Search Results (577)

Background: Human metapneumovirus (HMPV) is a major pathogen responsible for causing severe acute respiratory infections (SARI). Whole-genome sequencing can better identify transmission events and outbreaks. In this study, we aimed to investigate the epidemiology and genetic diversity of HMPV in SARI cases in Ningxia, China. Methods: We collected respiratory tract samples from hospitalized patients with SARI from October 2023 to September 2024 in Ningxia, China. Nasopharyngeal swabs were tested for respiratory viruses with qRT-PCR. Whole-genome sequences were determined for samples with high viral loads using an amplicon-based method. Results: We enrolled 2873 SARI patients from October 2023 to September 2024, and found an HMPV-positive proportion of 3.06% (88/2873). Children aged 4 years were particularly susceptible to HMPV infection, with a positive proportion of 10.92% (13/119). HMPV exhibits distinct seasonal characteristics, consistent with its established epidemiological pattern, with a peak incidence occurring during winter months. Sixteen complete HMPV genome sequences were obtained. Among these, 81.25% (13/16) were identified as genotype A (A2.2.2: 92.31%, 12/13; A2.2.1: 7.69%, 1/13) and 18.75% (3/16) as genotype B1. Notably, the dominant strain was 111nt-dup in genotype A2.2.2. Sequence analysis of HMPV genes revealed divergent G-gene sequence identities between different genotypes. Additionally, the potential glycosylation sites of the G protein varied across genotypes. Conclusions: In this study, we found that the 111nt-dup strain was the dominant one in genotype A, and multiple genotypes co-circulated in Ningxia from October 2023 to September 2024. The HMPV G protein exhibited the highest level of inter-strain diversity between genotypes. These findings provide valuable insights into the prevention and control of HMPV infections in China. Full article

The repeated occurrence of SARS-CoV-2 variants, largely driven by virus–host interactions, was and will remain a public health concern. Spike protein mutations shaped viral infectivity, transmissibility, and immune escape. From February 2022 to April 2024, a local genomic surveillance program in Verona, Italy, was conducted on 1333 SARS-CoV-2-positive nasopharyngeal swabs via next generation full-length genome sequencing. Spike protein mutations were classified based on their prevalence over time. Mutations were grouped into five categories: fixed, emerging, fading, transient, and divergent. Notably, some divergent mutations displayed a “Lazarus effect,” disappearing and later reappearing in new lineages, indicating potential adaptive advantages in specific genomic contexts. This two-year surveillance study highlights the dynamic nature of spike protein mutations and their role in SARS-CoV-2 evolution. The findings underscore the need for ongoing mutation-focused genomic monitoring to detect early signals of variant emergence, especially among mutations previously considered disadvantageous. Such efforts are critical for driving public health responses and guiding future vaccine and therapeutic strategies. Full article

Background/Objectives: Due to the significant overlap in symptoms between COVID-19 and other respiratory infections, a multiplex PCR-based platform was developed to simultaneously detect 22 respiratory pathogens. Target sequences were retrieved from the GenBank database and aligned using Clustal Omega 2.1 to identify conserved regions prioritized for primer design. Primers were designed using Primer Express^® 3.0.1 and evaluated in Primer Explorer to ensure specificity and minimize secondary structures. A multiplex strategy organized primers into three groups, each labeled with distinct fluorophores (FAM, VIC, or NED), allowing for detection by conventional PCR or capillary electrophoresis (CE). Methods: After reverse transcription for RNA targets, amplification was performed in a single-tube reaction. A total of 340 clinical samples—nasopharyngeal and saliva swabs—were collected from patients, during the COVID-19 pandemic period. The automated analysis of electropherograms enabled precise pathogen identification. Results: Of the samples analyzed, 57.1% tested negative for all pathogens. SARS-CoV-2 was the most frequently detected pathogen (29%), followed by enterovirus (6.5%). Positive results were detected in both nasopharyngeal and saliva swabs, with SARS-CoV-2 predominating in saliva samples. Conclusions: This single-tube multiplex PCR-CE assay represents a cost-effective and robust approach for comprehensive respiratory pathogen detection. It enables rapid and simultaneous diagnosis, facilitating targeted treatment strategies and improved patient outcomes. Full article

Since late 2023, an increase in Bordetella pertussis infections has been noticed in Europe, particularly among children. Our data showed the upward trend of B. pertussis cases in the Lazio region, even among adults with severe influenza-like illnesses, highlighting the necessity for maintaining high vaccination rates across both children and adults. These findings underscore the urgent need for clinicians to maintain a high index of suspicion for B. pertussis in patients with respiratory symptoms, prioritize nasopharyngeal swabs for accurate diagnosis, assess for co-infections, verify booster vaccination status in adults, and support timely reporting to public health authorities. Full article

Background: Human metapneumovirus (hMPV) is a respiratory pathogen that causes illness ranging from mild upper respiratory tract infections to severe pneumonia, particularly in individuals with comorbidities. Fatal cases of hMPV-induced hemorrhagic pneumonia are rare and likely under-reported. Diagnosis is often delayed due to overlapping symptoms with other respiratory viruses and the rapid progression of the disease. Case presentation: We report the case of a 55-year-old man with a complex medical history, including liver cirrhosis and diabetes mellitus, who developed acute viral pneumonia. Initial symptoms appeared three days before a sudden clinical deterioration marked by shortness of breath, hemoptysis, and respiratory failure. A nasopharyngeal swab taken on the third day of illness tested positive for hMPV by qRT-PCR. The patient died the following day. Postmortem molecular testing confirmed hMPV in lung tissue and alveolar contents. Autopsy revealed bilateral hemorrhagic pneumonia with regional lymphadenopathy. Histopathological examination showed alveolar hemorrhage, multinucleated cells, neutrophilic infiltration, activated autophagy in macrophages, and numerous cytoplasmic eosinophilic viral inclusions. Conclusions: This is the first documented case of fatal hMPV pneumonia in Armenia. It highlights the potential severity of hMPV in adults with chronic health conditions and emphasizes the need for timely molecular diagnostics. Postmortem identification of characteristic viral inclusions may serve as a cost-effective histopathological marker of hMPV-associated lung pathology. Full article

Human respiratory syncytial virus (HRSV) is a highly contagious RNA virus that causes respiratory infections, especially in children. This study evaluated the impact of COVID-19 control measure changes on HRSV infection patterns in Hangzhou by comparing epidemiological and clinical characteristics. We conducted a retrospective analysis of 12,993 pediatric nasopharyngeal swab samples from children with acute respiratory infections at The Children’s Hospital of Zhejiang University School of Medicine. These samples, collected between February 2022 and January 2024, were screened for HRSV and 12 other respiratory pathogens using capillary electrophoresis technology. From February 2022 to January 2023, the HRSV positivity rate was 7.06%. In 2023, it increased to 9.26%. The highest positivity rates were in infants aged 0–6 months and children aged 6 months to 1 year. Coinfections were most common with rhinovirus in 2022 and Mycoplasma pneumoniae in 2023. HRSV positivity rates were low from April to September 2022, peaking in December. In 2023, the peak occurred from April to September. Symptoms ranged from mild to severe pneumonia, with higher hospitalization rates in children with underlying conditions. The study revealed significant changes in HRSV infection rates following pandemic restriction relaxations, emphasizing the need for the early identification and prevention of severe cases. Full article

Post-COVID-19 syndrome (PCS) is a common outcome of severe COVID-19 infection; however, less is known about PCS following mild COVID-19. Healthcare workers (HCWs) are more susceptible to acquiring COVID-19 and potentially suffering physical and psychological morbidity secondary to their role. We surveyed HCWs at four hospitals in northeast England at two timepoints during the pandemic, assessing physical and psychophysiological symptoms of PCS, alongside associated factors, whilst also testing for COVID-19 status by SARS-CoV-2 serology and reviewing evidence of infection from previous PCR nasopharyngeal swabs. Of the 379 participants at baseline and 250 HCWs recruited 18 months later, 46% and 64% (respectively) had evidence of previous COVID-19, with no significant associations between COVID-19 status or demographics and symptom scores or self-described PCS. Depression and fatigue were more common later in the pandemic. Furthermore, 20% self-described having PCS, 34% of whom had no evidence of previous COVID-19. Scores for fatigue, pain, mobility, anxiety, and depression were significantly worse in the PCS group compared to those without ongoing symptoms. Significant proportions of HCWs continued to suffer debilitating symptoms during the later pandemic period, although a significant minority had no evidence of previous COVID-19 infection, suggesting that other factors may be involved in their symptomatology. Full article

Introduction: An effective vaccination strategy requires monitoring serotype changes by geography and age. This study analyzed Streptococcus pneumoniae serotypes in healthy children under 6 years of age vaccinated with PCV10 in Bulgaria from October 2021 to May 2025. Methods: A total of 569 children were screened for the lytA and cpsA genes viareal-time polymerase chain reaction (real-time PCR). Positive samples were typed using relevant kits, and 76 serotypes/serogroups of S. pneumoniae were identified. Results: Nasopharyngeal swabs from 232 children (40.8%) were found to carry S. pneumoniae, and a total of 255 serotypes were detected, with 19B/19C (17.2%), 6C (10.7%), and 15B/15C (9.8%) being the most prevalent. Of these, 91 serotypes (15.9%) were included in at least one vaccine, while the remaining 164 serotypes (25.4%) were not. The carriage rate reduced to 22% in 2023 but increased to 47% in 2024. Overall, younger children had lower carriage rates (p < 0.05), with serotype 6C being more common in children under 12 months of age (25%). Approximately 9.1% of pneumococcal carriage cases involved co-detected serotypes, with significantly higher co-detection rates for 19B/19C, 15B/15C, 10B, 10F/C, 23B, 7C/40, 23A, and 24A compared with mono-detection rates (p < 0.05). Conclusions: 19B/19C, 6C, 15B/15C, and 19A were identified as the main serotypes. Children over 3 years of age were also more likely to carry multiple pneumococci. These findings emphasize the need to reassess childhood vaccination strategies to curb the spread of antibiotic-resistant serotypes. Full article

Background/Objectives: Genetic variants in cytokine genes such as IL1B, IL6, and TNF may influence inflammatory responses to SARS-CoV-2 and affect disease severity. This study investigates the role of these variants in relation to COVID-19 outcomes, including hospitalization, ICU admission, and mortality. Methods: A total of 500 unvaccinated individuals from southern Brazil diagnosed with COVID-19 via RT-PCR were analyzed. DNA was extracted from nasopharyngeal swabs and genotyped for functional variants selected based on evidence of regulatory function and prior associations with inflammatory outcomes—IL1B (rs4848306, rs1143623, rs16944, rs1143627), IL6 (rs1800795, rs2069832, rs2069840, rs2069845), and TNF (rs1799964, rs1800630, rs1799724, rs1800629, rs361525). Multivariate logistic regression analysis, adjusted for sex and age, was employed to assess the association between these genetic variants and severe clinical outcomes. Results: The results indicated that the IL1B rs16944-AG (OR: 1.98 [95% CI: 1.22–3.23], p = 0.006) and TNF rs1799964-CT (OR: 1.97 [95% CI: 1.22–3.22], p = 0.006) genotypes were associated with the need for hospitalization, while TNF rs1800630-AA (OR: 2.37 [95% CI: 1.08–5.33], p = 0.034) was associated with ICU admission. Additionally, the CC genotype of TNF rs1799964 was associated with a higher risk of mortality (OR: 3.73 [95% CI: 1.21–14.37], p = 0.034). Conclusions: Genetic variants—specifically IL1B rs16944 and rs1143627, and TNF rs1799964 and rs1800630—were associated with COVID-19 severity and should be further investigated in larger studies to evaluate their potential as predictive markers of severe outcomes in COVID-19. Full article

(1) Background: A safe and effective nucleic acid sample transportation method was developed that is suitable for underdeveloped areas which lack advanced sequencing capabilities, specifically for virus genomic sequencing and infectious disease monitoring. (2) Methods: This study evaluated the use of Flinders Technology Associates (FTA) cards for transporting amplified whole-genome DNA from 120 SARS-CoV-2-positive nasopharyngeal swab samples in Sierra Leone. Nucleic acid extraction and whole-genome amplification were conducted at a local laboratory. Amplified products were applied to FTA Elute cards for room temperature shipment to China CDC for elution and sequencing. (3) Results: The FTA card method achieved a 9.6% recovery rate for amplicons, sufficient for viral genome sequencing. In total, 86 (71.7%) high-quality SRAS-CoV-2 genomic sequences were obtained, with the majority reaching depths exceeding 100X. Sequence analysis revealed co-circulation of Delta, Omicron, and B.1 lineages. Higher Ct values in the original sample significantly reduced coverage and depth, with Ct ≤ 27; 73.6% of samples yielded effective sequences. (4) Conclusions: Transportation of amplified nucleic acid samples using FTA cards enables virus genomic sequencing in resource-limited areas. This approach can potentially improve local virus surveillance and outbreak response capabilities. Further optimizations could improve sequence recovery rate. Implementing this method could significantly enhance sequencing accessibility in underdeveloped regions. Full article

Background/Objectives: The COVID-19 pandemic, caused by SARS-CoV-2, required the rapid development of diagnostic tests. SARS-CoV-2, part of the betacoronavirus genus, shares characteristics with SARS-CoV-1, including its ability to survive on surfaces, facilitating the spread of the infection. This study analyzes the technique of nasopharyngeal secretion collection for SARS-CoV-2 diagnosis and compares the accuracy of rapid antigen and molecular tests. Methods: This study had two components: study A assessed the healthcare personnel training in collecting nasopharyngeal secretions and the discomfort associated with applying a questionnaire. Study B compared rapid antigen test accuracy with RT-PCR among children, through a retrospective analysis. The data were statistically analyzed to assess compliance with the testing protocols. Results: In study A, 88 healthcare workers achieved an average compliance score of 7.60 out of 10 regarding the collection procedure. Over 70% of participants correctly followed the fundamental steps of the procedure. Many patients who underwent sample collection reported pain and symptoms such as coughing or sneezing. In study B, 198 pediatric patients were tested using rapid antigen tests, collected simultaneously with RT-PCR. The rapid tests showed a 50% sensitivity and 97.5% specificity. Conclusions: This study indicates that nasopharyngeal specimen collection techniques are based on international recommendations, but improvements could be made to reduce discomfort. Rapid antigen tests are helpful for screening due to their high specificity and negative predictive value. Continuous healthcare personnel training and the monitoring of diagnostic techniques remain essential in managing SARS-CoV-2 and other viral infections. Full article

Parainfluenza virus (PIV) infections contribute to the overall childhood morbidity from acute respiratory illness, yet virus-specific epidemiologic data are lacking across many regions globally. Here, we describe the clinical manifestations, seasonality, and meteorologic associations with PIV infections in Ecuadorian children. Between July 2018 and July 2023, we documented demographic and clinical information from children younger than 5 years seen in a single public health clinic with signs and symptoms consistent with an acute respiratory infection. Nasopharyngeal swabs collected at study enrollment underwent multiplex polymerase chain reaction-based diagnostic testing (Biofire FilmArray v. 1.7™). Regional meteorological data from the same period were provided by Ecuador’s Instituto Nacional de Meteorologia e Hidrologia. Parainfluenza viruses were detected in 9% of the 1251 enrolled subjects. PIVs were most frequently detected between March and July, with no change in seasonality following SARS-CoV-2 pandemic onset. Clinical manifestations of PIV infections included non-specific upper respiratory illness (82%), laryngotracheitis (3%), and bronchiolitis (11%). Events of PIV detection were negatively associated with ambient temperature and rainfall. Our findings highlight the contribution that PIVs play in the morbidity associated with pediatric medically attended outpatient respiratory tract infection and provide new insights into the seasonal epidemiology of PIV infections in coastal Ecuador. Full article

Background: adenoviruses (AdVs) are DNA viruses that typically cause mild infections in immunocompetent children, and typically involve the respiratory and gastrointestinal tract. Adenoviral pharyngitis is a common paediatric illness, particularly in children under 4 years old. The aim of our 7-year retrospective study, conducted at a tertiary care paediatric emergency department (ED), was to describe the clinical and laboratory characteristics and management of patients with pharyngeal AdV infections. Specifically, we examined how the management of patients with adenoviral pharyngitis has evolved following the introduction of a rapid antigen nasopharyngeal swab test for AdVs, which has been performed directly in the ED since 2023. Methods: in this single-centre retrospective observational study, the demographic and clinical information for children discharged from the ED who had been diagnosed with a pharyngeal AdV infection between 1 January 2017 and 31 December 2023 were retrospectively reviewed. Moreover, we compared data before and after the introduction of rapid AdV antigenic swabs, which have been directly performed in the ED since the beginning of 2023. Statistical analysis was undertaken using the Student’s t-test and Pearson and Fisher’s exact test, as appropriate. Significance was set at p-value < 0.05. Results: during the study period, 172 children were diagnosed with adenoviral pharyngitis based on a positive swab. All patients were febrile, with a median duration of fever of 4 days. Blood tests were requested for 84.9% of patients at admission, resulting in a mean WBC count of 13,250/mmc and a mean CRP of 70.6 mg/L. The highest CRP median values were found on the third day of fever. Out of 383 swabs performed during 2017–2022, 13.6% were positive vs a 32% positive rate for the 372 swabs performed in 2023. The mean duration of observation in the ED before 2023 was 31.4 h vs. 10.4 h in 2023. Similarly, 9% of patients with adenoviral pharyngitis were admitted to a paediatric ward before 2023 and only 0.8% in 2023. Conclusions: the primary reason for ED admission in cases of adenoviral pharyngitis is fever lasting several days due to hyperinflammation. Differential diagnosis with bacterial infection is essential to limit the number of hospitalisations and inappropriate antibiotic therapy. The introduction of the rapid antigen nasopharyngeal swab has simplified the diagnosis of adenoviral pharyngitis, enabling timely and accurate differentiation from bacterial causes. Full article

Background. Despite the high transmissibility of SARS-CoV-2, some individuals remain uninfected despite prolonged exposure to a high viral load, suggesting the involvement of an innate resistance mechanism, possibly underpinned by the host’s genetic factors. The angiotensin-converting enzyme-1 (ACE1), ACE2, and C-C Chemokine Receptor 5 (CCR5) polymorphisms have been shown to influence susceptibility to the infection. In this study, the role of ACE1, ACE2, and CCR5 gene polymorphisms in modulating susceptibility to SARS-CoV-2 infection within the context of intimate contact was evaluated. Methods. A cohort of heterosexual couples from Northern Sardinia, characterized by a homogenous genetic background, was recruited during the initial pandemic wave (March–June 2020). In each couple, one partner (index case) tested positive for SARS-CoV-2 by at least two consecutive independent molecular tests (real-time polymerase chain reaction: RT-PCR) on nasopharyngeal swabs. Bed-sharing partners of SARS-CoV-2 positive index cases, resistant and susceptible to the infection, were genotyped for ACE1 287 bp Alu repeat insertion/deletion (I/D) polymorphism, ACE2 G8790A (rs2285666) variant, and a 32-base pair deletion (Δ32) of CCR5. Resistant and susceptible partners to the infection were compared for polymorphisms. Results. Out of 63 couples, 30 partners acquired SARS-CoV-2 infection, while 33 remained uninfected despite intimate exposure. Clinical history was minimal for current or past illnesses. SARS-CoV-2-infected index spouses and partners who acquired the infection developed a mild disease, not requiring hospitalization. The observed distribution of ACE1 I/D and ACE2 G8790A genotypes was consistent with previously reported frequencies in Sardinia and across European populations. None of the study participants carried the CCR5-Δ32 variant. No statistically significant differences (p > 0.05) in the allelic or genotypic frequencies of these polymorphisms were observed between the infected and resistant partners. Conclusions. No differences in the distribution of ACE1, ACE2, and CCR5 polymorphisms between the two groups were detected. These findings suggest that resistance is likely multifactorial, involving a complex interplay of genetic, immunological, and environmental factors. Full article

The COVID-19 pandemic has had a profound impact on healthcare systems worldwide, with severe consequences on the global economy and society. The clinical presentation of SARS-CoV-2 infection varies widely, ranging from asymptomatic cases to severe disease and death. Coinfection with other respiratory pathogens in SARS-CoV-2-positive individuals may exacerbate symptom severity and lead to poorer clinical outcomes. Background/Objectives: This study is the first to investigate the prevalence of viral and bacterial co-infections in SARS-CoV-2-positive individuals in Cyprus. Methods: A total of 1111 SARS-CoV-2-positive nasopharyngeal swab samples collected from non-hospitalized patients were analyzed for the presence of 18 viral and 3 bacterial respiratory pathogens. Results: Of these, 51 samples (4.6%) were found to have at least one additional respiratory pathogen. The most frequently detected viruses were rhinovirus/enterovirus (n = 28; 2.5%) and adenovirus (n = 8; 0.7%), while the bacterial pathogens identified were Legionella pneumophila (n = 1; 0.1%) and Bordetella pertussis (n = 1; 0.1%). The highest proportion of co-infections was observed in the youngest age group (<10 years), where 52.9% of co-infections were identified, followed by the 30–39 age group, which accounted for 15.7% of cases. Among single respiratory virus co-infections, rhinovirus/enterovirus (27.5%) and adenovirus (13.7%) were the most frequently detected in the <10 age group, followed by RSV (3.9%), bocavirus, influenza B, HMPV A + B, and coronavirus NL63 (each at 2%). Conclusions: The current study underscores the importance of simultaneous testing for SARS-CoV-2 and other respiratory pathogens, as this may have significant implications for both individual patient care and healthcare services. Full article