Association Between Preceding Viral Respiratory Infection and Subsequent Respiratory Illnesses Among Children: A Prospective Cohort Study in the Philippines

Risk of Subsequent Respiratory Virus Detection After Primary Virus Detection in a Community Household Study-King County, Washington, 2019-2021

BACKGROUND

The epidemiology of respiratory viral infections is complex. How infection with one respiratory virus affects risk of subsequent infection with the same or another respiratory virus is not well described.

METHODS

From October 2019 to June 2021, enrolled households completed active surveillance for acute respiratory illness (ARI), and participants with ARI self-collected nasal swab specimens; after April 2020, participants with ARI or laboratory-confirmed severe acute respiratory syndrome coronavirus 2 and their household members self-collected nasal swab specimens. Specimens were tested using multiplex reverse-transcription polymerase chain reaction for respiratory viruses. A Cox regression model with a time-dependent covariate examined risk of subsequent detections following a specific primary viral detection.

RESULTS

Rhinovirus was the most frequently detected pathogen in study specimens (406 [9.5%]). Among 51 participants with multiple viral detections, rhinovirus to seasonal coronavirus (8 [14.8%]) was the most common viral detection pairing. Relative to no primary detection, there was a 1.03-2.06-fold increase in risk of subsequent virus detection in the 90 days after primary detection; risk varied by primary virus: human parainfluenza virus, rhinovirus, and respiratory syncytial virus were statistically significant.

CONCLUSIONS

Primary virus detection was associated with higher risk of subsequent virus detection within the first 90 days after primary detection.

Comparison of Rhinovirus A-, B-, and C-Associated Respiratory Tract Illness Severity Based on the 5'-Untranslated Region Among Children Younger Than 5 Years

Background

Rhinoviruses (RVs) are among the most frequently detected viruses from hospitalized children with severe acute respiratory infections, being classified into RV-A, RV-B, and RV-C (4 clades: C, GAC1, GAC2, and A2). This study aimed to compare the clinical characteristics and respiratory tract illness severity between the RV species and RV-C clades in children in primary care and hospital settings in rural communities in the Philippines.

Methods

Clinical samples and information of children <5 years old in the Philippines were collected from 2014 to 2016. The samples were tested by reverse-transcription polymerase chain reaction (RT-PCR) targeting the 5′-untranslated region. PCR-positive samples were sequenced, and RV species were identified by phylogenetic analysis.

Results

Overall, 3680 respiratory tract illness episodes in 1688 cohort children were documented; 713 of those were RV positive and identified as RV-A (n = 271), RV-B (n = 47), and RV-C (n = 395: C [n = 76], GAG1 [n = 172], GAG2 [n = 8], A2 [n = 138], and unidentified [n = 1]). Severe illnesses, low oxygen saturation, cough, and wheezing were more common in patients with RV-C, especially with GAC1, than in those with RV-A or RV-B. Furthermore, severe illness was significantly more common in RV-C (GAC1)–positive cases than in RV-A–positive cases (odds ratio, 2.61 [95% CI, 1.17–4.13]).

Conclusions

Children infected with RV-C had more severe illnesses than children infected with RV-A and RV-B. Moreover, emerging clades of RV-C were associated with increased severity.

Incidence of lower respiratory tract infection and associated viruses in a birth cohort in the Philippines

Background

Lower respiratory tract infection (LRTI) is an important cause of morbidity and mortality in infants and young children. However, the etiological role of viruses and the timing of developing LRTI are not well defined.

Methods

We analyzed the data of a prospective cohort study in the Philippines as a birth cohort. We detected LRTI among children who visited healthcare facilities with respiratory symptom, and collected nasopharyngeal swabs for virus detection. We analyzed the incidence rates (IRs) and cumulative proportion of LRTI and severe LRTI by age group and each virus detected.

Results

A total of 350 LRTI episodes were observed from 473 child-years yielded from 419 children. The IRs of LRTI were 70.8, 70.7, and 80.8 per 100 child-years for 0–5, 6–11, and 12–23 months of age, respectively. By 12 months of age, 45% of children developed LRTI at least once. Rhinovirus and respiratory syncytial virus were the most frequently detected viruses in all age groups. However, the IRs of influenza virus were low especially at 0–5 months of age.

Conclusions

We identified various patterns of age-specific IRs of LRTI and severe LRTI for different viruses, which should be considered to establish more effective interventions including vaccinations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07289-3.

[Comprehensive understanding of viral diseases by field, molecular, and theoretical studies]

Viral diseases are responsible for substantial morbidity and mortality and continue to be of great concern. To ensure better control of viral infections, I have been tackling the issue as a medical doctor, an academic researcher, and a public health officer. Especially, I have studied respiratory viruses, such as the influenza virus, from the perspectives of molecular virology, theoretical modeling, and field epidemiology. RNA biology and its involvement with viral life-cycle and pathogenicity are central topics of molecular study, while mathematical models of transmission dynamics and phylogenetics are major components of theoretical research. As a field epidemiologist, I work with public health authorities during viral disease outbreaks. I was deployed to West Africa for viral hemorrhagic fever outbreak responses as a WHO consultant, and I have served the Japanese Government as an advisor for COVID-19 countermeasures. I would like to integrate various approaches from clinical medicine to epidemiology, theoretical modeling, evolutionary biology, genetics, and molecular biology in my research. In that way, we could gain a more comprehensive understanding of viral diseases. I hope these findings will help ease the disease burden of viral infections around the world.

Near-Complete Genome Sequencing of Influenza C Virus in the Philippines between 2014 and 2019

We report 19 nearly complete genome sequences of influenza C virus isolated from clinical samples recovered from children in the Philippines between 2014 and 2019.

Risk of Transmission and Viral Shedding From the Time of Infection for Respiratory Syncytial Virus in Households

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infection worldwide, but reports of temporal changes in the risk of transmission among close contacts has been scarce. This study aimed to examine an association between the viral load trajectory and transmission risk to develop a better control strategy for the disease spread. We conducted a household-based prospective cohort study in Biliran Province, the Philippines, and enrolled 451 participants to observe the development of acute respiratory infection. Including the cases found at the health-care facility, we analyzed the data of viral loads with symptom records obtained from 172 followed participants who had household member positive for RSV with a rapid test during an RSV outbreak in 2018-2019. We developed a model estimating a temporal change in the viral shedding from the infection and evaluated transmission dynamics. We found that most transmission events occurred within approximately 7 days of the household exposure, including potential presymptomatic transmissions. The inferred risk of infection among those younger than 5 years was 3.5 times higher than that of those older than 5 years. This finding suggested that the initial week after the household exposure is particularly important for preventing RSV spread.

Complete Genome Sequences of Enterovirus D68 Clade A and D Strains in the Philippines

Complete genome sequences were determined for 4 clade A and 12 clade D enterovirus D68 strains detected in nasopharyngeal swabs from children with acute respiratory illness in the Philippines. These sequence data will be useful for future epidemiological monitoring, including watching for viral evolution.

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 (aOR 1.10, 95% CI 0.98, 1.23) or when limited to index ARI with respiratory viruses detected (aOR 1.03, 95% CI 0.86, 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 0.87, 1.27).

DISCUSSION

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.

Epidemiology and Seasonality of Childhood Respiratory Syncytial Virus Infections in the Tropics

Infections caused by respiratory syncytial virus (RSV) are a major cause of morbidity and mortality in young children worldwide. Understanding seasonal patterns of region-specific RSV activity is important to guide resource allocation for existing and future treatment and prevention strategies. The decades of excellent RSV surveillance data that are available from the developed countries of the world are incredibly instructive in advancing public health initiatives in those regions. With few exceptions, these developed nations are positioned geographically across temperate regions of the world. RSV surveillance across tropical regions of the world has improved in recent years, but remains spotty, and where available, still lacks the necessary longitudinal data to determine the amount of seasonal variation expected over time. However, existing and emerging data collected across tropical regions of the world do indicate that patterns of infection are often quite different from those so well described in temperate areas. Here, we provide a brief summary regarding what is known about general patterns of RSV disease activity across tropical Asia, Africa and South America, then offer additional country-specific details using examples where multiple reports and/or more robust surveillance data have become available.

Relationship of Viral Detection with Duration of Ventilation in Critically Ill Infants with Lower Respiratory Tract Infection

RATIONALE

Although respiratory virus testing is frequent done for critically ill infants with bronchiolitis, the prognostic value of this testing is unknown for those requiring positive pressure ventilation (PPV).

OBJECTIVES

To determine the differences in PPV utilization according to viral detection and to explore the association between viral detection and duration of PPV in critically ill children with presumed respiratory infection.

METHODS

This is a retrospective cohort study in a quaternary pediatric intensive care unit from February 2014 until February 2017. We evaluated 984 children < 1 year of age who received PPV for presumed respiratory infection without significant congenital heart disease, care limitations, baseline PPV usage, or tracheostomy. Respiratory viruses were identified using a PCR panel. Analyses of duration of PPV according to viral etiology were performed using univariate and multivariable logistic regression and truncated negative binomial regression with calculated mean marginal effect (MME).

RESULTS

Overall, 85 (9%) infants had no viruses identified, 629 (64%) had a single virus detected, most commonly respiratory syncytial virus (RSV) (417, 42%) followed by rhinovirus/enterovirus (RV/EV) (145, 15%), 230 (23%) had 2 viruses detected, and 40 (4%) had three viruses detected. Compared to those with 1 or no virus detected, infants with ≥2 viruses received longer total PPV duration in adjusted analysis [RR:1.4 (95% CI 1.2-1.6); p<0.001, MME=29 hours]. Detection of RV/EV alone, compared to RSV alone, was associated with significantly shorter duration of total PPV [RR:0.7 (95% CI 0.62, 0.87); p=<0.001, MME= -23 hours], noninvasive PPV [RR: 0.7 (95% CI 0.60, 0.85); p<0.001 MME = -15 hours], and invasive PPV [RR 0.7 (95% CI 0.54, 0.83); p<0.001, MME = -54 hours) when adjusted for weight, prematurity, and administration of early antibiotic therapy.

CONCLUSIONS

Identification of viral type and number in severe bronchiolitis is an important predictor of duration of PPV.

Evaluation of a novel rapid TRC assay for the detection of influenza using nasopharyngeal swabs and gargle samples

We evaluated a novel transcription-reverse transcription concerted reaction (TRC) assay that can detect influenza A and B within 15 min using nasopharyngeal swab and gargle samples obtained from patients with influenza-like illness, between January and March 2018 and between January and March 2019. Based on the combined RT-PCR and sequencing results, in the nasal swabs, the sensitivity and specificity of TRC for detecting influenza were calculated as 1.000 and 1.000, respectively. In the gargle samples, the sensitivity and specificity of TRC were 0.946 and 1.000, respectively. The TRC assay showed comparable performance to RT-PCR in the detection of influenza viruses.

Factors associated with diarrhoea and acute respiratory infection in children under-5 years old in Ghana: an analysis of a national cross-sectional survey

BACKGROUND

Diarrhoea and acute respiratory infection (ARI) are major causes of morbidity and mortality in children under-5 years old in Ghana. The aim of the study was to assess factors associated with diarrhoea and ARI in children under-5 years old.

METHODS

We analysed nationally representative data from the 2017-2018 Ghana Multiple Indicator Cluster Survey (MICS) on 8879 children under-5 years old. Multivariable logistic regression was used to assess the factors associated with diarrhoea and ARI. We applied sample weights, stratification and clustering to account for the sampling design of the MICS.

RESULTS

The prevalence of diarrhoea was 17.0% (95% CI: 15.70, 18.24%). Children aged 6-11 months [Adjusted prevalence odds ratio (aPOR): 2.06, 95% CI: 1.45, 2.92], and 12-23 months (aPOR: 2.37, 95% CI: 1.67, 3.35), had higher prevalence of diarrhoea compared to children aged 0-5 months. Children whose mothers had a college or higher education (aPOR: 0.41, 95% CI: 0.22, 0.78), and a secondary education (aPOR: 0.66, 95% CI: 0.51, 0.86), had 59% and 34% lower odds of diarrhoea respectively, compared to children whose mothers had no formal education. Children from the richest households (aPOR: 0.58, 95% CI: 0.39, 0.86), had 42% lower odds of diarrhoea compared to children from the poorest households. Children resident in rural areas had 22% lower odds of diarrhoea compared to their peers in urban areas (aPOR: 0.78, 95% CI: 0.63, 0.98). The prevalence of ARI was 33.3% (95% CI: 31.72, 34.82%). Children aged 6-11 months (aPOR: 1.43, 95% CI: 1.06, 1.93), and 12-23 months (aPOR: 1.41, 95% CI: 1.10, 1.82), had higher prevalence of ARI compared to children aged 0-5 months.

CONCLUSIONS

This study suggests that the prevalence of diarrhoea and ARI among children aged 6-11 and 12-23 months was higher compared to children aged 0-5 months. Children under-5 years old whose mothers had a secondary or higher education had a lower prevalence of diarrhoea compared to children whose mothers had no formal education.

Epidemiological and clinical characteristics of children with acute respiratory viral infections in the Philippines: a prospective cohort study

OBJECTIVES

Viral acute respiratory infection (ARI) remains a major global health problem, especially among children in low- and middle-income countries. The study was conducted to reveal aetiological significance of respiratory viruses among both non-hospitalized and hospitalized children.

METHODS

A cohort study of children with ARI at the household, primary healthcare facility, and hospital levels was conducted alongside a hospital-based study including non-cohort children from 2014 to 2016 in the Philippines. The ARI cases were recorded at households and healthcare facilities, and a clinical investigation was performed. Nasopharyngeal swabs were collected from the symptomatic children and tested for respiratory viruses via polymerase chain reaction. Then, the association between healthcare facility utilization and viral detection was investigated.

RESULTS

Overall, 18,514 ARI cases were enrolled in the cohort study, and samples were collected from 4735 of these cases. The hospital-based study detected 648 ARI cases, all of which were sampled. Rhinovirus (22.2%; 1052/4735) was most frequently detected followed by respiratory syncytial virus (12.0%; 566/4735). Enterovirus (adjusted odds ratio, 1.8; 95% confidence interval, 1.1-2.8), human metapneumovirus (2.1, 1.4-3.2), rhinovirus (2.1, 1.8-2.6), and respiratory syncytial virus (1.6, 1.2-1.9) were significantly more prevalent in the ARI cases at healthcare facilities than in those in households. Of all ARI cases, 0.6% required hospitalization while 1.8% were hospitalized among the respiratory syncytial virus-positive cases (3.8, 3.0-4.9).

CONCLUSIONS

We determined the prevalence of respiratory viruses among children with ARIs at the household, primary healthcare facility, and hospital levels and the association with clinical characteristics. In particular, we discovered a significant disease burden and impact of respiratory syncytial virus infections as well as a considerable aetiological implication of rhinovirus infections.

Underdetection of laboratory-confirmed influenza-associated hospital admissions among infants: a multicentre, prospective study

BACKGROUND

Since influenza often presents non-specifically in infancy, we aimed to assess the extent to which existing respiratory surveillance platforms might underestimate the frequency of severe influenza disease among infants.

METHODS

The Influenza and Respiratory Syncytial Virus in Infants (IRIS) study was a prospective observational study done at four hospitals in Albania, Jordan, Nicaragua, and the Philippines. We included acutely ill infants aged younger than 1 year admitted to hospital within 10 days or less of illness onset during two influenza seasons (2015-16 and 2016-17) in Albania, Jordan, and Nicaragua, and over a continuous 34 week period (2015-16) in the Philippines. We assessed the frequency of influenza virus infections by real-time RT-PCR (rRT-PCR) and serology. The main study outcome was seroconversion, defined as convalescent antibody titres more than or equal to four-fold higher than acute sera antibody titres, and convalescent antibody titres of 40 or higher. Seroconverison was confirmed by haemagglutination inhibition assay for influenza A viruses, and by hemagglutination inhibition assay and microneutralisation for influenza B viruses.

FINDINGS

Between June 27, 2015, and April 21, 2017, 3634 acutely ill infants were enrolled, of whom 1943 were enrolled during influenza seasons and had complete acute-convalescent pairs and thus were included in the final analytical sample. Of the 1943 infants, 94 (5%) were influenza-positive by both rRT-PCR and serology, 58 (3%) were positive by rRT-PCR-only, and 102 (5%) were positive by serology only. Seroconversion to at least one of the influenza A or B viruses was observed among 196 (77%) of 254 influenza-positive infants. Of the 254 infants with influenza virus, 84 (33%) only had non-respiratory clinical discharge diagnoses (eg, sepsis, febrile seizures, dehydration, or other non-respiratory viral illness). A focus on respiratory diagnoses and rRT-PCR-confirmed influenza underdetects influenza-associated hospital admissions among infants by a factor of 2·6 (95% CI 2·0-3·6). Findings were unchanged when syndromic severe acute respiratory infection criteria were applied instead of clinical diagnosis.

INTERPRETATION

If the true incidence of laboratory-confirmed influenza-associated hospital admissions among infants is at least twice that of previous estimates, this substantially increases the global burden of severe influenza and expands our estimates of the preventive value of maternal and infant influenza vaccination programmes.

FUNDING

US Centers for Disease Control and Prevention.

Age-specific incidence rates and risk factors for respiratory syncytial virus-associated lower respiratory tract illness in cohort children under 5 years old in the Philippines

Background

Respiratory syncytial virus (RSV) is one of the main viral causes of lower respiratory tract illness (LRTI), especially in young children. RSV vaccines, including maternal and infant vaccines, are under development; however, more epidemiological studies are needed to develop effective vaccination strategies.

Objectives

To estimate detailed age‐specific incidence rates and severity of RSV‐associated LRTI (RSV‐LRTI) using data from a community‐based prospective cohort study in the Philippines.

Patients/Methods

Cohort children who visited health facilities due to acute respiratory symptoms were identified, and nasopharyngeal swabs were collected to detect RSV. The severity of RSV‐LRTI was assessed using the severity definition proposed by the World Health Organization. Risk factors for developing RSV‐LRTI and contribution of SpO₂ measurement were also evaluated.

Results

A total of 395 RSV episodes which occurred in children aged 2‐59 months were categorised as 183 RSV‐LRTI, 72 as severe RSV‐LRTI and 29 as very severe RSV‐LRTI. Children aged 3‐5 months had the highest incidence rate of RSV‐LRTI, at 207.4 per 1000 child‐years (95% CI: 149.0‐279.5). Younger age group, place of living and low educational level of caregivers were associated with developing RSV‐LRTI. Clinical manifestations had low levels of agreement with hypoxaemia as measured by pulse oximeter.

Conclusion

The highest burden of RSV was observed in young infants aged 3‐5 months, whereas the burden was also high in those aged 12‐20 months. Future vaccination strategies should consider the protection of older children, especially those aged one year, as well as young infants.

Chemical and Biological Components of Urban Aerosols in Africa: Current Status and Knowledge Gaps

Aerosolized particulate matter (PM) is a complex mixture that has been recognized as the greatest cause of premature human mortality in low- and middle-income countries. Its toxicity arises largely from its chemical and biological components. These include polycyclic aromatic hydrocarbons (PAHs) and their nitro-derivatives (NPAHs) as well as microorganisms. In Africa, fossil fuel combustion and biomass burning in urban settings are the major sources of human exposure to PM, yet data on the role of aerosols in disease association in Africa remains scarce. This review is the first to examine studies conducted in Africa on both PAHs/NPAHs and airborne microorganisms associated with PM. These studies demonstrate that PM exposure in Africa exceeds World Health Organization (WHO) safety limits and carcinogenic PAHs/NPAHs and pathogenic microorganisms are the major components of PM aerosols. The health impacts of PAHs/NPAHs and airborne microbial loadings in PM are reviewed. This will be important for future epidemiological evaluations and may contribute to the development of effective management strategies to improve ambient air quality in the African continent.

Transmission of Respiratory Syncytial Virus Among Children Under 5 Years in Households of Rural Communities, the Philippines

Background

To develop a more effective vaccination strategy for reducing the impact of respiratory syncytial virus (RSV) infection, especially in young infants (<6 months old), it is necessary to understand the transmission dynamics of RSV.

Methods

We conducted a community-based prospective cohort study from 2014 to 2016 in Biliran Province, the Philippines, on children <5 years old. We collected nasopharyngeal swabs from symptomatic children with acute respiratory infection (ARI) during household visits and at health facilities. In households (n = 181) with RSV-positive ARI cases (RSV-ARI), we also identified ARI episodes among other children <5 years old in the same household. In addition, we determined the serial interval to estimate the basic reproduction number (R₀), the average number of secondary cases generated by a single primary case.

Results

In the 181 households analyzed, we found 212 RSV-ARI in 152 households with a single case and 29 households with multiple cases, which included 29 1st RSV-ARI and 31 2nd RSV-ARI. We also found possible index cases among children <5 years old in the same household for 29.0% (18 of 62) of young infants with RSV-ARI. The estimated mean serial interval was 3.2 days, and R₀ was estimated to be 0.92–1.33 for RSV-A and 1.04–1.76 for RSV-B, which varied between different times (2014 and 2015) and places.

Conclusions

Young infants are likely to acquire RSV infection from older children in the same household. Therefore, vaccination targeting older children might protect infants from RSV infection.