Epidemiology of Human Seasonal Coronaviruses Among People With Mild and Severe Acute Respiratory Illness in Blantyre, Malawi, 2011-2017.

BACKGROUND: The aim of this study was to characterize the epidemiology of human seasonal coronaviruses (HCoVs) in southern Malawi. METHODS: We tested for HCoVs 229E, OC43, NL63, and HKU1 using real-time polymerase chain reaction (PCR) on upper respiratory specimens from asymptomatic controls and individuals of all ages recruited through severe acute respiratory illness (SARI) surveillance at Queen Elizabeth Central Hospital, Blantyre, and a prospective influenza-like illness (ILI) observational study between 2011 and 2017. We modeled the probability of having a positive PCR for each HCoV using negative binomial models, and calculated pathogen-attributable fractions (PAFs). RESULTS: Overall, 8.8% (539/6107) of specimens were positive for ≥1 HCoV. OC43 was the most frequently detected HCoV (3.1% [191/6107]). NL63 was more frequently detected in ILI patients (adjusted incidence rate ratio [aIRR], 9.60 [95% confidence interval {CI}, 3.25-28.30]), while 229E (aIRR, 8.99 [95% CI, 1.81-44.70]) was more frequent in SARI patients than asymptomatic controls. In adults, 229E and OC43 were associated with SARI (PAF, 86.5% and 89.4%, respectively), while NL63 was associated with ILI (PAF, 85.1%). The prevalence of HCoVs was similar between children with SARI and controls. All HCoVs had bimodal peaks but distinct seasonality. CONCLUSIONS: OC43 was the most prevalent HCoV in acute respiratory illness of all ages. Individual HCoVs had distinct seasonality that differed from temperate settings.

Vaccine Effectiveness Against Influenza A-Associated Hospitalization, Organ Failure, and Death: United States, 2022-2023.

BACKGROUND: Influenza circulation during the 2022-2023 season in the United States largely returned to pre-coronavirus disease 2019 (COVID-19)-pandemic patterns and levels. Influenza A(H3N2) viruses were detected most frequently this season, predominately clade 3C.2a1b.2a, a close antigenic match to the vaccine strain. METHODS: To understand effectiveness of the 2022-2023 influenza vaccine against influenza-associated hospitalization, organ failure, and death, a multicenter sentinel surveillance network in the United States prospectively enrolled adults hospitalized with acute respiratory illness between 1 October 2022, and 28 February 2023. Using the test-negative design, vaccine effectiveness (VE) estimates against influenza-associated hospitalization, organ failures, and death were measured by comparing the odds of current-season influenza vaccination in influenza-positive case-patients and influenza-negative, SARS-CoV-2-negative control-patients. RESULTS: A total of 3707 patients, including 714 influenza cases (33% vaccinated) and 2993 influenza- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-negative controls (49% vaccinated) were analyzed. VE against influenza-associated hospitalization was 37% (95% confidence interval [CI]: 27%-46%) and varied by age (18-64 years: 47% [30%-60%]; ≥65 years: 28% [10%-43%]), and virus (A[H3N2]: 29% [6%-46%], A[H1N1]: 47% [23%-64%]). VE against more severe influenza-associated outcomes included: 41% (29%-50%) against influenza with hypoxemia treated with supplemental oxygen; 65% (56%-72%) against influenza with respiratory, cardiovascular, or renal failure treated with organ support; and 66% (40%-81%) against influenza with respiratory failure treated with invasive mechanical ventilation. CONCLUSIONS: During an early 2022-2023 influenza season with a well-matched influenza vaccine, vaccination was associated with reduced risk of influenza-associated hospitalization and organ failure.

Epidemiology of Respiratory Syncytial Virus in Adults and Children With Medically Attended Acute Respiratory Illness Over Three Seasons.

BACKGROUND: Data on the true prevalence of respiratory syncytial virus (RSV) among medically attended acute respiratory illnesses (MAARI) has been limited by the lack of regular clinical testing of mild to moderate illnesses. Here we present a prospective evaluation of the epidemiology of RSV-associated MAARI across age groups and multimorbidity status over 3 seasons, which is informative in light of the recommendations for shared decision making for vaccination in older adults. METHODS: Ambulatory patients ≥6 months of age meeting a common MAARI case definition were prospectively enrolled in the Michigan Ford Influenza Vaccine Effectiveness (MFIVE) study, a subsite of the US Influenza Vaccine Effectiveness Network. All participants were tested by nasal-throat swab for RSV and influenza, including subtype, independently from clinician-directed testing. Participant illness characteristics and calculated multimorbidity-weighted index (MWI) were collected by in-person survey and electronic medical record review. RESULTS: Over 3 surveillance seasons (fall 2017 to spring 2020), 9.9% (n = 441) of 4442 participants had RSV detected. RSV-associated MAARI was more prevalent than influenza for participants 6 months to 4 years of age. Adults with RSV-MAARI had higher median MWI scores overall compared to influenza-MAARI and controls with neither virus (1.62, 0.40, and 0.64, respectively). CONCLUSIONS: RSV is a significant, underrecognized cause of MAARI in both children and adults presenting for ambulatory care. Multimorbidity is an important contributor to RSV-associated MAARI in outpatient adults, providing information to support shared clinical decision making for vaccination.

Prospective clinical surveillance for severe acute respiratory illness and COVID-19 vaccine effectiveness in Kenyan hospitals during the COVID-19 pandemic.

BACKGROUND: There are limited data from sub-Saharan Africa describing the demographic characteristics, clinical features and outcome of patients admitted to public hospitals with severe acute respiratory infections during the COVID-19 pandemic. METHODS: We conducted a prospective longitudinal hospital-based sentinel surveillance between May 2020 and December 2022 at 16 public hospitals in Kenya. All patients aged above 18 years admitted to adult medical wards in the participating hospitals were included. We collected data on demographic and clinical characteristics, SARS-CoV-2 infection and COVID-19 vaccination status and, admission episode outcomes. We determined COVID-19 vaccine effectiveness (VE) against admission with SARS-CoV-2 positive severe acute respiratory illness (SARI) (i.e., COVID-19) and progression to inpatient mortality among patients admitted with SARI, using a test-negative case control design. RESULTS: Of the 52,636 patients included in the study, 17,950 (34.1%) were admitted with SARI. The median age was 50 years. Patients were equally distributed across sexes. Pneumonia was the most common diagnosis at discharge. Hypertension, Human Immunodeficiency Virus (HIV) infection and Diabetes Mellitus were the most common chronic comorbidities. SARS-CoV-2 test results were positive in 2,364 (27.9%) of the 8,471 patients that underwent testing. After adjusting for age, sex and presence of a chronic comorbidity, SARI patients were more likely to progress to inpatient mortality compared to non-SARI patients regardless of their SARS-CoV-2 infection status (adjusted odds ratio (aOR) for SARI and SARS-CoV-2 negative patients 1.22, 95% CI 1.10-1.37; and aOR for SARI and SARS-CoV-2 positive patients 1.32, 95% CI 1.24-1.40). After adjusting for age, sex and presence of a chronic comorbidity, COVID-19 VE against progression to inpatient mortality following admission with SARI for those with a confirmed vaccination status was 0.59 (95% CI 0.27-0.77). CONCLUSION: We have provided a comprehensive description of the demographic and clinical pattern of admissions with SARI in Kenyan hospitals during the COVID-19 pandemic period as well as the COVID-19 VE for these patients. These data were useful in providing situational awareness during the first three years of the pandemic in Kenya and informing national response measures.

Decreased risk of non-influenza respiratory infection after influenza B virus infection in children.

Previous studies suggest that influenza virus infection may provide temporary non-specific immunity and hence lower the risk of non-influenza respiratory virus infection. In a randomized controlled trial of influenza vaccination, 1 330 children were followed-up in 2009-2011. Respiratory swabs were collected when they reported acute respiratory illness and tested against influenza and other respiratory viruses. We used Poisson regression to compare the incidence of non-influenza respiratory virus infection before and after influenza virus infection. Based on 52 children with influenza B virus infection, the incidence rate ratio (IRR) of non-influenza respiratory virus infection after influenza virus infection was 0.47 (95% confidence interval: 0.27-0.82) compared with before infection. Simulation suggested that this IRR was 0.87 if the temporary protection did not exist. We identified a decreased risk of non-influenza respiratory virus infection after influenza B virus infection in children. Further investigation is needed to determine if this decreased risk could be attributed to temporary non-specific immunity acquired from influenza virus infection.

Nasal high flow therapy in remote hospitals: guideline development using a modified Delphi technique.

INTRODUCTION: In remote Australian hospitals there are no onsite paediatric intensive care units (PICUs), increasing the reliance on aeromedical retrieval to access tertiary care. Nasal high flow (NHF) therapy is an oxygen therapy used in tertiary hospitals to treat paediatric patients with respiratory conditions. In rural and remote Queensland, Australia, the use of NHF therapy is inconsistent and there are no guidelines on how this therapy should be implemented in practice. Therefore, three remote hospitals within the Torres Strait and Cape York commenced a project to improve consistent and equitable access to NHF therapy. Implementing NHF therapy in remote hospitals may improve health and social outcomes for children with acute respiratory distress. A clinical guideline for the use of NHF therapy in the three participating remote hospitals was published on 28 October 2021. This study aimed to develop a clinical guideline for the use of NHF therapy in three remote hospitals. METHODS: A modified Delphi technique was used to develop the guideline. Remote medicine and nursing clinicians at the three study sites, retrieval experts, a receiving tertiary-based paediatrician, PICU specialists and NHF therapy experts made up the expert panel of participants. These experts participated in an iterative round table discussion to develop remote-specific guidelines for the use of NHF therapy. Prior to the meeting, panellists were provided with an executive summary of the current literature on NHF therapy implementation with key questions for consideration. Participants were able to add relevant issues ad hoc. A final guideline representing the panellists' recommendations was submitted to the Torres and Cape Health Service for ratification. RESULTS: Remote-specific decisions on the following topics were produced: environment of care, nasogastric tube usage, timings of chest X-ray, automatic approvals to arrange courier services for pathology, medication use, staff training; staff ratios, observations regimes, both tertiary and local medical consultation frequency and the experience level of the medical officer required to attend to these consultations, location of the on-call medical officer, documentation, escalation of care considerations and disposition of the patient in relation to retrievals. DISCUSSION: Decisions were made to mitigate two highly representative remote factors: delays in the workplace practices, such as time to arrange treatment locally and delays in retrievals; and burden of the lack of access to services, such as lack of access to trained staff, staffing levels on-shift, adequate oxygen and equipment/consumable supplies. CONCLUSION: The aim was to develop a clinical guideline that was contextualised to the remote hospital. This outcome was achieved by using a modified Delphi technique, with a panel of experts providing the decision-making for the guideline. Consistency and safety were addressed by reducing delays in workplace practices; examples were time to arrange treatment locally and mitigate delays in an unknown time to retrievals, access to trained staff, staffing levels, and communication between remote and tertiary teams.

Work Attendance with Acute Respiratory Illness Before and During COVID-19 Pandemic, United States, 2018-2022.

Both SARS-CoV-2 and influenza virus can be transmitted by asymptomatic, presymptomatic, or symptomatic infected persons. We assessed effects on work attendance while ill before and during the COVID-19 pandemic in the United States by analyzing data collected prospectively from persons with acute respiratory illnesses enrolled in a multistate study during 2018-2022. Persons with previous hybrid work experience were significantly less likely to work onsite on the day before through the first 3 days of illness than those without that experience, an effect more pronounced during the COVID-19 pandemic than during prepandemic influenza seasons. Persons with influenza or COVID-19 were significantly less likely to work onsite than persons with other acute respiratory illnesses. Among persons with positive COVID-19 test results available by the second or third day of illness, few worked onsite. Hybrid and remote work policies might reduce workplace exposures and help reduce spread of respiratory viruses.

Antibiotic prescribing practices for acute respiratory illness in children less than 24 months of age in Kenema, Sierra Leone: is it time to move beyond algorithm driven decision making?

BACKGROUND: Lower respiratory tract infections are the leading cause of mortality in young children globally. In many resource-limited settings clinicians rely on guidelines such as IMCI or ETAT + that promote empiric antibiotic utilization for management of acute respiratory illness (ARI). Numerous evaluations of both guidelines have shown an overall positive response however, several challenges have also been reported, including the potential for over-prescribing of unnecessary antibiotics. The aims of this study were to describe the antibiotic prescribing practices for children less than 24 months of age with symptoms of ARI, that were admitted to Kenema Government Hospital (KGH) in the Eastern Province of Sierra Leone, and to identify the number of children empirically prescribed antibiotics who were admitted to hospital with ARI, as well as their clinical signs, symptoms, and outcomes. METHODS: We conducted a prospective study of children < 24 months of age admitted to the KGH pediatric ward with respiratory symptoms between October 1, 2020 and May 31, 2022. Study nurses collected data on demographic information, medical and medication history, and information on clinical course while hospitalized. RESULTS: A total of 777 children were enrolled. Prior to arrival at the hospital, 224 children (28.8%) reported taking an antibiotic for this illness without improvement. Only 15 (1.9%) children received a chest radiograph to aid in diagnosis and 100% of patients were placed on antibiotics during their hospital stay. CONCLUSIONS: Despite the lives saved, reliance on clinical decision-support tools such as IMCI and ETAT + for pediatric ARI, is resulting in the likely over-prescribing of antibiotics. Greater uptake of implementation research is needed to develop strategies and tools designed to optimize antibiotic use for ARI in LMIC settings. Additionally, much greater priority needs to be given to ensuring clinicians have the basic tools for clinical diagnosis, as well as greater investments in essential laboratory and radiographic diagnostics that help LMIC clinicians move beyond the sole reliance on algorithm based clinical decision making.

Association of recent respiratory illness and influenza with acute myocardial infarction among the Bangladeshi population: A case-control study.

Current evidence suggests that recent acute respiratory infections and seasonal influenza may precipitate acute myocardial infarction (AMI). This study examined the potential link between recent clinical respiratory illness (CRI) and influenza, and AMI in Bangladesh. Conducted during the 2018 influenza season at a Dhaka tertiary-level cardiovascular (CV) hospital, it included 150 AMI cases and two control groups: 44 hospitalized cardiac patients without AMI and 90 healthy individuals. Participants were matched by gender and age groups. The study focused on self-reported CRI and laboratory-confirmed influenza ascertained via quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) within the preceding week, analyzed using multivariable logistic regression. Results showed that cases reported CRI, significantly more frequently than healthy controls (27.3% vs. 13.3%, adjusted odds ratio (aOR): 2.21; 95% confidence interval (CI): 1.05-4.06), although this was not significantly different from all controls (27.3% vs. 22.4%; aOR: 1.19; 95% CI: 0.65-2.18). Influenza rates were insignificantly higher among cases than controls. The study suggests that recent respiratory illnesses may precede AMI onset among Bangladeshi patients. Infection prevention and control practices, as well as the uptake of the influenza vaccine, may be advocated for patients at high risk of acute CV events.

Housing and health outcomes: evidence on child morbidities from six Sub-Saharan African countries.

BACKGROUND: The connection between healthy housing status and health is well established. The quality of housing plays a significant role in infectious and non-communicable as well as vector-borne diseases. The global burden of disease attributable to housing is considerable with millions of deaths arising from diarrheal and respiratory diseases annually. In sub-Saharan Africa (SSA), the quality of housing remains poor although improvements have been documented. There is a general dearth of comparative analysis across several countries in the sub-region. We assess in this study, the association between healthy housing and child morbidity across six countries in SSA. METHODS: We use the Demographic and Health Survey (DHS) data for six countries where the most recent survey collected health outcome data on child diarrhoea, acute respiratory illness, and fever. The total sample size of 91,096 is used in the analysis (representing 15, 044 for Burkina Faso, 11, 732 for Cameroon, 5, 884 for Ghana, 20, 964 for Kenya, 33, 924 for Nigeria, and 3,548 for South Africa). The key exposure variable is healthy housing status. We control for various factors associated with the three childhood health outcomes. These include quality housing status, residency (rural/urban), age of the head of the household, mother's education, mother's BMI status, marital status, mother's age, and religious status. Others include the child's gender, age, whether the child is from multiple or single births, and breastfeeding status. Inferential analysis using survey-weighted logistic regression is employed. RESULTS: Our findings indicate that housing is an important determinant of the three outcomes investigated. Compared to unhealthier housing, healthy housing status was found to be associated with reduced odds of diarrhoea in Cameroon [Healthiest: aOR = 0.48, 95% CI, (0.32,0.71), healthier: aOR = 0.50, 95% CI,(0.35,0.70), Healthy: aOR = 0.60, 95% CI, (0.44,0.83), Unhealthy: aOR = 0.60, 95% CI, (0.44,0.81)], Kenya [Healthiest: aOR = 0.68, 95% CI, (0.52,0.87), Healtheir: aOR = 0.79, 95% CI, (0.63,0.98), Healthy: aOR = 0.76, 95% CI, (0.62,0.91)], South Africa[Healthy: aOR = 0.41, 95% CI, (0.18, 0.97)], and Nigeria [Healthiest: aOR = 0.48, 95% CI,(0.37,0.62), Healthier: aOR = 0.61, 95% CI,(0.50,0.74), Healthy: aOR = 0.71, 95%CI, (0.59,0.86), Unhealthy: aOR = 0.78, 95% CI, (0.67,0.91)], and reduced odds of Acute Respiratory Infection in Cameroon [Healthy: aOR = 0.72, 95% CI,(0.54,0.96)], Kenya [Healthiest: aOR = 0.66, 95% CI, (0.54,0.81), Healthier: aOR = 0.81, 95% CI, (0.69,0.95)], and Nigeria [Healthiest: aOR = 0.69, 95% CI, (0.56,0.85), Healthier: aOR = 0.72, 95% CI, (0.60,0.87), Healthy: aOR = 0.78, 95% CI, (0.66,0.92), Unhealthy: aOR = 0.80, 95% CI, (0.69,0.93)] while it was associated with increased odds in Burkina Faso [Healthiest: aOR = 2.45, 95% CI, (1.39,4.34), Healthy: aOR = 1.55, 95% CI, (1.09,2.20)] and South Africa [Healthy: aOR = 2.36 95% CI, (1.31, 4.25)]. In addition, healthy housing was significantly associated with reduced odds of fever among children in all countries except South Africa [Healthiest: aOR = 2.09, 95% CI, (1.02, 4.29)] where children living in the healthiest homes had more than double the odds of having fever. In addition, household-level factors such as the age of the household head, and place of residence were associated with the outcomes. Child-level factors such as breastfeeding status, age, and sex, and maternal-level factors such as education, age, marital status, body mass index (BMI), and religion were also associated with the outcomes. CONCLUSIONS: The dissimilarity of findings across similar covariates and the multiple relations between healthy housing and under 5 morbidity patterns show unequivocally the heterogeneity that exists across African countries and the need to account for different contexts in efforts to seek an understanding of the role of healthy housing in child morbidity and general health outcomes.

Assessing the Impact of Acute Respiratory Illnesses on the Risk of Subsequent Respiratory Illness.

BACKGROUND: Whether acute respiratory illnesses (ARIs), often associated with virus detection, are associated with lower risk for subsequent ARI remains unclear. We assessed the association between symptomatic ARI and subsequent ARI in young children. METHODS: In a prospective cohort of Peruvian children <3 years, we examined the impact of index ARI on subsequent ARI risk. Index ARI were matched with ≤3 asymptomatic observations and followed over 28 days. We compared risk of subsequent ARI between groups using conditional logistic regression adjusting for several covariates, accounting for repeat observations from individual children. RESULTS: Among 983 index ARI, 339 (34%) had an ARI event during follow-up, compared with 876/2826 (31%) matched asymptomatic observations. We found no significant association of index ARI and subsequent ARI risk during follow-up overall (adjusted odds ratio [aOR], 1.10; 95% confidence interval [CI], .98-1.23) or when limited to index ARI with respiratory viruses detected (aOR, 1.03; 95% CI, .86-1.24). Similarly, when the outcome was limited to ARI in which viruses were detected, no significant association was seen (aOR, 1.05; 95% CI, .87-1.27). CONCLUSIONS: ARIs were not associated with short-term protection against subsequent ARI in these children. Additional longitudinal studies are needed to understand drivers of recurrent ARI in young children.

Neurocognitive Outcome Following Recovery from Severe Acute Respiratory Syndrome - Coronavirus-1 (SARS-CoV-1).

OBJECTIVE: Severe acute respiratory syndrome (SARS) is a highly contagious viral respiratory illness associated with hypoxia and dyspnea. Many of those who contracted and recovered from SARS during the 2002-2003 outbreak reported persistent physical, psychological, and cognitive difficulties. Here, we investigated the residual influences of SARS on cognition for a subset of healthcare professionals who recovered and were referred for neuropsychological evaluation through their workplace insurance. METHOD: Twenty-eight healthcare professionals were evaluated on neuropsychological and mood functioning approximately 1.5 years post-recovery from a severe respiratory illness. Test scores were compared with age-matched normative data, and correlations were examined between mood, self-report memory scales, subjective complaints (e.g., poor concentration, pain, fatigue), illness severity (i.e., length of hospitalization, oxygen use during hospital stay), and cognitive performance. RESULTS: Participants performed within age expectations on the majority of cognitive measures including overall memory ability. Although processing speed was generally within normal limits, 43% showed significant speed-accuracy trade-offs favoring accuracy over maintaining speed. Deficits were observed on measures of complex attention, such as working memory and the ability to sustain attention under conditions of distraction. Participants endorsed poorer memory ability than same-age peers on a meta-memory measure and mild to moderate depression and anxiety symptoms. Objective test performance was largely uncorrelated with self-reports, mood, or illness severity, except for moderate correlations between complex attention and participants' subjective ratings of Everyday Task-Oriented Memory. CONCLUSIONS: These findings demonstrate specific long-term cognitive deficits associated with SARS and provide further evidence of the cognitive effects of hypoxic illnesses.

Sentinel surveillance for influenza A viruses in Lahore District Pakistan in flu season 2015-2016.

BACKGROUND: Influenza A virus (IAV) remains an important global public health threat with limited epidemiological information available from low-and-middle-income countries. The major objective of this study was to describe the proportions, temporal and spatial distribution, and demographic and clinical characteristics of IAV positive patients with influenza like illness (ILI) and severe acute respiratory illness (SARI) in Lahore, Pakistan. METHODS: Prospective surveillance was established in a sentinel hospital from October 2015 to May 2016. All eligible outpatients and inpatients with ILI or SARI were enrolled in the study. Nasal and/or throat swabs were collected along with clinico-epidemiological data. Samples were tested by real-time RT-PCR (rRT-PCR) to identify IAV and subtype. The descriptive analysis of data was done in R software. RESULTS: Out of 311 enrolled patients, 284 (91.3%) were ILI and 27 (8.7%) were SARI cases. A distinct peak of ILI and SARI activity was observed in February. Fifty individuals (16%) were positive for IAV with peak positivity observed in December. Of 50 IAV, 15 were seasonal H3N2, 14 were H1N1pdm09 and 21 were unable to be typed. The majority of IAV positive cases (98%) presented with current or history of fever, 88% reported cough and 82% reported sore throat. The most common comorbidities in IAV positive cases were hepatitis C (4%), obesity (4%) and tuberculosis (6%). The highest incidence of patients reporting to the hospital was seen three days post symptoms onset (66/311) with 14 of these (14/66) positive for IAV. CONCLUSION: Distinct trends of ILI, SARI and IAV positive cases were observed which can be used to inform public health interventions (vaccinations, hand and respiratory hygiene) at appropriate times among high-risk groups. We suggest sampling from both ILI and SARI patients in routine surveillance as recommended by WHO.

Household level of air pollution and its impact on the occurrence of Acute Respiratory Illness among children under five: secondary analysis of Demographic and Health Survey in West Africa.

BACKGROUND: One out of ten deaths of children under five are attributable to indoor air pollution. And Acute Respiratory Illness (ARI) is among the direct causes. OBJECTIVE: This study showed the possibilities of characterizing indoor air pollution in West African Economic and Monetary Union (WAEMU) area and it also made it possible to estimate its impact on the occurrence of ARI in children under five. METHODS: It has been a secondary analysis based on Demographic and Health Surveys (DHSs) from WAEMU countries' data.. "Household level of air pollution" is the created composite variable, from questions on the degradation factors of indoor air quality (domestic combustion processes) which served to characterize indoor air pollution and to measure its impact by a logistic regression. RESULTS: Burkina Faso stands out with a greater number of households with a high level of pollution (63.7%) followed by Benin (43.7%) then Togo (43.0%). The main exposure factor "Household level of air pollution" was associated with ARI symptoms (Togo: prevalence = 51.3%; chi-squared test's p-value < 0.001). Exposure to high level of pollution constitutes a risk (AOR [95 CI]), even though it is not significant ( Ivory Coast: 1.29 [0.72-2.30], Senegal: 1.39 [0.94-2.05] and Togo: 1.15 [0.67-1.95]) and this could be explained by the high infectious etiology of the ARI.

Respiratory syncytial virus: host genetic susceptibility and factors associated with disease severity in a cohort of pediatric patients.

BACKGROUND: Respiratory syncytial virus (RSV) infections are the leading cause of hospitalization in young children. We assessed the epidemiology, severity, clinical characteristics, molecular profile and genetic factors of RSV infections compared to acute respiratory illness (ARI) caused by other respiratory viruses. METHODS: Prospective cohort study was conducted from 2017 to 2018 with children under 2 years old hospitalized with ARI. Detection of respiratory viruses was carried out using RT-PCR. RSVs were genotyped via nucleotide sequencing, and host interleukin 28B (IL28B) single nucleotide polymorphisms (SNPs) were determined using SNP TaqMan® Genotyping Assays. RESULTS: A total of 468 children were included; 288 (61.5%) had an infection by a single virus: 202 (70.1%) cases by RSV followed by rhinovirus 36 (12.5%) and influenza 16 (5.6%). Of the RSV cases, 36% were genotyped with a higher prevalence of RSV B (62.1%). The RSV group presented median age of 2.7 months (1.6-6.8), higher frequency in: intensive care unit admission (p = 0.004), mechanical ventilation use (p = 0.018), wheezing (p < 0.001), antimicrobial use (p < 0.001) and low oxygen saturation (p < 0.001). Prematurity (27.2%) was the most frequent comorbidity. RSV patients without comorbidities demonstrated a higher frequency in the combination of IL28B rs12979860 CT/IL28B rs8099917 TG and IL28B rs12979860 TT/IL28B rs8099917 TT genotypes. Viral coinfection was detected in 27 (5.7%) children, with the most frequent being RSV and rhinovirus (14.2%). CONCLUSIONS: This study highlighted the burden of RSV infection in children under 2 years of age, without comorbidities, with a higher need for pediatric ICU admission. Some IL28B allele combinations had a significant association with RSV frequency of infections.

Augmentation of Transcriptomic Data for Improved Classification of Patients with Respiratory Diseases of Viral Origin.

To better understand the molecular basis of respiratory diseases of viral origin, high-throughput gene-expression data are frequently taken by means of DNA microarray or RNA-seq technology. Such data can also be useful to classify infected individuals by molecular signatures in the form of machine-learning models with genes as predictor variables. Early diagnosis of patients by molecular signatures could also contribute to better treatments. An approach that has rarely been considered for machine-learning models in the context of transcriptomics is data augmentation. For other data types it has been shown that augmentation can improve classification accuracy and prevent overfitting. Here, we compare three strategies for data augmentation of DNA microarray and RNA-seq data from two selected studies on respiratory diseases of viral origin. The first study involves samples of patients with either viral or bacterial origin of the respiratory disease, the second study involves patients with either SARS-CoV-2 or another respiratory virus as disease origin. Specifically, we reanalyze these public datasets to study whether patient classification by transcriptomic signatures can be improved when adding artificial data for training of the machine-learning models. Our comparison reveals that augmentation of transcriptomic data can improve the classification accuracy and that fewer genes are necessary as explanatory variables in the final models. We also report genes from our signatures that overlap with signatures presented in the original publications of our example data. Due to strict selection criteria, the molecular role of these genes in the context of respiratory infectious diseases is underlined.

Upper Respiratory Infections in Schools and Childcare Centers Reopening after COVID-19 Dismissals, Hong Kong.

A large number of common cold outbreaks in Hong Kong schools and childcare centers during October-November 2020 led to territorywide school dismissals. Increased susceptibility to rhinoviruses during prolonged school closures and dismissals for coronavirus disease and varying effectiveness of nonpharmaceutical interventions may have heightened transmission of cold-causing viruses after school attendance resumed.

Rapid High-Throughput Whole-Genome Sequencing of SARS-CoV-2 by Using One-Step Reverse Transcription-PCR Amplification with an Integrated Microfluidic System and Next-Generation Sequencing.

The long-lasting global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Here, we report a simple and efficient workflow for whole-genome sequencing utilizing one-step reverse transcription-PCR (RT-PCR) amplification on a microfluidic platform, followed by MiSeq amplicon sequencing. The method uses Fluidigm integrated fluidic circuit (IFC) and instruments to amplify 48 samples with 39 pairs of primers, including 35 custom-designed primer pairs and four additional primer pairs from the ARTIC network protocol v3. Application of this method on RNA samples from both viral isolates and clinical specimens demonstrates robustness and efficiency in obtaining the full genome sequence of SARS-CoV-2.

Epidemiology of influenza B infection in the state of Rio Grande do Sul, Brazil, from 2003 to 2019.

Influenza B virus (IBV) causes respiratory tract infections with mild, moderate, or life-threatening symptoms. This study describes the epidemiology of IBV infection in Rio Grande do Sul (RS), Brazil, over 17 years. Nasopharyngeal samples were collected from outpatients presenting acute respiratory illness (ARI) between 2003 and 2019, and from inpatients with severe acute respiratory infection (SARI) from 2009 to 2019. IBV was detected by immunofluorescence assay or quantitative real-time polymerase chain reaction; demographic and clinical data were analyzed. In total, 48,656 cases of respiratory infection were analyzed, of which 20.45% were ARI, and 79.46% were SARI. Respiratory viruses accounted for 22.59% and 37.47% of the cases of ARI and SARI, respectively. Considering respiratory viral infections, 17.10% of ARI and 3.06% of SARI were associated with IBV. IBV circulated year-round in RS, with an increase in autumn and winter, peaking in July (p = .005). IBV infection showed an association with age, and most outpatients positive for IBV were between 10 and 49 years old, whereas IBV infection in SARI affected mainly individuals ≤ 1 year or ≥ 60 years old. No significant association was found between sex and IBV infection. Coryza, sore throat, and myalgia were associated with ARI (p < .001). Moreover, 3.18% of the deaths associated with respiratory virus infection were positive for IBV; notably, cardiopathy (p < .001), metabolic disease (p < .001), and smoking (p = .003) were associated to fatality in IBV infection. IBV is an important cause of severe respiratory infections, and the fatality risk is high in individuals with cardiopathy and metabolic diseases.

Clinical features of parainfluenza infections among young children hospitalized for acute respiratory illness in Amman, Jordan.

BACKGROUND: Parainfluenza virus (PIV) is a leading cause of acute respiratory illness (ARI) in children. However, few studies have characterized the clinical features and outcomes associated with PIV infections among young children in the Middle East. METHODS: We conducted hospital-based surveillance for ARI among children < 2 years of age in a large referral hospital in Amman, Jordan. We systematically collected clinical data and respiratory specimens for pathogen detection using reverse transcription polymerase chain reaction. We compared clinical features of PIV-associated ARI among individual serotypes 1, 2, 3, and 4 and among PIV infections compared with other viral ARI and ARI with no virus detected. We also compared the odds of supplemental oxygen use using logistic regression. RESULTS: PIV was detected in 221/3168 (7.0%) children hospitalized with ARI. PIV-3 was the most commonly detected serotype (125/221; 57%). Individual clinical features of PIV infections varied little by individual serotype, although admission diagnosis of 'croup' was only associated with PIV-1 and PIV-2. Children with PIV-associated ARI had lower frequency of cough (71% vs 83%; p < 0.001) and wheezing (53% vs 60% p < 0.001) than children with ARI associated with other viruses. We did not find a significant difference in supplemental oxygen use between children with PIV-associated infections (adjusted odds ratio [aOR] 1.12, 95% CI 0.66-1.89, p = 0.68) and infections in which no virus was detected. CONCLUSIONS: PIV is frequently associated with ARI requiring hospitalization in young Jordanian children. Substantial overlap in clinical features may preclude distinguishing PIV infections from other viral infections at presentation.