Search Results (67)

Endemic human coronaviruses (HCoVs) are important contributors to respiratory infections, yet genomic data from sub-Saharan Africa remain limited. We analyzed 13,530 nasopharyngeal samples collected through the national influenza sentinel surveillance network in Côte d’Ivoire between 2022 and 2024 to characterize the circulation and genomic diversity of endemic HCoVs. A subset of 52 RT-qPCR-positive samples with Ct values ≤ 28 was selected for targeted hybrid-capture sequencing using the Twist Bioscience Respiratory Virus Research Panel. Genome recovery metrics were available for 28 samples, including HCoV-NL63 (n = 9), HCoV-229E (n = 8), HCoV-OC43 (n = 9), and HCoV-HKU1 (n = 2). Endemic HCoVs circulated throughout the study period, with temporal variation across species and increased detections during several rainy-season months. No co-presence of multiple endemic HCoV species was identified in the final analytical dataset. Genome recovery differed by species, with broader and more consistent coverage for HCoV-OC43 and HCoV-NL63 than for HCoV-229E and HCoV-HKU1. Phylogenetic analysis showed that all recovered HCoV-229E genomes clustered within genotype L6 and all recovered HCoV-HKU1 genomes within genotype A, whereas HCoV-OC43 and HCoV-NL63 were distributed across multiple genotypes among recovered genomes. To our knowledge, these findings provide the first genomic data on endemic HCoVs from Côte d’Ivoire and support the feasibility and further targeted integration of targeted hybrid-capture sequencing into routine genomic surveillance of respiratory viruses. Full article

In Cambodia, farmers construct artificial household bat roosts to collect and sell guano as fertilizer. We investigated farming practices and attendant spillover risks using (1) surveys on guano production; (2) an estimation of bat population size and species present using carcasses, visual identification, and audio recordings; (3) surveys of guano-producing and neighboring households on water, sanitation, and hygiene practices; and (4) the testing of guano and household food, water, and surfaces for coronaviruses using RT-qPCR. Bat roosts are constructed using dried palm leaves with coconut tree and/or steel/concrete supports. Roosting areas ranged from 42 to 327 m², bat abundance varied from 0 to 11,187, guano production was between 5 and 120 kg/week, guano yields were from 0.15 to 0.4 kg/m²/week, and farmers earned USD ~100–200/household/month. Higher guano production in the peak (normally wet) season was associated with greater bat abundance (p = 0.016). The lesser Asiatic yellow house bat (Scotophilus kuhlii) was the only bat species identified. Roosts were <20 m from guano-producing households. Neighbors and households’ hygiene risks included not having handwashing stations and not covering food in storage/while drying. Coronaviruses (Alphacoronaviruses or Infectious Bronchitis Virus) were detected in 14.6%, 17.3%, 2.9%, 1.4%, and 0.0% of guano, urine, household surface, food, and water samples, respectively. While guano farming offers economic benefits, spillover risks exist. Safe guano collection and storage, handwashing, and food covering in guano-producing communities are necessary to mitigate spillover risks. Full article

Seasonal human coronaviruses (HCoVs) continue to undergo adaptive evolution under structural and immune-mediated constraints. We investigated the molecular epidemiology and spike (S) protein structural variation of circulating coronaviruses in Riyadh, Saudi Arabia, during the 2025–2026 winter season, with particular emphasis on genotype persistence and glycosylation architecture in HCoV-OC43. Among 293 nasopharyngeal aspirates (NPAs) collected from hospitalized patients with acute respiratory illness, HCoV-OC43 was detected in 26 cases (8.87%), whereas other seasonal coronaviruses were not identified. Partial sequencing of the S gene revealed 97.84–98.23% nucleotide identity relative to the prototype strain VR-759, with amino acid substitutions distributed at discrete positions rather than within extended variable domains, indicating structural conservation. Phylogenetic reconstruction demonstrated that all Riyadh isolates clustered within genotype C, together with previously circulating local strains, supporting sustained endemic persistence and in situ evolution. In silico analysis of the S protein glycosylation landscape identified four invariant N-linked glycosylation motifs (N-X-S/T) at residues 46, 121, 134, and 190, reflecting strong structural constraints on glycan-dependent folding and antigenic configuration. A genotype-associated K68N substitution generated an additional N-glycosylation motif (68NGTD) in multiple Riyadh isolates, potentially modifying local glycan shielding without disrupting the overall glycosylation framework. The preservation of core glycosylation sites alongside selective motif acquisition suggests evolutionary fine-tuning of S surface topology rather than large-scale structural remodeling. Collectively, these findings indicate that genotype C persistence in Riyadh is accompanied by conserved S architecture and subtle glycosylation adjustments that may modulate immune recognition while maintaining structural integrity. Continued high-resolution molecular surveillance will be critical for defining the functional consequences of S microevolution in endemic HCoVs. Full article

The coronavirus disease 19 pandemic disrupted pediatric respiratory infections through non-pharmaceutical interventions and altered contact patterns. Long-term comparisons across the pandemic timeline in children remain limited. In this study, we analyzed 15,657 respiratory specimens from patients ≤ 18 years at Dankook University Hospital (2007–2023) using multiplex polymerase chain reaction assays targeting 15 viruses. Age-stratified positivity rates were compared across pandemic phases. Children ≤ 6 years comprised 88.61% of the study population. Human rhinovirus showed the highest detection rate (24.06%), followed by adenovirus (12.33%), respiratory syncytial virus-subtypes A and B (RSV-A: 11.13%; RSV-B: 8.65%), human parainfluenza virus-type 3 (HPIV-3; 6.21%), human metapneumovirus (HMPV; 5.33%), and enterovirus (2018–2023; EV; 10.96%). Monthly distributions differed (p < 0.001). RSV peaked in late autumn and winter; influenza and seasonal coronaviruses in winter and spring; HMPV, HPIV-3, EV, and human bocavirus in summer and fall. Positivity declined during the pandemic, rebounding in 2023, most prominently among children aged 1–6 years (84.91%). HPIV-3 and EV increased (p < 0.001). RSV-A predominated pre-pandemic, whereas RSV-B showed a non-significant relative increase post-pandemic; no subtype differences occurred during the pandemic. Findings demonstrate pathogen-specific shifts in predominance and seasonality and support ongoing surveillance and pediatric care planning. Full article

Respiratory infections represent one of the leading causes of pediatric consultations and hospitalizations in Chile, where rapid etiological identification is essential for clinical decision-making. We evaluated the impact of implementing the BIOFIRE^® SPOTFIRE^® Respiratory (R) Panel in the pediatric Emergency Department of a public referral hospital in Santiago, using a pre–post cross-sectional design comparing two winter periods (July 2023 vs. July 2024). Clinical records, laboratory data, and operational indicators were analyzed to assess changes in diagnostic yield, turnaround time, hospitalizations, discharges, supplementary test requests, and antimicrobial use. A total of 470 patients were included (224 in 2023; 246 in 2024). The etiological detection rate increased from 58.0% to 87.8% after the implementation of Spotfire^® (p < 0.0001), with marked increases in the identification of adenovirus, RSV, rhinovirus/enterovirus, and seasonal coronaviruses. Rapid molecular testing was associated with a significant rise in emergency department discharges (23.7% vs. 57.3%; p < 0.0001) and a reduction in hospitalizations (76.3% vs. 42.7%; p < 0.0001) and readmissions (9.2% vs. 0.5%; p < 0.0001). Requests for complete blood counts, chest X-rays, and antimicrobial prescriptions at discharge also decreased significantly. These effects persisted in key subgroups, including infants and children with comorbidities. In this high-demand winter setting, the BIOFIRE^® SPOTFIRE^® R Panel improved diagnostic performance and supported more efficient and targeted clinical management. Full article

Background: Viral respiratory tract infections (RTIs) frequently lead to emergency department (ED) presentations and hospital admissions, particularly among older adults and individuals with underlying health conditions. Identifying patients at increased risk for hospitalization is essential for optimizing triage and resource allocation. This study aimed to determine independent demographic, clinical, and virological predictors of hospital admission among adults presenting with confirmed viral RTIs. Methods: A retrospective cohort study was conducted at a tertiary hospital between September 2022 and May 2024. Adult patients with molecularly confirmed viral RTIs were included. Demographic, clinical, and microbiological data were extracted from electronic medical records. Predictors of admission were assessed using univariate and multivariate logistic regression. Results: Among 311 patients, 147 (47.3%) required hospitalization. Hospitalized patients were significantly older and more likely to present with fever, cough, tachypnea, dyspnea, chest pain, comorbidities, and lower or mixed respiratory tract infections (all p < 0.001). In multivariate analysis, older age, fever, cough, and lower or mixed RTIs were strong independent predictors of admission. Several viral pathogens, including human rhinovirus, non–SARS-CoV-2 coronaviruses, influenza A, and parainfluenza virus, were associated with reduced odds of hospitalization. Conclusions: Age, comorbidity burden, and lower respiratory tract involvement are key determinants of hospitalization in viral RTIs. Integrating clinical and virological data may improve risk stratification and guide ED triage during seasonal and emerging respiratory virus activity. Full article

Seasonal human coronaviruses (HCoVs), including HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1, circulate globally in an epidemic pattern and account for a substantial proportion of common cold cases, particularly in infants, the elderly, and immunocompromised individuals. Although clinical manifestations are typically mild, these HCoVs exhibit ongoing antigenic drift and have demonstrated the potential to cause severe diseases in certain populations, underscoring the importance of developing targeted and broad-spectrum vaccines. This review systematically examines the pathogenesis, epidemiology, genomic architecture, and major antigenic determinants of seasonal HCoVs, highlighting key differences in receptor usage and the roles of structural proteins in modulating viral tropism and host immunity. We summarize recent advances across various vaccine platforms, including inactivated, DNA, mRNA, subunit, viral-vectored, and virus-like particle (VLP) approaches, in the development of seasonal HCoV vaccines. We specifically summarize preclinical and clinical findings demonstrating variable cross-reactivity between SARS-CoV-2 and seasonal HCoV vaccines. Evidence indicates that cross-reactive humoral and cellular immune responses following SARS-CoV-2 infection or vaccination predominantly target conserved epitopes of structural proteins, supporting strategies that incorporate conserved regions to achieve broad-spectrum protection. Finally, we discuss current challenges in pathogenesis research and vaccine development for seasonal HCoVs. We propose future directions for the development of innovative pan-coronavirus vaccines that integrate both humoral and cellular antigens, aiming to protect vulnerable populations and mitigate future zoonotic spillover threats. Full article

We investigated respiratory virus epidemiology in older adults across pre-pandemic (2007–2019), pandemic (2020–2022), and post-pandemic (2023–2024) periods, focusing on how public health interventions shaped surveillance, prevalence, and sex-specific trends. We conducted a retrospective cross-sectional study at a 1000-bed tertiary hospital in the Republic of Korea during 2007–2024, analyzing 4692 nasopharyngeal swab specimens collected from adults aged ≥ 65 years with suspected respiratory infections during 2007–2024. The specimens were tested for 15 respiratory viruses using multiplex real-time polymerase chain reaction. The outcomes included virus-specific detection rates and seasonal, sex-based and temporal trends before and after the COVID-19 pandemic. During the pre-pandemic period, older adults accounted for 13.2% of the tested individuals, which significantly increased to 52.0% in the later periods. Influenza A was the most frequently detected virus, followed by rhinovirus and human metapneumovirus. Influenza, RSV A/B, and coronaviruses 229E and OC43 showed peak positivity in winter, parainfluenza virus type 3 peaked in summer, and rhinovirus circulated year-round. Virus circulation was markedly suppressed during 2020–2022 and partially rebounded during 2023–2024. This study highlights the shift in diagnostic access and epidemiologic patterns of respiratory virus infections in older adults following the COVID-19 pandemic. Full article

This study evaluated the epidemiology and seasonal patterns of respiratory viruses in adults hospitalized with acute respiratory tract infections during two consecutive post-COVID-19 pandemic seasons. A retrospective study was conducted at the University Hospital “P. Giaccone”, Palermo, from September 2022 to September 2024. Multiplex molecular assays were used to detect the ten respiratory viruses most relevant from an epidemiological perspective in respiratory samples (n = 1110) of 1081 patients. A respiratory viral infection was identified in 29.6% of patients. The highest viral infection rate was observed in the 31–50 age group. Human rhinovirus/enterovirus (HRV/EV) was the most frequently detected (40%), followed by influenza A virus (IAV; 18.4%) and human coronaviruses (HuCoVs; 12.8%). Viral co-infections were identified in 10.9% of positive cases, with HRV/EV, adenovirus (ADV), and parainfluenza virus (PIV) being most frequently involved. Influenza and respiratory syncytial viruses (RSVs) showed a winter seasonality, while diverse circulation patterns were revealed for the other viruses. This study demonstrated a sustained circulation of respiratory viruses in adults hospitalized with severe respiratory symptoms, with HRV/EV accounting for most of them. Syndromic multiplex molecular testing, although limited to the detection of a small fraction of epidemiologically relevant known viruses, has proven to be a valuable tool, not only for diagnostic purposes but also for acquiring genotyping data and implementing epidemiological information from sentinel surveillance systems. Full article

Since the emergence of SARS-CoV-2, the interplay of human behavior, environmental factors, viral evolution, and public health interventions has resulted in unexpected changes in the timing, intensity, and geography of respiratory virus outbreaks. For example, respiratory syncytial viruses (RSV) exhibited a surge during atypical summer months in several countries. Influenza, on the other hand, nearly vanished in the early years of the pandemic, but returned with unusual strength and altered seasonal patterns. Concurrently, new variants of concern in coronaviruses have demonstrated increased airborne transmissibility, greater resilience to environmental conditions, and the ability to evade both natural and vaccine-induced immunity. In this review article, we have synthesized the current understanding of the aerobiology of respiratory infectious viruses, with a particular emphasis on the paradoxical trends observed in recent years. We examined various aspects, including viral morphology and environmental survivability, shifts in seasonality, the drivers of mutation and resistance, and the impact of environmental and climatic factors. Key issues we explored include viral morphology adaptation in response to airborne selective pressures and climate variability influence on the ecology of airborne viruses. Lastly, we investigated future risks and proposed an interdisciplinary framework for monitoring and mitigating airborne viral threats in an ever-changing world. Full article

Background/Objectives: mRNA vaccines have demonstrated strong immunogenicity and efficacy against SARS-CoV-2. However, the extent of antibody cross-reactivity against human seasonal coronaviruses, such as NL63, remains unclear. Furthermore, it is unknown whether pre-existing antibody responses against NL63 might influence the outcome of SARS-CoV-2 mRNA vaccination. Methods: We used a flow cytometry-based serological assay and an in vitro neutralization assay to analyze NL63 antibody responses in sera from SARS-CoV-2 mRNA-vaccinated mice and plasma samples from a vaccinated human cohort. Results: We found that the Moderna mRNA-1273 vaccine can generate cross-reactive antibodies against NL63. Importantly, SARS-CoV-2 mRNA vaccination did not boost pre-existing anti-NL63 responses in humans, and pre-existing NL63 antibody levels did not affect the antibody response induced by SARS-CoV-2 mRNA vaccination. Conclusions: These findings suggest that while SARS-CoV-2 mRNA vaccination can induce cross-reactive antibodies against NL63, pre-existing immunity to this seasonal coronavirus does not appear to significantly impact vaccine immunogenicity. These findings contribute to our understanding of the complex interplay between pre-existing immunity to seasonal coronaviruses and the immune response generated by SARS-CoV-2 mRNA vaccines. Full article

Background: Vaccines against COVID-19 target the spike protein. There is minimal information on longitudinal COVID-19 immune profiling in recovered versus naïve and vaccinated versus non-vaccinated healthcare workers (HCWs). Methods: This is a prospective longitudinal observational cohort of pediatric HCWs (pHCWs) conducted during 2020–2022 at an academic center, exploring the impact of COVID-19 vaccination on immunoglobulin G (IgG) antibody titers over time and cross-reactivity with other coronaviruses, including SARS-CoV-1, MERS-CoV, and seasonal coronaviruses (HCoV-HKU1 and HCoV-OC43). Results: A total of 642 pHCWs initially enrolled, and 337 participants had repeat IgG titers measured post-vaccine and post-booster. Most participants were female, median age range of 31–40 years. Anti-spike was higher in all vaccinated individuals versus non-vaccinated (p < 0.0001) and naïve versus infected (p < 0.0001). A single dose of vaccine was sufficient to attain maximum titers in recovered participants versus naïve who received both doses of vaccine. Anti-spike titers dropped significantly at 9 months after the primary series, whereas sustained anti-spike titers were observed at 9 months post-booster. Conclusions: All vaccinated pHCWs developed antibodies to spike. COVID-19 infection and/or vaccination yielded antibodies that cross-reacted to SARS-CoV-1, MERS-CoV, HCoV-HKU1, and HCoV-OC43. Anti-spike titers were more durable post-booster compared to the primary series. Longitudinal immune profiling of COVID-19 responses provides vital data to shape public health policies, optimize vaccine strategies, and strengthen pandemic preparedness. Full article

Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900–1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses. Full article

Acute respiratory infection is one of the leading causes of morbidity and mortality among children in low- and middle-income countries. Due to limited diagnostic capability, many respiratory pathogens causing influenza-like illness go undetected. This study aims to detect enterovirus, respiratory syncytial virus, seasonal coronavirus and respiratory pathogens other than influenza in patients with influenza-like illness. A total of 997 (54.3%) respiratory samples (collected in the years 2016–2018) were randomly selected from 1835 influenza-negative samples. The xTAG Respiratory Viral Panel (RVP) FAST v2 panel was used to detect respiratory pathogens including enterovirus/rhinovirus (EV/RV), respiratory syncytial virus (RSV) and seasonal coronavirus (HKU1, OC43, NL63 and 229E). A total of 78.7% (785/997) were positive for respiratory viruses. Of these viruses, EV/RV was detected in 36.3% (362/997), which is the highest number, followed by RSV in 13.7% (137/997). The seasonal coronaviruses HKU1 and OC43 (1.5%, 15/997), NL63 (1.2%, 12/997) and 229E (1%, 10/997) were also detected. The EV/RV-positive samples were sequenced, of which 16.7% (5/30) were confirmed as EVs and were identified as coxsackievirus (CV) types CVB5, CVB3, CV21 and CVB2. The findings of this study highlight the importance of strengthening influenza-like illness surveillance programs in the region by including other respiratory viruses in their scope besides seasonal human influenza viruses. Full article

Emerging viral diseases, including seasonal illnesses and pandemics, pose significant global public health risks. Respiratory viruses, particularly coronaviruses and influenza viruses, are associated with high morbidity and mortality, imposing substantial socioeconomic burdens. This review focuses on the current landscape of respiratory viruses, particularly influenza and SARS-CoV-2, and their antiviral treatments. It also discusses the potential for pandemics and the development of new antiviral vaccines and therapies, drawing lessons from past outbreaks to inform future strategies for managing viral threats. Full article