UNASSIGNED: Human metapneumovirus (HMPV) is a common respiratory pathogen that causes respiratory tract infections. In India, HMPV has been identified as one of the leading causes of morbidity and mortality in infants and young children with respiratory tract infections. The most reported sublineages of HMPV in India are B1, B2, A2b and A2c.
UNASSIGNED: A retrospective study was conducted to determine the circulating genotypes of HMPV among SARI cases from January 2016 to December 2018.
UNASSIGNED: Positive throat swab samples were confirmed with real-time RT-PCR. Subsequently, these samples were analysed using semi-nested conventional RT-PCR targeting the G gene, followed by sequencing and phylogenetic analysis. Clinical data analysis was also performed using SPSS 15.0 software.
UNASSIGNED: All 20 samples from the SARI cases were classified under the A2c sublineage of HMPV. Phylogenetic analysis indicated that these strains were genetically related to those circulating in Japan, China, and Croatia. Among the samples, ten showed 111-nucleotide duplications, while the other ten had 180-nucleotide duplications.
UNASSIGNED: Clinical analysis showed that four cases had coinfections with other pathogens. Our extensive analysis of patient samples determined that HMPV, especially the A2c genotype, significantly contributed to SARI cases within our study population, which signifies the importance of considering HMPV as a probable aetiological agent when investigating SARI outbreaks.

Pregnant women (PW) are at a higher risk of diseases and hospitalization from viral respiratory infections, particularly influenza and SARS-CoV-2, due to cardiopulmonary and immunological changes. This study assessed the impact of viral respiratory infections on PW hospitalized with severe acute respiratory infection (SARI) prior to the COVID-19 pandemic. It is a cross-sectional study with 42 PW and 85 non-pregnant women (NPW) admitted with SARI to two tertiary hospitals between January 2015 and December 2019. The rates of virus prevalence, SARI hospitalization, length of hospital stay, oxygen supplementation, intensive care unit (ICU) admission, and death were comparable between PW and NPW. A multivariate analysis showed that PW had a higher rate of viral SARI hospitalizations (OR = 2.37; 95% CI = 1.02-5.48) as compared to NPW, with the influenza virus being the most prevalent (aOR = 7.58; 95% CI = 1.53-37.66). The length of hospital stays (aOR = 0.83; 95% CI = 0.73-0.95) and admissions to the ICU (aOR = 0.028; 95% CI = 0.004-0.25) were lower in PW as compared to hospitalized NPW. The influenza virus had a greater impact on the frequency of SARI in the group of PW, and these had a better outcome than NPW due to the earlier antiviral treatment they received.

In December 2023, we observed through hospital-based surveillance a severe outbreak of enterovirus D68 infection in pediatric inpatients in Dakar, Senegal. Molecular characterization revealed that subclade B3, the dominant lineage in outbreaks worldwide, was responsible for the outbreak. Enhanced surveillance in inpatient settings, including among patients with neurologic illnesses, is needed.

BACKGROUND: Changes in the epidemiology of illnesses caused by respiratory syncytial virus (RSV) infection following the COVID-19 pandemic are reported. The New Zealand (NZ) COVID-19 situation was unique; RSV community transmission was eliminated with the 2020 border closure, with a rapid and large increase in hospitalizations following the relaxation of social isolation measures and the opening of an exclusive border with Australia.
METHODS: This active population-based surveillance compared the age-specific incidence and seasonality of RSV-associated hospitalizations in Auckland, NZ, for 2 years before and after the 2020 border closures. Hospitalisation rates between years were compared by age, ethnicity (European/other, Māori, Pacific and Asian) and socioeconomic group (1 = least, 5 = most deprived).
RESULTS: There was no RSV transmission in 2020. In all other years, hospitalisation rates were highest for people of Pacific versus other ethnic groups and for people living in the most deprived quintile of households. RSV hospitalisation rates were higher in 2021 and 2022 than in 2018-19. The epidemic peak was higher in 2021, but not 2022, and the duration was shorter than in 2018-19. In 2021, the increase in RSV hospitalisation rates was significant across all age, sex, ethnic and socioeconomic groups. In 2022, the increase in hospitalisation rates was only significant in one age (1- < 3 years), one ethnic (Asian) and one socioeconomic group (quintile 2).
CONCLUSIONS: COVID pandemic responses altered RSV-related hospitalisation seasonal patterns. Atypical features of RSV hospitalisation epidemiology were the increase in rates in older children and young adults, which lessened in 2022. Despite these variations, RSV hospitalisations in NZ continue to disproportionately affect individuals of Pacific ethnicity and those living in more socioeconomically deprived households. Whilst future public health strategies focused on RSV disease mitigation need to consider the potential shifts in epidemiological patterns when the transmission is disrupted, these variances must be considered in the context of longer-standing patterns of unequal disease distribution.

OBJECTIVE:  Beginning in December 2019, COVID-19 rapidly emerged as a global pandemic. Though its severity in children was reported to be less than that in adults, data on its epidemiology in relation to severe acute respiratory illness (SARI) caused by other microbes needed to be generated. This study compares the clinical profile and outcome of children hospitalized with COVID-19-positive and negative SARI.
METHODS:  This is a prospective observational analytical study involving children 1 month to 18 years old, hospitalized with COVID-19-positive and negative SARI during the pandemic. All eligible patients were enrolled after obtaining informed parental consent. Their clinical manifestations, investigations, and outcomes were documented on a predesigned case record form. A nasopharyngeal swab sample for COVID-19 reverse transcription polymerase chain reaction was sent, and results were noted.
RESULTS:  From May 2020 to July 2021, 267 children were hospitalized with a diagnosis of SARI. Out of these, 146 (54.7%) were boys and 78.7% were under five years of age. Other presentations included fever and cough, breathlessness, nausea, vomiting, diarrhea, rash, seizures, and altered sensorium. Twenty-eight patients (10.5%) tested positive for COVID-19. COVID-19 patients were similar in terms of demographic characteristics and presenting symptoms to non-COVID-19 patients but had a lower absolute lymphocyte count (p = 0.019) and higher serum alanine transaminase levels (p = 0.013). Acute respiratory distress syndrome (OR, 4.3; 95% CI, 1.8-10.0), shock (OR, 3.9; 95% CI, 1.9-7.9), and need for intensive care unit admission (OR, 9.9; 95% CI, 6.9-14) were more common in COVID-19 SARI patients. Death occurred in 18% of COVID-19 and 9% of non-COVID-19 patients (p = 0.07). SARI nonsurvivors had significantly lower blood pH and platelet counts than survivors.
CONCLUSIONS: Comparison of COVID-19-positive and negative SARI patients showed subtle differences between the two groups, with COVID-19-positive children having an increased severity of illness. Also, laboratory evidence of multiorgan dysfunction at admission was associated with higher mortality.

OBJECTIVE: Endemic SARS-CoV-2 infections still burden the healthcare system and represent a considerable threat to vulnerable patient cohorts, in particular immunocompromised (IC) patients. This study aimed to analyze the in-hospital outcome of IC patients with severe SARS-CoV-2 infection in Germany.
METHODS: This retrospective, observational study, analyzed administrative data from inpatient cases (n = 146,324) in 84 German Helios hospitals between 1 January 2022 and 31 December 2022 with regard to in-hospital outcome and health care burden in IC patients during the first 12 months of Omicron dominance. As the primary objective, in-hospital outcomes of patients with COVID-19-related severe acute respiratory infection (SARI) were analyzed by comparing patients with (n = 2037) and without IC diagnoses (n = 14,772). Secondary analyses were conducted on IC patients with (n = 2037) and without COVID-19-related SARI (n = 129,515). A severe in-hospital outcome as a composite endpoint was defined per the WHO definition if one of the following criteria were met: intensive care unit (ICU) treatment, mechanical ventilation (MV), or in-hospital death.
RESULTS: In total, 12% of COVID-related SARI cases were IC patients, accounting for 15% of ICU admissions, 15% of MV use, and 16% of deaths, resulting in a higher prevalence of severe in-hospital courses in IC patients developing COVID-19-related SARI compared to non-IC patients (Odds Ratio, OR = 1.4, p < 0.001), based on higher in-hospital mortality (OR = 1.4, p < 0.001), increased need for ICU treatment (OR = 1.3, p < 0.001) and mechanical ventilation (OR = 1.2, p < 0.001). Among IC patients, COVID-19-related SARI profoundly increased the risk for severe courses (OR = 4.0, p < 0.001).
CONCLUSIONS: Our findings highlight the vulnerability of IC patients to severe COVID-19. The persistently high prevalence of severe outcomes in these patients in the Omicron era emphasizes the necessity for continuous in-hospital risk assessment and monitoring of IC patients.

Respiratory diseases, including influenza and coronaviruses, pose recurrent global threats. This study delves into the respiratory surveillance systems, focusing on the effectiveness of SARI sentinel surveillance for total and severe cases incidence estimation. Leveraging data from the COVID-19 pandemic in Chile, we examined 2020-2023 data (a 159-week period) comparing census surveillance results of confirmed cases and hospitalizations, with sentinel surveillance. Our analyses revealed a consistent underestimation of total cases and an overestimation of severe cases of sentinel surveillance. To address these limitations, we introduce a nowcasting model, improving the precision and accuracy of incidence estimates. Furthermore, the integration of genomic surveillance data significantly enhances model predictions. While our findings are primarily focused on COVID-19, they have implications for respiratory virus surveillance and early detection of respiratory epidemics. The nowcasting model offers real-time insights into an outbreak for public health decision-making, using the same surveillance data that is routinely collected. This approach enhances preparedness for emerging respiratory diseases by the development of practical solutions with applications in public health.

The lockdown enforced amid the COVID-19 pandemic has affected the occurrence and trends of various respiratory virus infections, with a particular focus on influenza. Our study seeks to analyze the repercussions of the COVID-19 pandemic on the positivity of the influenza virus throughout a 4-year span, encompassing both the pre-COVID-19 era (2018 and 2019) and the COVID-19 period (2020 and 2021). Data collected from patients clinically diagnosed with Influenza-like Illness and Severe Acute Respiratory Illness (SARI) from January 2018 to December 2021 for influenza virus detection were acquired and analyzed through multiplex RT-qPCR. The statistical analysis was conducted using SPSS (Statistical Package for Social Sciences) Version 21.0 Software. A total of 4464 samples were tested over 4 years (2018-2021), with 3201 samples from the pre-COVID era and 1263 samples from the COVID era. Influenza A positivity dropped from 17.7 to 9.57% and Influenza B positivity decreased from 3.74 to 2.61%. Subtyping revealed changes in prevalence for both viruses. Seasonal variations showed more pronounced peaks in the pre-COVID-19 era with reduced activity during lockdown. Influenza A saw a resurgence in August 2021. Throughout the COVID-19 pandemic (2020-2021) SARI cases did not decrease. The positivity rate for Influenza A slightly rose to 7.79% from 4.23% in the COVID period (2020-2021). This increase correlates with heightened hospitalization rates during the pandemic, sparking concerns of potential coinfection with coronavirus and Influenza A. The notable drop in influenza cases in 2020-2021 is likely due to stringent precautions, lockdowns, drug repurposing, and prioritized testing, indicating no reduction in influenza transmission. Increased influenza positivity in SARI patients during COVID-19 highlights a heightened risk of coinfection. Emphasizing solely on COVID-19 may lead to underreporting of other respiratory pathogens, including influenza viruses.

BACKGROUND: Data from the sentinel surveillance system of severe acute respiratory infections in Spain were used to estimate the impact of administration of nirsevimab to children born from 1 April 2023 onwards.
METHODS: Estimated RSV hospitalisations in < 1-year-olds during weeks 40, 2023, to 8, 2024, were compared to the number that would be expected after accounting for the background change in RSV circulation in the 2023/24 season, compared to 2022/23.
RESULTS: We estimated 9364-9875 RSV hospitalisations less than expected, corresponding to a 74%-75% reduction.

Metagenomic next-generation sequencing (mNGS) is a valuable technique for identifying pathogens. However, conventional mNGS requires the separate processing of DNA and RNA genomes, which can be resource- and time-intensive. To mitigate these impediments, we propose a novel method called DNA/RNA cosequencing that aims to enhance the efficiency of pathogen detection. DNA/RNA cosequencing uses reverse transcription of total nucleic acids extracted from samples by using random primers, without removing DNA, and then employs mNGS. We applied this method to 85 cases of severe acute respiratory infections (SARI). Influenza virus was identified in 13 cases (H1N1: seven cases, H3N2: three cases, unclassified influenza type: three cases) and was not detected in the remaining 72 samples. Bacteria were present in all samples. Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii were detected in four influenza-positive samples, suggesting coinfections. The sensitivity and specificity for detecting influenza A virus were 73.33% and 95.92%, respectively. A κ value of 0.726 indicated a high level of concordance between the results of DNA/RNA cosequencing and SARI influenza virus monitoring. DNA/RNA cosequencing enhanced the efficiency of pathogen detection, providing a novel capability to strengthen surveillance and thereby prevent and control infectious disease outbreaks.