasopharyngeal density of respiratory viruses was not significantly higher in children with pneumonia than those without; however, the odds of being a case increased with increased density for some viruses. The utility of viral density, alone, in defining pneumonia was limited.

Common respiratory viral infections: Bilateral versus unilateral bronchoalveolar lavage versus endotracheal aspiration

Data about the diagnostic efficiency of bilateral bronchoalveolar lavage (BAL) samples and endotracheal aspirates (EA) testing for common viral respiratory infections are scarce. We analyzed data from 167 cases, where bilateral BAL samples were tested, and from 101 cases, where BAL samples and EA were tested. Multiplex polymerase chain reaction (PCR) was performed with the fast track diagnostics viral respiratory panel, producing data on the adenovirus, coronavirus, enterovirus, human metapneumovirus, bocavirus, influenza virus, parainfluenza virus, rhinovirus, and respiratory syncytial virus status of patients with respiratory disease symptoms. In the bilateral BAL cohort, 46 (27.5%) cases were positive for at least one of the viruses mentioned above in both samples. Discrepant results (virus not detected on one side) were seen in six (3.6%) cases. In the BAL versus EA cohort, 12 (11.9%) cases were positive in both materials, discrepant results (only one material being positive) were observed in 11 (10.9%) cases, with seven (63.6%) BAL samples, and four (36.4%) EA being positive. Bilateral sampling does not significantly improve the diagnostic efficiency of BAL for the detection of common respiratory viral pathogens via PCR. The diagnostic quality of EA and BAL samples for the detection of common viral respiratory pathogens is comparable.

Evaluation of PCR cycle threshold values by patient population with the quidel lyra SARS-CoV-2 assay

The Lyra SARS-CoV-2 assay was the primary method for molecular testing performed at Barnes-Jewish Healthcare System in St. Louis, Missouri during the initial COVID-19 surge from mid-March to late-April 2020. We performed a retrospective analysis of 1,043 positive Lyra SARS-CoV-2 results during these 36 days to investigate associations between cycle threshold (C_T)  value and patient characteristics. Total RNA were extracted from NP or OP swabs using either the EasyMag or KingFisher automated extraction systems and quantified with RotorGene Q (Qiagen) or Applied Biosystems 7500 Fast Dx thermocyclers respectively. Notably, we found lower a significant median lower C_T for samples tested on the KingFisher-ABI 7500 fastDX (KF/ABI) system compared to the EasyMag/RotorGene (EM/RGQ) platform. Since 77.5% of our tests were ran on the EM/RGQ pipeline we then perform additional analysis on these values and found that C _T values in outpatient care settings compared to samples obtained in the emergency department or inpatient had significantly lower C _T values. These collective findings suggests a difference in viral load amongst various patient populations.

Aging correlates with lower threshold cycle values for RdRP/RdRP+S genes during molecular detection of SARS-CoV-2

RT-qPCR is the most reliable molecular method for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we analyzed results of RT-qPCR obtained for 3044 patients diagnosed as SARS-CoV-2-positive using four different molecular tests utilizing five RNA sequences. The analysis showed that patients' age inversely correlates with threshold cycle (Ct) values for RdRP gene (LightMix® Modular Wuhan CoV RdRP-gene by Roche Diagnostics) and RdRP+S genes (MutaPLEX® Coronavirus RT-PCR kit by Immundiagnostic). At the same time, there was no correlation between age and Ct values for E, N, and ORF1ab genes. When patients were grouped by age, mean Ct values for RdRP gene in older patients were significantly lower compared with younger individuals. Collectively, our report indicates that older SARS-CoV-2-infected individuals exhibit higher viremia at diagnosis than younger patients, which may reflect impaired functioning of their immune response and predispose to more severe disease and worse prognosis.

Association of Viral Load With Disease Severity in Outpatient Children With Respiratory Syncytial Virus Infection

BACKGROUND

There are scarce data on whether viral load affects the severity of respiratory syncytial virus (RSV) disease in outpatient children.

METHODS

We analyzed the association between viral load and disease severity among children who participated in a prospective cohort study of respiratory infections. The children were examined and nasal swabs for the detection of RSV were obtained during each respiratory illness. Quantification of RSV load was based on the cycle threshold (Ct) value. For the primary analysis, the children were divided into 2 groups: higher (Ct < 27) and lower viral load (Ct ≥ 27).

RESULTS

Among 201 episodes of RSV infection, children with higher viral load had significantly longer median durations of rhinitis (8 vs 6 days; P = .0008), cough (8 vs 6 days; P = .034), fever (2 vs 1 days; P = .018), and any symptom (10 vs 8 days; P = .024) than those with lower viral load. There were statistically significant negative correlations between the Ct values and durations of all measured symptoms.

CONCLUSIONS

Our findings support the concept that viral load drives the severity of RSV disease in children. Reducing the viral load by RSV antivirals might provide substantial benefits to outpatient children.

Estimating epidemiologic dynamics from cross-sectional viral load distributions

Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but incidence data used for such estimation are confounded by variable testing practices. We show instead that the population distribution of viral loads observed under random or symptom-based surveillance, in the form of cycle threshold (Ct) values, changes during an epidemic and that Ct values from even limited numbers of random samples can provide improved estimates of an epidemic's trajectory. Combining multiple such samples and the fraction positive improves the precision and robustness of such estimation. We apply our methods to Ct values from surveillance conducted during the SARS-CoV-2 pandemic in a variety of settings and demonstrate new approaches for real-time estimates of epidemic trajectories for outbreak management and response.

Associations Between Relative Viral Load at Diagnosis and Influenza A Symptoms and Recovery

BACKGROUND

Rapid point-of-care polymerase chain reaction (PCR) diagnostic tests generally provide a qualitative result of positive or negative only. Additional information about the relative viral load could be calculated. Such quantitative information might be useful for making treatment decisions.

METHODS

We enrolled students at a university health center who presented with cough and 1 additional flu-like symptom from December 2016 to February 2017. Data were collected before, during, and 5 days after the clinic visit. All those enrolled in the study received a point-of-care PCR test (cobas Liat). For those patients that tested positive for influenza A, we investigated correlations between the relative viral load and measures of disease severity and recovery.

RESULTS

One hundred thirty-five students tested positive for influenza A. We found a positive correlation between viral load and body temperature. Time since symptom onset seemed to have a negative correlation but was not statistically significant. We did not find any correlations between viral load and overall symptom severity or outcomes related to recovery.

CONCLUSIONS

Although we found a correlation between relative viral load and body temperature, for our study population of young, overall healthy adults, we did not find that relative viral load provided additional information that could help in determining treatment and disease outcomes. It could be that viral load does provide useful additional information for other groups of patients, such as young children or older adults. Further studies on those populations are warranted.

Respiratory Syncytial Virus Disease Severity in Young Children

BACKGROUND

Respiratory syncytial virus (RSV) is the leading cause of acute respiratory infections (ARI) in hospitalized children. Although prematurity and underlying medical conditions are known risk factors, most of these children are healthy, and factors including RSV load and subgroups may contribute to RSV-ARI severity. Therefore, we aimed to evaluate the role of RSV in ARI disease severity and determine factors associated with increased RSV-ARI severity in young children.

METHOD

Children less than five years with fever and/or ARI symptoms were recruited from the emergency department (ED) or inpatient settings at Vanderbilt Children's Hospital. Nasal and/or throat swabs were tested by qRT-PCR for common respiratory viruses, including RSV. A severity score was calculated for RSV-positive children.

RESULTS

From 11/2015 through 07/2016, 898 participants were enrolled, and 681 (76%) had at least one virus detected, with 191 (28%) testing positive for RSV. RSV-positive children were more likely to be hospitalized, require intensive care unit (ICU) admission, and receive oxygen compared to other-virus-positive children. Higher viral load, White race, younger age, and higher severity score were independently associated with hospitalization in RSV-positive children. No differences in disease severity were noted among children infected with RSV A and B.

CONCLUSION

RSV was associated with increased ARI severity in young children enrolled from ED and inpatient settings, but no differences in disease severity were noted between RSV A and B. . These findings emphasize the need for effective antiviral therapy and/or preventive measures such as vaccines against RSV in young children.

Initial SARS-CoV-2 PCR crossing point does not predict hospitalization and duration of PCR positivity

This study aimed to determine if the crossing point of the initial positive SARS-CoV-2 PCR test correlated with patient demographics, subsequent hospitalization, or duration of positivity. Seventy-three patients with two or more positive PCR tests had a median time of 23 days to two consecutive negative results.

Human Polyomavirus 6 Detected in Cases of Eosinophilic Pustular Folliculitis

BACKGROUND

Human polyomaviruses (HPyVs) have been associated with several cutaneous inflammatory conditions. More investigation is needed to identify further presentations of cutaneous pathology associated with HPyVs. Our aim was to investigate the possible association of skin-tropic HPyVs with folliculitis, particularly eosinophilic pustular folliculitis (EPF).

METHODS

This study included 55 Japanese patients, comprising 13 patients with EPF and 42 patients with suppurative folliculitis. HPyV DNAs were detected by quantitative polymerase chain reaction. Expression of viral antigen and geographically related viral genotypes were also assessed.

RESULTS

Human polyomavirus 6 (HPyV6) DNA was found in 9 of 13 (69%) patients with EPF, a rate significantly higher than that found in suppurative folliculitis (1/42; 2%). Of the 7 HPyV6 DNA-positive EPF specimens analyzed, 4 were positive for HPyV6 small tumor antigen. All the HPyV6 strains detected in this study were of the Asian/Japanese genotype.

CONCLUSIONS

The predominant detection of HPyV6 DNA and the expression of viral antigen suggest a possible association between HPyV6 infection and EPF in a subset of patients. Worldwide studies are warranted to determine whether Asian/Japanese genotype HPyV6 is associated preferentially with the incidence and pathogenesis of this eosinophil-related skin disease that has an ethnic predilection for the East Asian population.

Stability of MERS-CoV RNA on spin columns of RNA extraction kit at room temperature

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus causing a highly fatal respiratory disease in humans. Confirmation of MERS-CoV infection and molecular study on the virus may require transportation of samples to specialized laboratories. While freezing at −80 °C is the gold standard method for RNA preservation, maintaining the integrity of viral RNA during transport will require additional precautions and, as a result, increase transport costs. We aimed at testing the stability of MERS-CoV RNA on spin columns of RNA extraction kit at room temperature for 16 weeks. Respiratory samples spiked with stock culture of MERS-CoV were extracted and loaded on QIAamp Viral RNA Mini Kit spin columns and preserved at room temperature. Amount of viral RNA was evaluated periodically by real-time quantitative reverse-transcription polymerase chain reaction. Minimal changes in cycle threshold values over the study period were noted, suggesting stability of viral RNA by this preservation method.

Accuracy of diagnostic tests for respiratory syncytial virus infection within a paediatric hospital population in Kilifi County, Kenya

Background: Respiratory syncytial virus (RSV)-induced lower respiratory tract disease is a prominent cause of hospitalisation among children aged <5 years in developing countries. Accurate and rapid diagnostic tests are central to informing effective patient management and surveillance efforts geared towards quantifying RSV disease burden. This study sought to estimate the sensitivity (Se), specificity (Sp) (along with the associated factors) and predictive values of a direct immunofluorescence test (IFAT), and two real-time reverse transcription polymerase chain reaction (rRT-PCR) assays for RSV infection within a paediatric hospital population: a multiplex rRT-PCR (MPX) and Fast-Track Diagnostics ® (FTD) Respiratory Pathogens 33 (Resp-33) rRT-PCR. Methods: The study enlisted 1458 paediatrics aged ≤59 months admitted with acute respiratory illness at the Kilifi County Hospital between August 2011 and December 2013. A Bayesian latent class modelling framework was employed to infer the tests' estimates based on the patients' diagnostic data from the three tests. Results: The tests posted statistically similar Se estimates: IFAT (93.7%, [90.7; 95.0]), FTD (97.8%, [94.6; 99.4]) and MPX (97.5%, [94.2; 99.3]). As for Sp, FTD registered a lower estimate (97.4%, [96.2; 98.2]) than MPX (99.7%, [99.0; 100.0]) but similar to IFAT (99.0%, [98.2; 99.6]). The negative and positive predictive values were strong (>91%) and closely mimicked the pattern given by the Se and Sp values respectively. None of the examined covariates (age, sex and pneumonia status) significantly influenced the accuracy of the tests. Conclusions: The evaluation found little to choose between the three diagnostic tests. Nonetheless, with its relative affordability, the conventional IFAT continues to hold promise for use in patient care and surveillance activities for RSV infection within settings where children are hospitalised with severe acute respiratory illness.

Elevated plasma levels of selective cytokines in COVID-19 patients reflect viral load and lung injury

A recent outbreak of pneumonia in Wuhan, China was found to be caused by a 2019 novel coronavirus (2019-nCoV or SARS-CoV-2 or HCoV-19). We previously reported the clinical features of 12 patients with 2019-nCoV infections in Shenzhen, China. To further understand the pathogenesis of COVID-19 and find better ways to monitor and treat the disease caused by 2019-nCoV, we measured the levels of 48 cytokines in the blood plasma of those 12 COVID-19 patients. Thirty-eight out of the 48 measured cytokines in the plasma of 2019-nCoV-infected patients were significantly elevated compared to healthy individuals. Seventeen cytokines were linked to 2019-nCoV loads. Fifteen cytokines, namely M-CSF, IL-10, IFN-α2, IL-17, IL-4, IP-10, IL-7, IL-1ra, G-CSF, IL-12, IFN-γ, IL-1α, IL-2, HGF and PDGF-BB, were strongly associated with the lung-injury Murray score and could be used to predict the disease severity of 2019-nCoV infections by calculating the area under the curve of the receiver-operating characteristics. Our results suggest that 2019-nCoV infections trigger extensive changes in a wide array of cytokines, some of which could be potential biomarkers of disease severity of 2019-nCoV infections. These findings will likely improve our understanding of the immunopathologic mechanisms of this emerging disease. Our results also suggest that modulators of cytokine responses may play a therapeutic role in combating the disease once the functions of these elevated cytokines have been characterized.

Lower respiratory tract infection in the community: associations between viral aetiology and illness course

OBJECTIVES

This study determined associations between respiratory viruses and subsequent illness course in primary care adult patients presenting with acute cough and/or suspected lower respiratory tract infection.

METHODS

A prospective European primary care study recruited adults with symptoms of lower respiratory tract infection between November 2007 and April 2010. Real-time in-house polymerase chain reaction (PCR) was performed to test for six common respiratory viruses. In this secondary analysis, symptom severity (scored 1 = no problem, 2 = mild, 3 = moderate, 4 = severe) and symptom duration were compared between groups with different viral aetiologies using regression and Cox proportional hazard models, respectively. Additionally, associations between baseline viral load (cycle threshold (Ct) value) and illness course were assessed.

RESULTS

The PCR tested positive for a common respiratory virus in 1354 of the 2957 (45.8%) included patients. The overall mean symptom score at presentation was 2.09 (95% confidence interval (CI) 2.07-2.11) and the median duration until resolution of moderately bad or severe symptoms was 8.70 days (interquartile range 4.50-11.00). Patients with influenza virus, human metapneumovirus (hMPV), respiratory syncytial virus (RSV), coronavirus (CoV) or rhinovirus had a significantly higher symptom score than patients with no virus isolated (0.07-0.25 points or 2.3-8.3% higher symptom score). Time to symptom resolution was longer in RSV infections (adjusted hazard ratio (AHR) 0.80, 95% CI 0.65-0.96) and hMPV infections (AHR 0.77, 95% CI 0.62-0.94) than in infections with no virus isolated. Overall, baseline viral load was associated with symptom severity (difference 0.11, 95% CI 0.06-0.16 per 10 cycles decrease in Ct value), but not with symptom duration.

CONCLUSIONS

In healthy, working adults from the general community presenting at the general practitioner with acute cough and/or suspected lower respiratory tract infection other than influenza impose an illness burden comparable to influenza. Hence, the public health focus for viral respiratory tract infections should be broadened.

Prevalence and Viral Loads of Cutaneous Human Polyomaviruses in the Skin of Patients With Chronic Inflammatory Skin Diseases

BACKGROUND

Human skin microorganisms have been associated with various skin diseases. However, most studies have focused on bacterial communities, and little is known about normally resident skin viruses such as the Polyomaviridae and their association with cutaneous disorders.

METHODS

We investigated the infection levels of Merkel cell polyomavirus (MCPyV), human polyomavirus 6 (HPyV6), and human polyomavirus 7 (HPyV7), using triplet skin swabs collected from lesional and nonlesional skins of 86 Japanese patients with inflammatory skin diseases and mycosis fungoides, and from 149 healthy control individuals.

RESULTS

This age-matched case-control study provides the first analyses of the loads of polyomaviruses in association with various skin diseases. The viral loads were significantly higher for HPyV6/HPyV7 and lower for MCPyV in patients with psoriasis. The viral load variation was observed not only at lesion sites, but also at clinically unaffected skin sites in most of the patients. The viral strains tested were all of the Asian/Japanese genotype.

CONCLUSIONS

Our findings suggest a covariation in the infection levels of cutaneous polyomaviruses in certain inflammatory skin conditions. Worldwide prospective longitudinal studies are warranted to understand the influence of such alterations on the pathogenesis of inflammatory skin disorders.

Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR

Acute respiratory tract infections are a major cause of respiratory morbidity and mortality in pediatric patients worldwide. However, accurate viral and immunologic markers to predict clinical outcomes of this patient population are still lacking. Droplet digital PCR assays for influenza and respiratory syncytial virus (RSV) were designed and performed in 64 respiratory samples from 23 patients with influenza virus infection and 73 samples from 19 patients with RSV infection. Samples of patients with hematologic malignancies, solid tumors, or sickle cell disease were included. Clinical information from institutional medical records was reviewed to assess disease severity. Samples from patients with fever or respiratory symptoms had a significantly higher viral loads than those from asymptomatic patients. Samples from patients with influenza virus and RSV infection collected at presentation had significantly higher viral loads than those collected from patients after completing a course of oseltamivir or ribavirin, respectively. RSV loads correlated positively with clinical symptoms in patients ≤5 years of age, whereas influenza viral loads were associated with clinical symptoms, irrespective of age. Patients receiving antivirals for influenza and RSV had a significant reduction in viral loads after completing therapy. Digital PCR offers an effective method to monitor the efficacy of antiviral treatment for respiratory tract infections in immunocompromised hosts.

Epidemiology of viral acute lower respiratory infections in a community-based cohort of rural north Indian children

Background

In India, community-based acute lower respiratory infections (ALRI) burden studies are limited, hampering development of prevention and control strategies.

Methods

We surveyed children <10 years old at home weekly from August 2012-August 2014, for cough, sore throat, rhinorrhoea, ear discharge, and shortness of breath. Symptomatic children were assessed for ALRI using World Health Organization definitions. Nasal and throat swabs were obtained from all ALRI cases and asymptomatic controls and tested using polymerase chain reaction for respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza viruses (PIV), and influenza viruses (IV). We estimated adjusted odds ratios (aOR) using logistic regression to calculate etiologic fractions (EF). We multiplied agent-specific ALRI incidence rates by EF to calculate the adjusted incidence as episodes per child-year.

Results

ALRI incidence was 0.19 (95% confidence interval (CI) = 0.18-0.20) episode per child-year. Association between virus and ALRI was strongest for RSV (aOR = 15.9; 95% CI = 7.3-34.7; EF = 94%) and least for IV (aOR = 4.6; 95% CI = 2.0-10.6; EF = 78%). Adjusted agent-specific ALRI incidences were RSV (0.03, 95% CI = 0.02-0.03), hMPV (0.02, 95% CI = 0.01-0.02), PIV (0.02, 95% CI = 0.01-0.02), and IV (0.01, 95% CI = 0.01-0.01) episode per child-year.

Conclusions

ALRI among children in rural India was high; RSV was a significant contributor.

Prevalence and Genetic Variability of Human Polyomaviruses 6 and 7 in Healthy Skin Among Asymptomatic Individuals

Background

Despite the pathogenetic potential of human polyomavirus 6 (HPyV6) and human polyomavirus 7 (HPyV7), they have been found in the normal skin of healthy individuals. However, little is known about the prevalence, infection levels, and geographical variations of these polyomaviruses in the skin.

Methods

Using skin swabs from 470 participants aged 2-98 years, we estimated the prevalence of copy numbers of HPyV6 and HPyV7 with respect to age and ethnicity. Phylogenetic analyses were conducted based on viral sequences obtained from Asian and white populations.

Results

This study provides the first analyses of the age-specific prevalence and levels of HPyV6 and HPyV7 infections in normal skin. Comparisons of age groups revealed that the prevalence and viral loads were significantly higher in elderly persons. Phylogenetic analyses demonstrated the existence of Asian/Japanese-specific strains genetically distinct from strains prevalent in the skin of the white population studied.

Conclusions

This large study suggests that HPyV6 and HPyV7 infections in the skin are highly prevalent in elderly adults. Further research is warranted to understand whether persistent infection with high viral loads in the skin could be a risk factor for the development of HPyV6- and HPyV7-associated skin disorders.

Role of Type I Interferon (IFN) in the Respiratory Syncytial Virus (RSV) Immune Response and Disease Severity

Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract disease in children <2 years of age. Increased morbidity and mortality have been reported in high-risk patients, such as premature infants, patients with cardiac disease, and severely immune compromised patients. Severe disease is associated with the virulence of the virus as well as host factors specifically including the innate immune response. The role of type I interferons (IFNs) in the response to RSV infection is important in regulating the rate of virus clearance and in directing the character of the immune response, which is normally associated with protection and less severe disease. Two RSV non-structural proteins, NS1 and NS2, as well as the envelope G glycoprotein are known to suppress type I IFN production and a robust type I IFN response to RSV does not occur in human infants or neonatal mouse models of RSV infection. Additionally, presence of type I IFNs are associated with mild symptoms in infants and administration of IFN-α prior to infection of neonatal mice with RSV reduces immunopathology. This evidence has driven RSV prophylaxis and therapeutic efforts to consider strategies for enhancing type I IFN production.

Respiratory Viral Infections in Patients With Cancer or Undergoing Hematopoietic Cell Transplant

Survival rates for pediatric cancer have steadily improved over time but it remains a significant cause of morbidity and mortality among children. Infections are a major complication of cancer and its treatment. Community acquired respiratory viral infections (CRV) in these patients increase morbidity, mortality and can lead to delay in chemotherapy. These are the result of infections with a heterogeneous group of viruses including RNA viruses, such as respiratory syncytial virus (RSV), influenza virus (IV), parainfluenza virus (PIV), metapneumovirus (HMPV), rhinovirus (RhV), and coronavirus (CoV). These infections maintain a similar seasonal pattern to those of immunocompetent patients. Clinical manifestations vary significantly depending on the type of virus and the type and degree of immunosuppression, ranging from asymptomatic or mild disease to rapidly progressive fatal pneumonia Infections in this population are characterized by a high rate of progression from upper to lower respiratory tract infection and prolonged viral shedding. Use of corticosteroids and immunosuppressive therapy are risk factors for severe disease. The clinical course is often difficult to predict, and clinical signs are unreliable. Accurate prognostic viral and immune markers, which have become part of the standard of care for systemic viral infections, are currently lacking; and management of CRV infections remains controversial. Defining effective prophylactic and therapeutic strategies is challenging, especially considering, the spectrum of immunocompromised patients, the variety of respiratory viruses, and the presence of other opportunistic infections and medical problems. Prevention remains one of the most important strategies against these viruses. Early diagnosis, supportive care and antivirals at an early stage, when available and indicated, have proven beneficial. However, with the exception of neuraminidase inhibitors for influenza infection, there are no accepted treatments. In high-risk patients, pre-emptive treatment with antivirals for upper respiratory tract infection (URTI) to decrease progression to LRTI is a common strategy. In the future, viral load and immune markers may prove beneficial in predicting severe disease, supporting decision making and monitor treatment in this population.

Prevalence of human respiratory syncytial virus infection in people with acute respiratory tract infections in Africa: A systematic review and meta-analysis

AIM

The epidemiology of human respiratory syncytial virus (HRSV) infection has not yet been systematically investigated in Africa. This systematic review and meta-analysis are to estimate the prevalence of HRSV infections in people with acute respiratory tract infections (ARTI) in Africa.

METHOD

We searched PubMed, EMBASE, Africa Journal Online, and Global Index Medicus to identify observational studies published from January 1, 2000, to August 1, 2017. We used a random-effects model to estimate the prevalence across studies. Heterogeneity (I2 ) was assessed via the chi-square test on Cochran's Q statistic. Review registration: PROSPERO CRD42017076352.

RESULTS

A total of 67 studies (154 000 participants) were included. Sixty (90%), seven (10%), and no studies had low, moderate, and high risk of bias, respectively. The prevalence of HRSV infection varied widely (range 0.4%-60.4%). The pooled prevalence was 14.6% (95% CI 13.0-16.4, I2  = 98.8%). The prevalence was higher in children (18.5%; 95% CI 15.8-21.5) compared to adults (4.0%; 95% CI 2.2-6.1) and in people with severe respiratory tract infections (17.9%; 95% CI 15.8-20.1) compared to those with benign forms (9.4%; 95% CI 7.4-11.5); P-values <0.0001. The HRSV prevalence was not associated with sex, subregion in Africa, setting, altitude, latitude, longitude, and seasonality.

CONCLUSION

This study suggests a high prevalence of HRSV in people with ARTI in Africa, particularly among children and people with severe clinical form. All innovative strategies to curb the burden should first focus on children which present the highest HRSV-related burden.

Contemporaneous data on the prevalence of Human Respiratory Syncytial Virus infection in people with acute respiratory tract infections in Africa (2000-2017)

Availability of accurate data on the burden of the Human Respiratory Syncytial Virus (HRSV) can help to implement better strategies to curb this burden in Africa continent among people with acute respiratory tract infections (ARTI). We summarize here available contemporaneous data published from January 1, 2000 to August 31, 2017 on the prevalence of HSRV infection among people with ARTI in the continent.

Human adenovirus load in respiratory tract secretions are predictors for disease severity in children with human adenovirus pneumonia

Background

Pneumonia is a serious public health issue and is concerned around the world. This study is to investigate the association between viral load in children with human adenovirus (HAdV) pneumonia and disease severity.

Methods

A total of 1313 cases of children hospitalized in Hunan Provincial People’s Hospital due to community acquired pneumonia (CAP) from April 2011 to May 2014 were enrolled in this study. Samples of nasopharyngeal aspirate were collected for the cohort. WHO criteria for CAP grading was emerged for pneumonia severity classification. Real-time fluorescence quantitative PCR (qRT-PCR) was used to detect 12 kinds of respiratory viruses. HAdV types were identified by nested PCR. The relationship between HAdV load and severity of disease was there by analyzed.

Results

Finally, 174 cases (174/1313, 13.3%) were positive for HAdV, and HAdV type 7 (HAdV-7) was the main serotype (76/174, 43.7%). Among the 174 cases, 70 cases were with HAdV infection alone and 104 cases were accompanied by other viruses. The patients were divided into mild pneumonia group (n = 108 cases) and severe pneumonia group (n = 66 cases). HAdV load of children in severe pneumonia group was higher than that in mild pneumonia group. Similar result was obtained in the 70 cases with HAdV infection alone after subgrouping. Relevant factors analysis results showed that severe pneumonia children presented lower onset age, more prone to fever, longer fever time, and longer hospital stay compared with that of mild pneumonia children. Children with HAdV-7 infection developed more frequently severe pneumonia. Multivariate regression analysis showed that HAdV load, age, and fever time were risk factors for pneumonia severity.

Conclusion

The severity of HAdV infection is significantly correlated with viral load and serotype.

Pathogen Clearance and New Respiratory Tract Infections Among Febrile Children in Zanzibar Investigated With Multitargeting Real-Time Polymerase Chain Reaction on Paired Nasopharyngeal Swab Samples

BACKGROUND

New molecular methods have revealed frequent and often polymicrobial respiratory infections in children in low-income settings. It is not known whether presence of multiple pathogens is due to prolonged infections or to frequent exposure. The aim of this study was to analyze short-term pathogen clearance from nasopharynx and the rate of new respiratory tract infections in febrile preschool children.

METHODS

Children (n = 207) with uncomplicated acute febrile illness 2-59 months of age presenting to a health center in Zanzibar, Tanzania, April-July 2011, were included. Paired nasopharyngeal swab samples, collected at enrolment and after 14 days, were analyzed by multiple real-time polymerase chain reaction for Adenovirus, bocavirus, Bordetella pertussis, Chlamydophila pneumoniae, Coronaviruses, Enterovirus, influenza A and B virus, metapneumovirus, measles virus, Mycoplasma pneumoniae, parainfluenza virus, Parechovirus, respiratory syncytial virus and Rhinovirus. An age-matched and geographically matched healthy control group (n = 166) underwent nasopharyngeal sampling on 1 occasion.

RESULTS

At baseline, 157/207 (76%) patients had at least 1 pathogen detected, in total 199 infections. At follow-up (day 14), 162/199 (81%) of these infections were not detected, including >95% of the previously detected infections with Enterovirus, influenza A virus, influenza B virus, metapneumovirus or parainfluenza virus. Still 115 (56%) children were positive for at least 1 pathogen at follow-up, of which 95/115 (83%) were not found at baseline. Detection of influenza B on day 14 was significantly associated with fever during follow-up.

CONCLUSION

The results suggest that children with acute febrile illness in Zanzibar rapidly clear respiratory tract infections but frequently acquire new infections within 14 days.

Role of viral and bacterial pathogens in causing pneumonia among Western Australian children: a case-control study protocol

INTRODUCTION

Pneumonia is the leading cause of childhood morbidity and mortality globally. Introduction of the conjugate Haemophilus influenzae B and multivalent pneumococcal vaccines in developed countries including Australia has significantly reduced the overall burden of bacterial pneumonia. With the availability of molecular diagnostics, viruses are frequently detected in children with pneumonia either as primary pathogens or predispose to secondary bacterial infection. Many respiratory pathogens that are known to cause pneumonia are also identified in asymptomatic children, so the true contribution of these pathogens to childhood community-acquired pneumonia (CAP) remains unclear. Since the introduction of pneumococcal vaccines, very few comprehensive studies from developed countries have attempted to determine the bacterial and viral aetiology of pneumonia. We aim to determine the contribution of bacteria and viruses to childhood CAP to inform further development of effective diagnosis, treatment and preventive strategies.

METHODS AND ANALYSIS

We are conducting a prospective case-control study (PneumoWA) where cases are children with radiologically confirmed pneumonia admitted to Princess Margaret Hospital for Children (PMH) and controls are healthy children identified from PMH outpatient clinics and from local community immunisation clinics. The case-control ratio is 1:1 with 250 children to be recruited in each arm. Nasopharyngeal swabs are collected from both cases and controls to detect the presence of viruses and bacteria by PCR; pathogen load will be assessed by quantitative PCR. The prevalence of pathogens detected in cases and controls will be compared, the OR of detection and population attributable fraction to CAP for each pathogen will be determined; relationships between pathogen load and disease status and severity will be explored.

ETHICS AND DISSEMINATION

This study has been approved by the human research ethics committees of PMH, Perth, Australia (PMH HREC REF 2014117EP). Findings will be disseminated at research conferences and in peer-reviewed journals.

Is Higher Viral Load in the Upper Respiratory Tract Associated With Severe Pneumonia? Findings From the PERCH Study

Background.

The etiologic inference of identifying a pathogen in the upper respiratory tract (URT) of children with pneumonia is unclear. To determine if viral load could provide evidence of causality of pneumonia, we compared viral load in the URT of children with World Health Organization–defined severe and very severe pneumonia and age-matched community controls.

Methods.

In the 9 developing country sites, nasopharyngeal/oropharyngeal swabs from children with and without pneumonia were tested using quantitative real-time polymerase chain reaction for 17 viruses. The association of viral load with case status was evaluated using logistic regression. Receiver operating characteristic (ROC) curves were constructed to determine optimal discriminatory viral load cutoffs. Viral load density distributions were plotted.

Results.

The mean viral load was higher in cases than controls for 7 viruses. However, there was substantial overlap in viral load distribution of cases and controls for all viruses. ROC curves to determine the optimal viral load cutoff produced an area under the curve of <0.80 for all viruses, suggesting poor to fair discrimination between cases and controls. Fatal and very severe pneumonia cases did not have higher viral load than less severe cases for most viruses.

Conclusions.

Although we found higher viral loads among pneumonia cases than controls for some viruses, the utility in using viral load of URT specimens to define viral pneumonia was equivocal. Our analysis was limited by lack of a gold standard for viral pneumonia.

Assessment of real-time PCR cycle threshold values in Microsporum canis culture-positive and culture-negative cats in an animal shelter: a field study

Objectives Real-time PCR provides quantitative information, recorded as the cycle threshold (Ct) value, about the number of organisms detected in a diagnostic sample. The Ct value correlates with the number of copies of the target organism in an inversely proportional and exponential relationship. The aim of the study was to determine whether Ct values could be used to distinguish between culture-positive and culture-negative samples. Methods This was a retrospective analysis of Ct values from dermatophyte PCR results in cats with suspicious skin lesions or suspected exposure to dermatophytosis. Results One hundred and thirty-two samples were included. Using culture as the gold standard, 28 were true positives, 12 were false positives and 92 were true negatives. The area under the curve for the pretreatment time point was 96.8% (95% confidence interval [CI] 94.2-99.5) compared with 74.3% (95% CI 52.6-96.0) for pooled data during treatment. Before treatment, a Ct cut-off of <35.7 (approximate DNA count 300) provided a sensitivity of 92.3% and specificity of 95.2%. There was no reliable cut-off Ct value between culture-positive and culture-negative samples during treatment. Ct values prior to treatment differed significantly between the true-positive and false-positive groups ( P = 0.0056). There was a significant difference between the pretreatment and first and second negative culture time points ( P = 0.0002 and P <0.0001, respectively). However, there was substantial overlap between Ct values for true positives and true negatives, and for pre- and intra-treatment time points. Conclusions and relevance Ct values had limited usefulness for distinguishing between culture-positive and culture-negative cases when field study samples were analyzed. In addition, Ct values were less reliable than fungal culture for determining mycological cure.