Harnessing three-dimensional (3D) cell culture models for pulmonary infections: State of the art and future directions.

Pulmonary infections have been a leading etiology of morbidity and mortality worldwide. Upper and lower respiratory tract infections have multifactorial causes, which include bacterial, viral, and rarely, fungal infections. Moreover, the recent emergence of SARS-CoV-2 has created havoc and imposes a huge healthcare burden. Drug and vaccine development against these pulmonary pathogens like respiratory syncytial virus, SARS-CoV-2, Mycobacteria, etc., requires a systematic set of tools for research and investigation. Currently, in vitro 2D cell culture models are widely used to emulate the in vivo physiologic environment. Although this approach holds a reasonable promise over pre-clinical animal models, it lacks the much-needed correlation to the in vivo tissue architecture, cellular organization, cell-to-cell interactions, downstream processes, and the biomechanical milieu. In view of these inadequacies, 3D cell culture models have recently acquired interest. Mammalian embryonic and induced pluripotent stem cells may display their remarkable self-organizing abilities in 3D culture, and the resulting organoids replicate important structural and functional characteristics of organs such the kidney, lung, gut, brain, and retina. 3D models range from scaffold-free systems to scaffold-based and hybrid models as well. Upsurge in organs-on-chip models for pulmonary conditions has anticipated encouraging results. Complexity and dexterity of developing 3D culture models and the lack of standardized working procedures are a few of the setbacks, which are expected to be overcome in the coming times. Herein, we have elaborated the significance and types of 3D cell culture models for scrutinizing pulmonary infections, along with the in vitro techniques, their applications, and additional systems under investigation.

A rapid and highly sensitive multiple detection of human adenovirus type 3, type 7 and respiratory syncytial virus by recombinase-aided reverse transcription PCR.

BACKGROUND: Polymerase chain reaction (PCR) has been widely used for many pathogen detection. However, PCR technology still suffers from long detection time and insufficient sensitivity. Recombinase-aided amplification (RAA) is a powerful nucleic acid detection tool with high sensitivity and amplification efficiency, but its complex probes and inability of multiplex detection hinder the further application of this technology. METHODS: In this study, we developed and validated the multiplex reverse transcription recombinase-aided PCR (multiplex RT-RAP) assay for human adenovirus 3 (HADV3), human adenovirus 7 (HADV7), and human respiratory syncytial virus (HRSV) within 1 h with Human RNaseP protein as a reference gene to monitor the whole process. RESULTS: Using recombinant plasmids, the sensitivity of multiplex RT-RAP for the detection of HADV3, HADV7, and HRSV was 18, 3, and 18 copies per reaction, respectively. The multiplex RT-RAP showed no cross-reactivity with other respiratory viruses, demonstrating its good specificity. A total of 252 clinical specimens were tested by multiplex RT-RAP and the results were found to be consistent with those of corresponding RT-qPCR assays. After testing serial dilutions of selected positive specimens, the detection sensitivity of multiplex RT-RAP was two to eightfold higher than that of corresponding RT-qPCR. CONCLUSION: We conclude the multiplex RT-RAP is a robust, rapid, highly sensitive, and specific assay with the potential to be used in the screening of clinical samples with low viral load.

In Vitro Potential Virucidal Effect Evaluation of Xibornol on Human Adenovirus Type 5, Human Rhinovirus Type 13, Human Coronavirus 229E, Human Parainfluenza Virus Type 1, and Human Respiratory Syncytial Virus.

The availability of virucidal compounds to reduce the impact of respiratory viruses is a relevant topic for public health, especially during the recent coronavirus disease (COVID-19) pandemic. Antimicrobial properties of Xibornol are known since the 1970s, but its activity on viruses is currently little explored. In this study, Xibornol activity at a fixed concentration of 0.03 mg/100 ml has been evaluated on five respiratory viruses (Human Adenovirus 5, Human Rhinovirus type 13, Human Coronavirus 229E, Human Parainfluenza Virus type 1, and Human Respiratory Syncytial Virus) through in vitro experiments based on adapted European standard UNI EN 14476-20019. The experiments were carried out under two different environmental conditions, one with the addition of fetal bovine serum to simulate an in vivo condition (dirty condition) and the other without the addition of any organic substances (clean condition). The viral abatement of Xibornol (expressed as Log10 reduction - LR) was statistically significant under both clean and dirty environmental conditions. Namely, in clean condition, LR ranged from 2.67 to 3.84, while in the dirty one the abatement was slightly lower (from 1.75 to 3.03). Parainfluenza Virus and Human Adenovirus were most resistant compared to the other viruses. The obtained data confirmed Xibornol activity and its use as topic substance for viral inactivation to prevent upper respiratory tract disease.

Diversity of respiratory viruses present in nasal swabs under influenza suspicion in respiratory disease cases of weaned pigs.

Respiratory diseases in weaned pigs are a common problem, with a complex etiology involving both viruses and bacteria. In the present study, we investigated the presence of eleven viruses in nasal swabs, collected from nurseries (55 cases) under the suspicion of swine influenza A virus (swIAV) and submitted by swine veterinarians for diagnosis. The other ten viruses included in the study were influenza B (IBV) and D (IDV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine respiratory coronavirus (PRCV), Porcine cytomegalovirus (PCMV), Porcine circovirus 2 (PCV2), 3 (PCV3) and 4 (PCV), Porcine parainfluenza 1 (PPIV1) and Swine orthopneumovirus (SOV). Twenty-six swIAV-positive cases and twenty-nine cases of swIAV-negative respiratory disease were primarily established. While IBV, IDV, PCV4 and PPIV1 were not found in any of the cases, PRCV, SOV, and PCMV were more likely to be found in swIAV-positive nurseries with respiratory disease (p < 0.05). Overall, PCV3, PRRSV, and PCMV were the most frequently detected agents at herd level. Taken individually, virus prevalence was: swIAV, 48.6%; PRCV, 48.0%; PRRSV, 31.6%; SOV, 33.8%; PCMV, 48.3%, PCV2, 36.0%; and PCV3, 33.0%. Moreover, low Ct values (<30) were common for all agents, except PCV2 and PCV3. When the correlation between pathogens was individually examined, the presence of PRRSV was negatively correlated with swIAV and PRCV, while was positively associated to PCMV (p < 0.05). Also, PRCV and SOV were positively correlated between them and negatively with PCMV. Besides, the analysis of suckling pig samples, collected in subclinically infected farrowing units under an influenza monitoring program, showed that circulation of PRCV, PCMV, SOV, and PCV3 started during the early weeks of life. Interestingly, in those subclinically infected units, none of the pathogens was found to be correlated to any other. Overall, our data may contribute to a better understanding of the complex etiology and epidemiology of respiratory diseases in weaners. This is the first report of SOV in Spain and shows, for the first time, the dynamics of this pathogen in swine farms.

Risk factors for infection with influenza A(H3N2) virus on a US university campus, October-November 2021.

BACKGROUND: Knowledge of the specific dynamics of influenza introduction and spread in university settings is limited. METHODS: Persons with acute respiratory illness symptoms received influenza testing by molecular assay during October 6-November 23, 2022. Viral sequencing and phylogenetic analysis were conducted on nasal swab samples from case-patients. Case-control analysis of a voluntary survey of persons tested was used to identify factors associated with influenza; logistic regression was conducted to calculate odds ratios and 95% CIs. A subset of case-patients tested during the first month of the outbreak was interviewed to identify sources of introduction and early spread. RESULTS: Among 3268 persons tested, 788 (24.1%) tested positive for influenza; 744 (22.8%) were included in the survey analysis. All 380 sequenced specimens were influenza A (H3N2) virus clade 3C.2a1b.2a.2, suggesting rapid transmission. Influenza (OR [95% CI]) was associated with indoor congregate dining (1.43 [1.002-2.03]), attending large gatherings indoors (1.83 [1.26-2.66]) or outdoors (2.33 [1.64-3.31]), and varied by residence type (apartment with ≥1 roommate: 2.93 [1.21-7.11], residence hall room alone: 4.18 [1.31-13.31], or with roommate: 6.09 [2.46-15.06], or fraternity/sorority house: 15.13 [4.30-53.21], all compared with single-dwelling apartment). Odds of influenza were lower among persons who left campus for ≥1 day during the week before their influenza test (0.49 [0.32-0.75]). Almost all early cases reported attending large events. CONCLUSIONS: Congregate living and activity settings on university campuses can lead to rapid spread of influenza following introduction. Isolating following a positive influenza test or administering antiviral medications to exposed persons may help mitigate outbreaks.

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia.

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic.  Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described  to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.

Comparison between Nasopharyngeal and Saliva Samples for the Detection of Respiratory Viruses in Children with Acute Lower Respiratory Tract Infections: A Pilot Study.

PURPOSE: During the COVID-19 pandemic, the use of salivary swabs (SS) to detect the SARS-CoV-2 virus has been implemented and widely studied in adults and children. However, the role of SS in detecting other common respiratory viruses in children is poorly investigated. METHODS: Children younger than 18 years of age admitted with respiratory signs and symptoms underwent both nasopharyngeal and SS procedures. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of SS were calculated, considering the nasopharyngeal swab result as the gold standard. RESULTS: A total of 83 patients (44 females, 53%) underwent both nasopharyngeal and SS procedures. Overall, the sensitivity of SS was 49.4%. Sensitivity according to different respiratory viruses ranged from 0% to 71.43%, while the specificity ranged from 96% to 100%. Negative predictive value ranged from 68.06% to 98.8%, while positive predictive value ranged from 0 to 100%. SS sensitivity in patients younger than 12 months of age was 39.47%, while in patients older than or equal to 12 months of age it was 57.78%. Patients with negative SS had a significantly lower median age (8.5 months (15.25) vs. 23 months (34), p = 0.001) and a significantly lower quantity of median saliva collected for salivary analysis (0 µL (213) vs. 300 µL (100), p < 0.001). CONCLUSIONS: SS has a relatively low sensitivity in detecting common respiratory viruses in children with LRTI, with a lower probability in younger children (and in particular those younger than 6 months of age) or those from whom we have collected lesser amounts of saliva. New strategies to improve saliva collection are needed for testing on a larger study population.

Surveillance of Viral Respiratory Infections in the Neonatal Intensive Care Unit-Evolution in the Last 5 Years.

Viral respiratory infections (VRIs) in very low birthweight infants can be associated with high rates of morbidity. The COVID-19 pandemic has exerted a strong impact on viral circulation. The purpose of this study is to report on VRIs during NICU admission in infants below 32 weeks' gestation and compare data collected between the pre-and post-COVID-19 pandemic periods. A prospective surveillance study was conducted at a tertiary NICU between April 2016 and June 2022. The COVID-19 post-pandemic period was established as being from March 2020 onwards. Respiratory virus detection was performed by real-time multiplex PCR assays in nasopharyngeal aspirates (NPAs). A total of 366 infants were enrolled. There were no statistical differences between periods regarding infants' birth weight, gestational age, gender distribution, or rates of bronchopulmonary dysplasia. Among the 1589 NPA collected during the pre-COVID-19 period, 8.9% were positive, and among the 1147 NPA collected during the post-pandemic period, only 3% were positive (p < 0.005). The type of viruses detected did not differ according to the study period (pre-COVID19 vs. post-COVID-19): rhinovirus (49.5% vs. 37.5%), adenovirus (22.6% vs. 25%), and human coronavirus (12.9% vs. 16.7%). SARS-CoV-2 was only detected in one patient. In conclusion, the viral profile causing VRI during the pre-COVID-19 and post-COVID-19 era was similar. However, the total number of VRI dropped significantly, most probably due to the global increase in infection prevention measures.

Linear spot Raman detector for the bi-channel immunochromatographic assay to simultaneously detect respiratory viruses

The rapid and accurate measurement of Raman signals on the test line (T-line) of surface-enhanced Raman scattering immunochromatography assay (SERS-ICA) strip is necessary for on-site detection based on SERS. Here, a novel linear spot Raman detector which can directly collect the SERS signals of the whole T-line on the dual-diagnostic SERS-ICA strip is developed for detection of multiple respiratory viruses via two magnetic SERS tags within 26min. The tags modified with two Raman reporter molecules can specifically recognize two viruses, thus enabling the simultaneous detection of both viruses on one T-line. Measured by the linear Raman detector, the limits of detection of the proposed dual-diagnostic SERS-ICA strip is as low as 870 and 263 copies/mL for severe acute respiratory syndrome coronavirus 2 and H1N1, respectively. The dual-diagnostic strip combined with the novel Raman detector herein are of great importance in the differential diagnosis of respiratory pathogens and show potential in the rapid and accurate diagnosis and control of emerging acute respiratory diseases.

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Result(s): Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion(s): Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.Copyright: © 2023 Jarju S et al.

Healthcare-associated Respiratory Syncytial Virus in Children's Hospitals.

BACKGROUND: Outbreaks of healthcare-associated respiratory syncytial virus (HA-RSV) infections in children are well described, but less is known about sporadic HA-RSV infections. We assessed the epidemiology and clinical outcomes associated with sporadic HA-RSV infections. METHODS: We retrospectively identified hospitalized children <18 years old with HA-RSV infections in six children's hospitals in the United States during the respiratory viral seasons October-April in 2016-2017, 2017-2018, and 2018-2019 and prospectively from October 2020 through November 2021. We evaluated outcomes temporally associated with HA-RSV infections including escalation of respiratory support, transfer to the pediatric intensive care unit (PICU), and in-hospital mortality. We assessed demographic characteristics and comorbid conditions associated with escalation of respiratory support. RESULTS: We identified 122 children (median age 16.0 months [IQR 6, 60 months]) with HA-RSV. The median onset of HA-RSV infections was hospital day 14 (IQR 7, 34 days). Overall, 78 (63.9%) children had two or more comorbid conditions; cardiovascular, gastrointestinal, neurologic/neuromuscular, respiratory, and premature/ neonatal comorbidities were most common. Fifty-five (45.1%) children required escalation of respiratory support and 18 (14.8%) were transferred to the PICU. Five (4.1%) died during hospitalization. In the multivariable analysis, respiratory comorbidities (aOR: 3.36 [CI95 1.41, 8.01]) were associated with increased odds of escalation of respiratory support. CONCLUSIONS: HA-RSV infections cause preventable morbidity and increase healthcare resource utilization. Further study of effective mitigation strategies for HA-respiratory viral infections should be prioritized; this priority is further supported by the impact of the COVID-19 pandemic on seasonal viral infections.

Simultaneous detection of SARS-CoV-2, influenza A, respiratory syncytial virus, and measles in wastewater by multiplex RT-qPCR.

A multiplex quantitative reverse transcription polymerase chain reaction (RT-qPCR)-based method was designed for the simultaneous detection of influenza A, SARS-CoV-2, respiratory syncytial virus, and measles virus. The performance of the multiplex assay was compared to four monoplex assays for relative quantification using standard quantification curves. Results showed that the multiplex assay had comparable linearity and analytical sensitivity to the monoplex assays, and the quantification parameters of both assays demonstrated minimal differences. Viral reporting recommendations for the multiplex method were estimated based on the corresponding limit of quantification (LOQ) and the limit of detection at 95 % confidence interval (LOD) values for each viral target. The LOQ was determined by the lowest nominal RNA concentrations where %CV values were ≤35 %. Corresponding LOD values for each viral target were between 15 and 25 gene copies per reaction (GC/rxn), and LOQ values were within 10 to 15 GC/rxn. The detection performance of a new multiplex assay was validated in the field by collecting composite wastewater samples from a local treatment facility and passive samples from three sewer shed locations. Results indicated that the assay could accurately estimate viral loads from various sample types, with samples collected from passive samplers showing a greater range of detectable viral concentrations than composite wastewater samples. This suggests that the sensitivity of the multiplex method may be improved when paired with more sensitive sampling methods. Laboratory and field results demonstrate the robustness and sensitivity of the multiplex assay and its applicability to detect the relative abundance of four viral targets among wastewater samples. Conventional monoplex RT-qPCR assays are suitable for diagnosing viral infections. However, multiplex analysis using wastewater provides a fast and cost-effective way to monitor viral diseases in a population or environment.

Mucosal vaccines for SARS-CoV-2: triumph of hope over experience.

Currently approved COVID-19 vaccines administered parenterally induce robust systemic humoral and cellular responses. While highly effective against severe disease, there is reduced effectiveness of these vaccines in preventing breakthrough infection and/or onward transmission, likely due to poor immunity elicited at the respiratory mucosa. As such, there has been considerable interest in developing novel mucosal vaccines that engenders more localised immune responses to provide better protection and recall responses at the site of virus entry, in contrast to traditional vaccine approaches that focus on systemic immunity. In this review, we explore the adaptive components of mucosal immunity, evaluate epidemiological studies to dissect if mucosal immunity conferred by parenteral vaccination or respiratory infection drives differential efficacy against virus acquisition or transmission, discuss mucosal vaccines undergoing clinical trials and assess key challenges and prospects for mucosal vaccine development.

Viral infections in critical care: a narrative review.

Viral infections form a substantial part of the intensive care workload, even before the recent and ongoing COVID-19 pandemic. The growing availability of molecular diagnostics for viral infections has led to increased recognition of these pathogens. This additional information, however, provides new challenges for interpretation and management. As the SARS-CoV-2 pandemic has amply demonstrated, the emergence and global spread of novel viruses are likely to provide continued challenges for critical care physicians into the future. This article will provide an overview of viral infections relevant to the critical care physician, discussing the diagnosis and management of respiratory viral infections, blood borne and enteric viruses. We will also discuss herpesviridae complications, commonly seen due to reactivation of latent infections. Further, we explore some rarer and emerging viruses, including recognition of viral haemorrhagic fevers, and briefly discuss post-viral syndromes which may present to the intensive care unit. Finally, we will discuss infection control and its importance in preventing nosocomial viral transmission.

Respiratory viral infections during Hajj seasons.

Respiratory viral infections pose a public health concern during mass gathering (MG) events. Sustainable and continuous surveillance of respiratory viruses remains a priority to early identify and prevent potential outbreaks. This article reviews recent literature addressed the prevalence and diversity of circulating respiratory viruses during Hajj pilgrimage, one of the largest planned religious MG events held annually in Saudi Arabia. The variation between studies with respect to study design, sample size, time of sample collection (pre-, during, and pos-Hajj), type of participants (e.g., symptomatic vs. a symptomatic pilgrims), and laboratory procedure was highlighted. The majority of these studies were conducted on the 2019 Hajj season or earlier, prior to the emergence of COVID-19 which had significant impact on the past three Hajj seasons (2020, 2021, and 2022). A summary about key aspects related to organization of Hajj during COVID-19 pandemic and the implementation of exceptional infection control strategies is provided.

In-Depth Analysis of the Re-Emergence of Respiratory Syncytial Virus at a Tertiary Care Hospital in Germany in the Summer of 2021 after the Alleviation of Non-Pharmaceutical Interventions Due to the SARS-CoV-2 Pandemic.

Following the extensive non-pharmaceutical interventions (NPIs) and behavioral changes in the wake of the SARS-CoV-2 pandemic, an interseasonal rise in respiratory syncytial virus (RSV) cases was observed in Germany in 2021. The aim of this study was to characterize the local molecular epidemiology of RSV infections in comparison to the three pre-pandemic seasons. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of RSV infections. RSV detections peaked in calendar week 40 of 2021, 18 weeks earlier than the usual peak observed in the three pre-pandemic seasons. Sequence analysis revealed a close phylogenetic relatedness regardless of the season of origin. A significantly higher amount of pediatric cases (88.9% of all cases, p < 0.001) was observed for season 2021/2022. For the pediatric cases, significant differences were observed for an increased number of siblings in the household (p = 0.004), a lower rate of fever (p = 0.007), and a reduced amount of co-infections (p = 0.001). Although the mean age of the adult patients was significantly younger (47.1 vs. 64.7, p < 0.001), high rates of comorbidities, lower respiratory tract infections and intensive care unit admissions prevailed. The NPIs in the wake of the SARS-CoV-2 pandemic had a tremendous impact on the epidemiologic characteristics and seasonality of RSV and warrant further epidemiologic studies of this important pathogen.

Effect of non-pharmaceutical interventions on the incidence of respiratory viruses at a tertiary cancer care center.

BACKGROUND: In March 2020, nonpharmaceutical interventions (NPIs) including face coverings and social distancing were adopted to curb the spread of SARS-CoV-2. Over the course of the pandemic, adherence to these NPIs has varied and eventually became optional in most non healthcare settings. We investigated the impact of relaxation of NPI on the incidence of respiratory viruses other than SARS-CoV-2 at a tertiary cancer care hospital. METHODS: This was a retrospective cohort study of respiratory viral panel results performed at between 08/01/2014-07/31/2022. Only one viral target result per patient per year was included. Poisson regression models were used to compare 2019-2020, 2020-2021, and 2021-2022 incidence of respiratory viruses to those of 2014-2019. Interrupted time series analysis was performed using autoregressive integrated moving average models in order to compare expected and observed positivity rates. RESULTS: A large reduction in the odds of testing positive for a respiratory virus was observed for most respiratory viruses when comparing results from 2019 to 2020 group to the corresponding period in 2014-2019. Subsequent seasons showed ongoing reductions in the odds of testing positive while slowly increasing over time back toward pre-pandemic levels. A time interrupted series analysis showed that the monthly positivity rate for all respiratory pathogens were reduced after 03/01/2020, when compared to the expected values forecast, except for adenovirus. CONCLUSIONS: This study provides valuable data that could be used to guide public health practices and support the efficacy of NPIs in curtailing the spread of novel and endemic respiratory viruses.

Nosocomial COVID-19 at a comprehensive cancer center during the first year of the pandemic: Lessons learned.

BACKGROUND: The spread of coronavirus disease 2019 (COVID-19) in health care settings endangers patients with cancer. As knowledge of the transmission of COVID-19 emerged, strategies for preventing nosocomial COVID-19 were updated. We describe our early experience with nosocomial respiratory viral infections (RVIs) at a cancer center in the first year of the pandemic (March 2020-March 2021). METHODS: Nosocomial RVIs were identified through our infection control prospective surveillance program, which conducted epidemiologic investigations of all microbiologically documented RVIs. Data was presented as frequencies and percentages or medians and ranges. RESULTS: A total of 35 of 3944 (0.9%) documented RVIs were determined to have been nosocomial acquired. Majority of RVIs were due to SARS CoV-2 (13/35; 37%) or by rhinovirus/enterovirus (12/35; 34%). A cluster investigation of the first 3 patients with nosocomial COVID-19 determined that transmission most likely occurred from employees to patients. Five patients (38%) required mechanical ventilation and 4 (31%) died during the same hospital encounter. CONCLUSIONS: Our investigation of the cluster led to enhancement of our infection control measures. The implications of COVID-19 vaccination on infection control policies is still unclear and further studies are needed to delineate its impact on the transmission of COVID-19 in a hospital setting.

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Method(s): Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Result(s): Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion(s): Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.Copyright © 2022 Jarju S et al.

Diagnostic des pneumonies aiguës communautaires aux urgences et distinction entre étiologie virale ou bactérienne

La pandémie actuelle liée à l'émergence du SARSCoV-2 en 2019 a considérablement modifié la perception des médecins de l'impact des virus respiratoires et de leur rôle dans les pneumonies aiguës communautaires (PAC). Alors que plus de 25 % des tableaux de PAC chez l'adulte étaient d'origine virale, les virus respiratoires étaient souvent perçus comme des agents pathogènes peu graves. Devant le défi que représente encore à nos jours la documentation microbiologique d'une PAC, l'instauration d'un traitement empirique par antibiotiques est souvent réalisée aux urgences. La pandémie de COVID-19 a surtout mis en exergue le rôle déterminant de la biologie moléculaire et du scanner thoracique dans l'algorithme diagnostique de la PAC. En effet, un diagnostic rapide et fiable est la clé pour améliorer les mesures de précaution et réduire la prescription inutile d'antibiotiques. Du fait de prises en charges très différentes, il est nécessaire de distinguer l'étiologie virale de la bactérienne d'une PAC.Alternate : The current pandemic linked to the emergence of SARS-CoV-2 in 2019 has considerably changed the perception of doctors of the impact of respiratory viruses and their role in community-acquired acute pneumonia (CAP). While more than 25% of CAP in adults were of viral origin, respiratory viruses were often perceived as harmless pathogens. Faced with the challenge that the microbiological documentation of a CAP still represents today, the establishment of empirical antibiotic treatment is often carried out in the emergency room. The COVID-19 pandemic has primarily highlighted the decisive role of molecular biology and chest CT in the diagnostic algorithm of CAP. Indeed, a rapid and reliable diagnosis is the key to improve isolation decisions and reducing the unnecessary prescription of antibiotics. Due to significantly different treatments, it is necessary to distinguish the viral etiology from the bacterial of a CAP.