SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses.
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ABSTRACT:
SUBMITTER: Swets MC
PROVIDER: S-EPMC8956294 | biostudies-literature | 2022 Apr
REPOSITORIES: biostudies-literature
Publications
SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses.
Swets Maaike C MC Russell Clark D CD Harrison Ewen M EM Docherty Annemarie B AB Lone Nazir N Girvan Michelle M Hardwick Hayley E HE Visser Leonardus G LG Openshaw Peter J M PJM Groeneveld Geert H GH Semple Malcolm G MG Baillie J Kenneth JK
Lancet (London, England) 20220325 10334
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Project description:BackgroundA mismatch between a widespread use of broad-spectrum antibiotic agents and a low prevalence of reported bacterial co-infections in patients with SARS-CoV-2 infections has been observed. Herein, we sought to characterize and compare bacterial co-infections at admission in hospitalized patients with SARS-CoV-2, influenza or respiratory syncytial virus (RSV) positive community-acquired pneumonia (CAP).MethodsA retrospective cohort study of bacterial co-infections at admission in SARS-CoV-2, influenza or RSV-positive adult patients with CAP admitted to Karolinska University Hospital in Stockholm, Sweden, from year 2011 to 2020. The prevalence of bacterial co-infections was investigated and compared between the three virus groups. In each virus group, length of stay, ICU-admission and 30-day mortality was compared in patients with and without bacterial co-infection, adjusting for age, sex and co-morbidities. In the SARS-CoV-2 group, risk factors for bacterial co-infection, were assessed using logistic regression models and creation of two scoring systems based on disease severity, age, co-morbidities and inflammatory markers with assessment of concordance statistics.ResultsCompared to influenza and RSV, the bacterial co-infection testing frequency in SARS-CoV-2 was lower for all included test modalities. Four percent [46/1243 (95% CI 3-5)] of all SARS-CoV-2 patients had a bacterial co-infection at admission, whereas the proportion was 27% [209/775 (95% CI 24-30)] and 29% [69/242 (95% CI 23-35)] in influenza and RSV, respectively. S. pneumoniae and S. aureus constituted the most common bacterial findings for all three virus groups. Comparing SARS-CoV-2 positive patients with and without bacterial co-infection at admission, a relevant association could not be demonstrated nor excluded with regards to risk of ICU-admission (aHR 1.53, 95% CI 0.87-2.69) or 30-day mortality (aHR 1.28, 95% CI 0.66-2.46) in adjusted analyses. Bacterial co-infection was associated with increased inflammatory markers, but the diagnostic accuracy was not substantially different in a scoring system based on disease severity, age, co-morbidities and inflammatory parameters [C statistic 0.66 (95% CI 0.59-0.74)], compared to using disease severity, age and co-morbidities only [C statistic 0.63 (95% CI 0.56-0.70)].ConclusionsThe prevalence of bacterial co-infections was significantly lower in patients with community-acquired SARS-CoV-2 positive pneumonia as compared to influenza and RSV positive pneumonia.
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Project description:SARS-CoV-2, influenza, and respiratory syncytial viruses (RSVs) cause acute respiratory infections with similar symptoms. Since the treatments and outcomes of these infections are different, the early detection and accurate differentiation of the viruses are clinically important for the prevention and treatment of the diseases. We previously demonstrated that clustered regularly interspaced short palindromic repeats (CRISPR) could rapidly and precisely detect SARS-CoV-2. The objective of this study was to develop CRISPR as a test for simultaneously detecting and accurately distinguishing the viruses. The CRISPR assay with an RNA guide against each virus was performed in the reference standards of SARS-CoV-2, influenza A and B, and RSV. The CRISPR assay had a limit of detection of 1-100 copies/µL for specifically detecting SARS-CoV-2, influenza A and B, and RSV without cross-reaction with other respiratory viruses. The validation of the test in nasopharyngeal specimens showed that it had a 90-100% sensitivity and 100% specificity for the detection of SARS-CoV-2, influenza A and B, and RSV. The CRISPR assay could potentially be used for sensitive detection and specific differentiation of the respiratory viruses.
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Project description:This retrospective study analysed the routine data obtained by multiplex real-time RT-qPCR methods for respiratory virus detection. A total of 4814 respiratory specimens collected during 1 September 2022-31 August 2023 were included in the study. A total of 38% of the specimens were positive for at least one target, with the incidence maximum (82%) for the small children (age group 0-4 years). The five dominant virus groups were rhinovirus (RV, 12%), influenza virus A (IAV, 7%), adenovirus (AdV, 6%), respiratory syncytial virus (RSV, 5%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, 5%). The specimens with multi-detections represented 19% of the positives, unevenly distributed (n = 225, 56, 43, 24) among the age groups 0-4, 5-14, 15-64, and 65< years, respectively. The dominant virus groups in multi-positive specimens were RV (53%), AdV (43%), and bocavirus (BoV, 35%)-in mutual pairs as well as all three together-followed by RSV (21%), and IAV (15%). Our study focused on the specimens with codetections and provides an insight into the variety of the respiratory virus interactions in Latvia during the first year since pandemic-related social restriction measures were eased. The observations also emphasise the need to consider the differentiation between rhinoviruses and enteroviruses, especially for the youngest patients in the age group 0-4.
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Project description:BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been raging since the end of 2019 and has shown worse outcomes in solid organ transplant (SOT) recipients. The clinical differences as well as outcomes between respiratory viruses have not been well defined in this population.MethodsThis is a retrospective cohort study of adult SOT recipients with nasopharyngeal swab or bronchoalveolar lavage PCR positive for either SARS-CoV-2, seasonal coronavirus, respiratory syncytial virus (RSV) or influenza virus from January 2017 to October 2020. The follow up period was 3 months. Clinical characteristics and outcomes were evaluated.ResultsA total of 377 recipients including 157 SARS-CoV-2, 70 seasonal coronavirus, 50 RSV and 100 influenza infections were identified. The most common transplanted organ was kidney 224/377 (59.4%). Lower respiratory tract infection (LRTI) was found in 210/377 (55.7%) and the risk factors identified with multivariable analysis were SARS-CoV-2 infection, steroid use, and older age. Co- and secondary infections were seen in 77/377 (20.4%) recipients with bacterial pathogens as dominant. Hospital admission was seen in 266/377 (67.7%) recipients without significant statistical difference among viruses, however, ICU admission, mechanical ventilation and mortality were higher with SARS-CoV-2 infection. In the multivariable model, the risk factors for mortality were SARS-CoV-2 infection and older age.ConclusionsWe found higher incidence of ICU admission, mechanical ventilation, and mortality among SARS-CoV-2 infected recipients. Older age was found to be the risk factor for lower respiratory tract infection and mortality for SARS-CoV-2, coronaviruses, RSV and influenza virus groups.
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Project description:BackgroundMore data is required to contextualise respiratory-syncytial-virus (RSV) disease burden, versus other vaccine-preventable respiratory-viral-infections (RVIs) in older adults. We aimed to compare severity of RSV in hospitalized adults versus influenza/boosted COVID-19.MethodsRetrospective population-based cohort study, including all adult RSV hospitalizations (2021-2023) in Singapore. Disease severity (28-day mortality/intensive-care-unit [ICU] admission) and healthcare utilization in RSV hospitalizations were compared with contemporaneous influenza hospitalizations and COVID-19 hospitalizations in 2023. Outcomes for COVID-19 were stratified by type/receipt of boosters. Comparative severity of RSV versus COVID-19/influenza was evaluated using multivariate logistic regression, adjusted for confounders. Generalized linear models were utilized to estimate excess length-of-stay/costs of RSV hospitalization versus COVID-19/influenza as a rate-ratio.Findings12,811 hospitalized adults were included (RSV: N = 1332; influenza: N = 3999; COVID-19: N = 7480). Amongst RSV hospitalizations, 5.4% (72/1332) died within 28 days; 3.8% (51/1332) required ICU. Median length-of-stay (RSV) was 5.0 days (IQR = 3.0-8.0). Older age/diabetes were associated with greater odds of 28-day mortality in RSV hospitalizations. Higher odds of 28-day mortality/ICU admission and higher healthcare utilization was observed in RSV hospitalizations versus influenza. Conversely, RSV was less severe than unboosted COVID-19, with lower odds of 28-day mortality (adjusted-odds-ratio, aOR = 0.56 [95% CI = 0.40-0.79]) and rate-ratio for length-of-stay/costs significantly <1. However, higher odds of ICU (aOR = 1.80 [95% CI = 1.07-3.00]) were observed in RSV hospitalizations, versus COVID-19 hospitalizations boosted <1 year prior with updated vaccines.InterpretationHospitalizations attributed to RSV were more severe than influenza. RSV disease was less severe versus COVID-19 in unboosted patients but severity was not significantly different from COVID-19 in boosted individuals.FundingNational Medical Research Council, Singapore.
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