The research team took advantage of whole blood transcriptomics, a technique that measures the activity of thousands of genes simultaneously in circulating immune cells. Rather than examining individual molecules in isolation, transcriptomics captures the coordinated behaviour of the entire immune system at a single moment, revealing which defensive programmes have been switched on, which have been silenced, and how the composition of the blood cell population itself has shifted in response to infection. This systems-level view is particularly valuable in paediatric respiratory disease, where clinical symptoms overlap considerably between viral and bacterial pathogens and where the biological drivers of severity remain poorly understood.

The study drew on children enrolled in the Drakenstein Child Health Study and the Pneumonia in South Africa Programme, longitudinal research platforms based in South Africa that have followed children in communities where the burden of lower respiratory tract illness is among the highest in the world. The investigators compared whole blood transcriptomes from 127 healthy children with those from 71 children who had mild or asymptomatic SARS-CoV-2 infection, 41 children hospitalised with severe SARS-CoV-2 disease, 47 children hospitalised with respiratory syncytial virus-associated lower respiratory tract illness, and 47 children with pulmonary tuberculosis. This design allowed the researchers to distinguish a general response to respiratory illness from pathogen-specific signatures and, crucially, to identify the molecular features that separate mild from severe COVID-19 in children.

The scale of the transcriptional differences was striking. The team identified more than 5,000 differentially expressed genes across the disease groups, all passing a stringent statistical threshold that controls the false discovery rate at below 5 percent. In children with severe SARS-CoV-2, standout genes included OLFM4, IFI27, CBX7, IGF2BP3 and OTOF. In RSV-associated lower respiratory tract illness, the most distinctive genes were IFI27, OTOF, SIGLEC1, IFI44L and USP18, several of which are well-known markers of interferon-driven antiviral activity. Pulmonary tuberculosis produced its own signature, dominated by MMP8, LTF, IGF2BP3, GPR84, CD177, C1QC and DEFA4, genes associated with neutrophil activation, granule release and the complement cascade, consistent with the intense myeloid inflammation that characterises tuberculous lung disease.

Pathway analysis of the severe COVID-19 group, compared with healthy uninfected children, revealed enrichment of neutrophil degranulation and interferon gamma signalling, alongside overexpression of genes encoding ribosomal proteins and a measurable depletion of general immune response programmes. Neutrophil degranulation refers to the release of toxic granule contents by these frontline white blood cells, a process that helps destroy pathogens but can also damage surrounding tissue when excessive. Interferon gamma, meanwhile, is a cytokine that orchestrates macrophage activation and antiviral defence. The combination of a strong neutrophil-driven inflammatory programme with signs of broader immune dysregulation echoes patterns previously documented in adults with severe COVID-19, and the authors note that severe disease in children exhibits a cellular response similar to that reported in adult patients.

To move beyond lists of individual genes, the researchers applied Weighted Gene Co-expression Network Analysis, a computational method that clusters genes into modules based on correlated patterns of expression across samples. Rather than treating each transcript as an independent variable, WGCNA identifies groups of genes that rise and fall together, which often reflects shared biological regulation. The analysis uncovered 10 such correlated gene modules that were shared across the different lower respiratory tract infections, suggesting that despite the distinct causative pathogens, the underlying response mechanisms in the blood draw on a common repertoire of immune programmes. This convergence helps explain why children with different infections can present with similar clinical pictures while still carrying pathogen-specific fingerprints detectable at the transcriptomic level.

The team also performed cellular decomposition analysis, a computational approach that infers the relative abundance of different immune cell types in whole blood from their gene expression patterns, avoiding the need for physical cell sorting. The results were sobering. Compared with healthy children, severe SARS-CoV-2 was associated with the depletion of 22 distinct cell populations, RSV-associated illness with 16, and pulmonary tuberculosis with 21. Depletion of circulating lymphocyte subsets is a recognised feature of severe respiratory viral infections and is thought to reflect both redistribution of cells to infected tissues and infection-induced cell death. The breadth of this depletion in severe paediatric COVID-19 underscores how profoundly the cellular architecture of the immune system is remodelled when disease becomes critical.

Perhaps the most clinically consequential finding is the set of genes capable of discriminating between disease states. The study identified transcripts that distinguish asymptomatic or mild SARS-CoV-2 infection from severe disease, that separate healthy children from those with severe COVID-19, and that differentiate RSV-associated illness and pulmonary tuberculosis from one another and from SARS-CoV-2. IFI27, an interferon-stimulated gene frequently implicated in antiviral responses, appears among the leading markers for both severe SARS-CoV-2 and RSV, while myeloid genes such as MMP8 and DEFA4 anchor the tubercular signature. The authors highlight these discriminators as potential future therapeutic targets, and they could also inform the development of diagnostic tests that distinguish bacterial from viral lower respiratory disease at the point of care, a longstanding goal in paediatric medicine where antibiotic stewardship is critical.

The work carries particular significance for low- and middle-income countries, where the study was conducted and where childhood pneumonia remains a leading cause of death. Most transcriptomic studies of COVID-19 have been performed in high-income settings with predominantly adult cohorts, leaving a gap in knowledge about immune responses in children from populations that bear a disproportionate burden of respiratory disease. By embedding this analysis within well-characterised South African birth and pneumonia cohorts, the researchers have generated reference data that reflect the epidemiological realities of the communities most affected. The study was approved by the research ethics committee of the University of Cape Town and the Western Cape Provincial Research Committee, with written informed consent obtained from mothers at enrolment and renewed annually, and secondary analysis approved by the University of Southampton.

As with any transcriptomic study, the findings describe associations between gene expression and disease state rather than proving causation, and whole blood sampling captures a systemic snapshot that may not fully mirror events within the lung itself. Nevertheless, the convergence of evidence, from differentially expressed genes through pathway enrichment, co-expression networks and cellular deconvolution, paints a coherent picture in which severe paediatric COVID-19 resembles the adult syndrome in its immunological architecture, while mild infection in children is marked by a far more restrained response. The gene signatures identified here, including OLFM4, IFI27, IGF2BP3 and their companions across disease groups, now provide a molecular framework for future studies of why some children deteriorate while most do not, and for the design of interventions aimed at tipping that balance.

Subject of Research: Immune gene expression differences in children with SARS-CoV-2 infection compared with other lower respiratory tract infections

Article Title: Immune transcriptomic differences in paediatric patients with SARS-CoV-2 compared to other lower respiratory tract infections

Article References: Kitaba, N. T., Workman, L., Cohen, C., Baralle, D., Kong, E., Botha, M., Johnson, M., Goldblatt, D., Nicol, M. P., Holloway, J. W., & Zar, H. J. (2026). Immune transcriptomic differences in paediatric patients with SARS-CoV-2 compared to other lower respiratory tract infections. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14343-x

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14343-x

Keywords: SARS-CoV-2, COVID-19, children, transcriptomics, gene expression, RSV, pulmonary tuberculosis, lower respiratory tract infection, neutrophil degranulation, interferon signalling, WGCNA, South Africa

The study relied on a single multiplex fluorescence polymerase chain reaction panel coupled with capillary electrophoresis, applied uniformly to every patient in the cohort. This platform detects 13 targets simultaneously: 11 respiratory viruses and two atypical bacteria, Mycoplasma pneumoniae and Chlamydia. Standardizing the diagnostic method across all five years is a technical strength, because it removes a common source of bias in longitudinal surveillance studies, where changes in assay sensitivity can be mistaken for genuine shifts in pathogen epidemiology. Of the 9,674 patients, 5,289, or 54.67 percent, had lower respiratory tract infections, while 4,385, or 45.33 percent, had upper respiratory tract infections, reflecting the case mix of a hospital-based population rather than a community sample.

The contrast in detection rates between the two anatomical compartments was striking. Pathogens were identified in 2,939 of 5,289 lower respiratory tract infection cases, a positivity rate of 55.57 percent, compared with only 677 of 4,385 upper respiratory tract infection cases, or 15.44 percent. That difference of 40.13 percentage points, with a 95 percent confidence interval of 38.40 to 41.80 and a P value below 0.001, indicates that lower tract disease in this cohort was far more likely to have an identifiable infectious cause. The authors suggest this may partly reflect the deeper sampling and higher pathogen loads associated with lower tract disease, as well as the inclusion of atypical bacteria that preferentially involve the lung parenchyma and bronchial tree.

Within the lower respiratory tract infections, Mycoplasma pneumoniae was the leading pathogen, detected in 954 of 5,289 cases, or 18.04 percent. Rhinovirus followed at 618 cases, or 11.68 percent, and influenza A virus ranked third at 456 cases, or 8.62 percent. In the upper respiratory tract, by contrast, rhinovirus predominated, found in 224 of 4,385 cases, or 5.11 percent. The prominence of Mycoplasma pneumoniae is notable because this cell-wall-less bacterium, which lacks the outer membrane targeted by beta-lactam antibiotics, requires macrolides or other alternative agents and has been associated with periodic epidemics worldwide, including a pronounced wave in East Asia following the end of COVID-19 restrictions. Its rise to the top of the pathogen ranking in this Chinese cohort mirrors reports from several neighboring countries during the same period.

The temporal analysis forms the core of the study’s contribution. During 2021 and 2022, when stringent containment measures and mass vaccination were maintained across China, both the volume of acute respiratory infection consultations and the proportion of tests returning positive remained low. Positivity stood at 326 of 1,180 tests, or 27.63 percent, in 2021 and fell to 283 of 1,161 tests, or 24.38 percent, in 2022. After the relaxation of non-pharmaceutical interventions, the picture changed abruptly. In 2023, 1,486 of 4,292 tests were positive, a rate of 34.62 percent, and by 2024 the positivity rate had climbed to 1,046 of 1,913 tests, or 54.68 percent. In 2025 the rate remained elevated at 475 of 1,128 tests, or 42.11 percent.

Because the number of patients tested varied substantially from year to year, the researchers adjusted for age group in a logistic regression model to determine whether the apparent resurgence was confounded by shifts in the demographic composition of the tested population. It was not. Compared with 2021, the odds of pathogen detection were significantly higher in 2023, with an odds ratio of 2.85 and a 95 percent confidence interval of 2.09 to 3.88; in 2024, with an odds ratio of 4.19 and a confidence interval of 3.01 to 5.84; and in 2025, with an odds ratio of 2.19 and a confidence interval of 1.53 to 3.15. The persistence of this signal after adjustment strengthens the interpretation that the rebound reflects genuine changes in pathogen circulation rather than changes in who was being tested.

This pattern is consistent with the concept of immunity debt, a hypothesis proposed early in the pandemic suggesting that prolonged reduction in exposure to common respiratory pathogens, combined with the aging of the cohort of infants and children who never encountered them, could produce a delayed and intensified wave of infections once transmission resumed. The study cannot directly measure population immunity, and the authors are careful to frame their findings as descriptive surveillance rather than proof of any single mechanism. Nevertheless, the sharp rise in positivity after December 2022, and the dominance of Mycoplasma pneumoniae, a pathogen known for cyclical epidemics at multi-year intervals, fit the broader pattern documented across the region after restrictions ended.

Perhaps the most clinically consequential findings concern the sickest patients. Among 79 patients who required intensive care for severe lower respiratory tract infection, at least one pathogen was detected in every single case, and bacterial or fungal co-infection was documented in 72 of them, or 91.14 percent. Even more alarming, multidrug-resistant organisms were identified in 42 of these ICU patients, or 53.16 percent. Severe disease in this cohort was characterized by advanced age and a heavy burden of secondary infection, underscoring a well-recognized but persistently difficult problem in respiratory critical care: viral injury to the respiratory epithelium creates conditions in which resistant hospital-associated and community-acquired bacteria and fungi can flourish, complicating treatment and worsening outcomes.

The high rate of co-infection in severe cases also carries implications for diagnostic and antimicrobial stewardship. Because mixed infections were more frequent in lower respiratory tract infections than in upper tract disease, the authors argue that multiplex molecular panels, which can identify several pathogens from a single specimen in a few hours, are particularly valuable in hospitalized patients, where distinguishing viral pneumonia from bacterial superinfection directly affects antibiotic decisions. The detection of multidrug-resistant organisms in more than half of the intensive care cohort adds urgency, since empiric broad-spectrum therapy in such patients must be balanced against the risk of further selecting for resistance.

The study’s limitations are those inherent to its retrospective, single-region design. The cohort comes from a hospital in Shijiazhuang, Hebei Province, and the 13-target panel does not cover all respiratory pathogens, notably excluding common bacteria such as Streptococcus pneumoniae and Haemophilus influenzae, so the true burden of bacterial co-infection in the wider population may differ. Hospital-based sampling also means the results describe patients ill enough to seek care rather than community transmission as a whole. Still, the five-year span, the uniform diagnostic method, and the age-adjusted analysis together offer a rigorous record of how one region’s respiratory pathogen landscape responded to the end of pandemic controls. The authors conclude that the suppression and resurgence they documented, together with the heavy burden of resistant co-infection in severe disease, argue for continued vigilance, sustained molecular surveillance, and optimized management of lower respiratory tract infections in the post-pandemic era.

Subject of Research: Respiratory pathogen epidemiology and co-infection patterns in acute respiratory infections during and after the COVID-19 pandemic

Article Title: Respiratory pathogen spectrum and co-infection patterns in patients with acute respiratory infection during and after the coronavirus COVID-19 pandemic: a five-year retrospective study, 2021–2025

Article References: Zhao, M.-W., Yang, J., Li, Y.-H., Qiu, P., Zhang, Y., Zhang, X.-W., Gao, S., Wang, J., & Zhao, P. (2026). Respiratory pathogen spectrum and co-infection patterns in patients with acute respiratory infection during and after the coronavirus COVID-19 pandemic: a five-year retrospective study, 2021–2025. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14526-6

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14526-6

Keywords: acute respiratory infection, Mycoplasma pneumoniae, rhinovirus, influenza A, co-infection, COVID-19, non-pharmaceutical interventions, lower respiratory tract infection, multidrug-resistant organisms, multiplex PCR, immunity debt, intensive care

The scale of the cohort allowed the investigators to divide patients into five age bands and compare clinical, laboratory, radiological, and microbiological features across the full pediatric spectrum, something earlier studies, which often focused narrowly on infants or preschool children, could not do. Among the 1,611 children, 57.4 percent were male, 301 children, or 18.7 percent, developed severe pneumonia, and 36 children, or 2.2 percent, required admission to the intensive care unit. The overall ICU admission rate appears modest, but the distribution across ages was strikingly uneven: infants aged zero to six months had the highest ICU admission rate at 7.9 percent, underscoring that the youngest airways, with their narrow caliber and immature immune responses, remain the most vulnerable to life-threatening hMPV disease.

At the opposite end of the pediatric age range, the picture changed dramatically. Children older than six years showed the highest proportions of atelectasis, at 22.4 percent, unilateral lung involvement, at 65.7 percent, and severe pneumonia, at 31.0 percent. This inversion of the usual risk pattern, in which severity is typically assumed to concentrate in infancy, suggests that school-aged children with human metapneumovirus infection should not be dismissed as low risk. The authors note that the very large radiological associations with severity may partly reflect overlap between imaging findings and the extent-based criteria used to define severe pneumonia, a methodological caveat that tempers but does not eliminate the clinical signal.

To identify which factors were independently associated with severe pneumonia, the team built a multivariable logistic regression model incorporating prespecified clinical, laboratory, and microbiological covariates, with selected laboratory variables analyzed as continuous measures. The results were internally coherent from an immunological standpoint. Atelectasis carried the strongest association, with an adjusted odds ratio of 47.52, followed by underlying chronic disease at 9.49, radiological consolidation at 6.82, fever at 3.29, and wheezing at 2.50. Mycoplasma pneumoniae co-detection nearly doubled the odds of severe pneumonia, with an adjusted odds ratio of 1.90. Higher absolute neutrophil counts, rising 1.47-fold per 5 × 10⁹ per liter, and higher C-reactive protein levels, rising 1.14-fold per 10 mg per liter, both pointed toward the heightened inflammatory activation that accompanies more severe lower airway disease.

Two findings ran in the opposite direction and are among the most intriguing in the study. Higher absolute monocyte counts were associated with lower odds of severe pneumonia, with an adjusted odds ratio of 0.71 per 1 × 10⁹ per liter, and bacterial co-detection as a broad category was also associated with reduced odds, at 0.60. The authors do not overinterpret these inverse associations, but they raise the possibility that a robust monocytic response reflects effective innate immune recruitment, while the broad bacterial co-detection category may be diluted by organisms of uncertain clinical significance detected by the highly sensitive sequencing platform. Targeted next-generation sequencing can identify low-abundance nucleic acids whose pathogenic role is ambiguous, a well-recognized challenge in molecular diagnostics that distinguishes colonization or contamination from true coinfection.

The age gradient of Mycoplasma pneumoniae co-detection was one of the clearest patterns in the entire dataset. Among infants aged zero to six months, only 6.0 percent of hMPV-positive children also tested positive for Mycoplasma pneumoniae, but this proportion climbed steadily with age, reaching 50.0 percent in children older than six years. This trajectory mirrors the known epidemiology of Mycoplasma pneumoniae, which is uncommon in early infancy and peaks in school-aged children and adolescents, likely reflecting cumulative exposure to this slow-growing, cell-wall-deficient bacterium in school and community settings. When human metapneumovirus damages the respiratory epithelium, it may facilitate Mycoplasma adherence and invasion of the lower airway, creating a viral-bacterial synergy that manifests as the higher odds of severe pneumonia observed after multivariable adjustment.

Importantly, the overall age-group term in the primary regression model did not reach statistical significance, meaning that age category per se was not an independent predictor of severity once other clinical and laboratory variables were accounted for. What differed across ages was the constellation of manifestations: young infants presented with the physiological fragility that drives ICU admission, while older children presented with the lobar consolidation, atelectasis, and mycoplasmal coinfection that drive classification as severe pneumonia. This distinction between age as a risk marker and age as a modifier of disease phenotype is a subtle but clinically meaningful contribution of the study, because it implies that clinicians should look for different warning signs at different ages rather than applying a single severity rubric uniformly.

Technically, the study relied on targeted next-generation sequencing of respiratory samples, including nasopharyngeal specimens and bronchoalveolar lavage fluid, to characterize the virome and bacteriome of each patient. Compared with conventional polymerase chain reaction panels, this approach captures a broader range of pathogens without requiring prior suspicion of a specific organism, which is precisely what enabled the systematic assessment of pathogen co-detection that formed a central aim of the work. The retrospective design, single-center setting, and reliance on clinically ordered testing all impose limitations, and the authors appropriately flag the potential circularity between radiological extent findings and the severity definition itself. Nevertheless, the internal consistency of the laboratory markers, with neutrophilia and elevated C-reactive protein tracking severity while monocyte counts inversely associated, lends biological plausibility to the model.

The practical implications for pediatric practice are concrete. For infants under six months with human metapneumovirus lower respiratory tract infection, the high ICU admission rate argues for close monitoring of respiratory status, including work of breathing, oxygen saturation trends, and feeding tolerance, even when the child appears initially stable. For school-aged children, the study suggests peri-admission chest imaging when clinically indicated, given the high frequency of atelectasis and unilateral involvement in this group, and prompt further clinical and microbiological evaluation when Mycoplasma pneumoniae is co-detected, since this combination roughly doubles the odds of severe pneumonia. As surveillance of human metapneumovirus intensifies worldwide, following its recognition as an increasingly appreciated cause of pediatric respiratory hospitalization, studies of this kind provide the age-specific evidence base that clinicians need to triage, investigate, and treat children with this common but heterogeneous infection.

Subject of Research: Age-stratified clinical features and risk factors for severe pneumonia in children hospitalized with human metapneumovirus lower respiratory tract infection

Article Title: Age-stratified clinical features and factors associated with severe pneumonia in hospitalized children with human metapneumovirus–associated lower respiratory tract infection

Article References: Zhang, J., Jiang, Q., Lei, M., Sun, Y., & Ma, X. (2026). Age-stratified clinical features and factors associated with severe pneumonia in hospitalized children with human metapneumovirus–associated lower respiratory tract infection. Virology Journal. https://doi.org/10.1186/s12985-026-03306-y

Image Credits: AI Generated

DOI: 10.1186/s12985-026-03306-y

Keywords: human metapneumovirus, lower respiratory tract infection, severe pneumonia, Mycoplasma pneumoniae, pathogen co-detection, children, next-generation sequencing, atelectasis, C-reactive protein, pediatric intensive care, risk factors, virology