Community-acquired viral respiratory infections amongst hospitalized inpatients during a COVID-19 outbreak in Singapore: co-infection and clinical outcomes

Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era

BACKGROUND

The concurrent circulation of SARS-CoV-2 with other respiratory viruses is unstoppable and represents a new diagnostic reality for clinicians and clinical microbiology laboratories. Multiplexed molecular testing on automated platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube is a useful approach for current and future diagnosis of respiratory infections in the clinical setting.

METHODS

Two time periods were included in the study: from February to April 2022, an early 2022 period, during the gradual lifting of COVID-19 prevention measures in the country, and from October 2022 to April 2023, the 2022/23 respiratory infections season. We analysed a total of 1,918 samples in the first period and 18,131 respiratory samples in the second period using a multiplex molecular assay for the simultaneous detection of Influenza A (Flu-A), Influenza B (Flu-B), Human Respiratory Syncytial Virus (HRSV) and SARS-CoV-2.

RESULTS

The results from early 2022 showed a strong dominance of SARS-CoV-2 infections with 1,267/1,918 (66.1%) cases. Flu-A was detected in 30/1,918 (1.6%) samples, HRSV in 14/1,918 (0.7%) samples, and Flu-B in 2/1,918 (0.1%) samples. Flu-A/SARS-CoV-2 co-detections were observed in 11/1,267 (0.9%) samples, and HRSV/SARS-CoV-2 co-detection in 5/1,267 (0.4%) samples. During the 2022/23 winter respiratory season, SARS-CoV-2 was detected in 1,738/18,131 (9.6%), Flu-A in 628/18,131 (3.5%), Flu-B in 106/18,131 (0.6%), and HRSV in 505/18,131 (2.8%) samples. Interestingly, co-detections were present to a similar extent as in early 2022.

CONCLUSION

The results show that the multiplex molecular approach is a valuable tool for the simultaneous laboratory diagnosis of SARS-CoV-2, Flu-A/B, and HRSV in hospitalized and outpatients. Infections with Flu-A/B, and HRSV occurred shortly after the COVID-19 control measures were lifted, so a strong reoccurrence of various respiratory infections and co-detections in the post COVID-19 period was to be expected.

Changes in seasonal respiratory viral infections among pediatric population around the COVID-19 pandemic; 2019-2023

PURPOSE

This study aims to describe the prevalence and the fluctuations of respiratory viral infections among the pediatric population in a tertiary care center during 2019-2023, parallel with the COVID-19 pandemic, and the specific preventative measures applied in the region during this time.

METHODS

In this observational study, we extracted all respiratory virus PCR tests collected from pediatric patients (< 15 years old) between January 2019 and March 2023. Data on the positivity rate and prevalence of 18 respiratory viruses were presented over the study period.

RESULTS

The lowest rate for the studied respiratory viruses was observed in 2020/2021 (during the COVID-19 pandemic), followed by a gradual increase in positive cases in the 2021/2022 season. Timing (seasonality) was altered during 2022/2023 with an early circulation of respiratory viruses in May-June followed by an early start of the usual respiratory viruses' season in September, leading to prolonged respiratory virus activity. Most respiratory viruses were circulating at unprecedented levels during the 2022/2023 season, with rhinovirus/enterovirus being the most commonly detected virus in all seasons. Other viruses that had atypical activity after the COVID-19 pandemic were influenza A(H3) virus, adenovirus, and parainfluenza 3 virus.

CONCLUSION

Our study demonstrates the extended influence of the COVID-19 pandemic and its associated community restriction measures on the timing and distribution of other respiratory viruses. Continuous monitoring of changes in the circulation of respiratory viruses is crucial for the success of related public health measures such as vaccination distributions and epidemic preparedness.

SARS-CoV-2 co-detection with influenza and human respiratory syncytial virus in Ethiopia: Findings from the severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance, January 01, 2021, to June 30, 2022

SARS-CoV-2 co-infection with the influenza virus or human respiratory syncytial virus (RSV) may complicate its progress and clinical outcomes. However, data on the co-detection of SARS-CoV-2 with other respiratory viruses are limited in Ethiopia and other parts of Africa to inform evidence-based response and decision-making. We analyzed 4,989 patients' data captured from the national severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance sites over 18 months period from January 01, 2021, to June 30, 2022. Laboratory specimens were collected from the patients and tested for viral respiratory pathogens by real-time, reverse transcription polymerase chain reaction (RT-PCR) at the national influenza center. The median age of the patients was 14 years (IQR: 1-35 years), with a slight preponderance of them being at the age of 15 to less than 50 years. SARS-CoV-2 was detected among 459 (9.2%, 95% CI: 8.4-10.0) patients, and 64 (1.3%, 95% CI: 1.0-1.6) of SARS-CoV-2 were co-detected either with Influenza virus (54.7%) or RSV (32.8%) and 12.5% were detected with both of the viruses. A substantial proportion (54.7%) of SARS-CoV-2 co-detection with other respiratory viruses was identified among patients in the age group from 15 to less than 50 years. The multivariable analysis found that the odds of SARS-CoV-2 co-detection was higher among individuals with the age category of 20 to 39 years as compared to those less than 20 years old (AOR: 1.98, 95%CI:1.15-3.42) while the odds of SARS-CoV-2 co-detection was lower among cases from other regions of the country as compared to those from Addis Ababa (AOR:0.16 95%CI:0.07-0.34). Although the SARS-CoV-2 co-detection with other respiratory viral pathogens was minimal, the findings of this study underscore that it is critical to continuously monitor the co-infections to reduce transmission and improve patient outcomes, particularly among the youth and patients with ILI.

The prevalence of 17 common respiratory viruses in patients with respiratory illness but negative for COVID-19: A cross-sectional study

Background and Aims

Second to COVID-19 pandemic, other viral respiratory infections are still important causes of human diseases or co-infections. Hence, the present study was carried out to investigate the common respiratory viruses in patients with respiratory illness diagnosed negative for severe acute respiratory syndrome coronavirus-2 in primary screening.

Methods

In a cross-sectional study, a real-time PCR was carried out using HiTeq. 17 Viro Respiratory pathogen One Step RT-PCR Kit (Genova, Bonda Faravar, Bioluence, Tehran, Iran).

Results

A total of 311 individuals (mean age ± SD: 48.2 ± 21.7 years, range: 1-97 years) underwent second PCR. Among these, 161 (51.7%) were female. In total, 55 (17.6%) cases (mean age ± SD: 45.7 ± 18.1 years) were found positive for respiratory viruses panel in the second PCR. The HCoV-OC43/HKU1 was in 5.4% (17/311), Flu A in 4.5% (14/311), HCoV-229E/NL63 in 2.8% (9/311), HMPV in 1.9% (6/311), HPiV 1, 2, 3 in 1.2% (4/311), HRSV in 0.9% (3/311), and HAdV in 0.6% (2/311) of the cases studies. Also, co-infection was detected in 4 samples (1.2%). In addition, sore throat (0.028), headache (p = 0.016), and body pain (p = 0.0001) were statistically the most significant symptoms in studied cases.

Conclusion

According to the findings of our study, respiratory virus infections and co-infections were 17.6% and 1.2% frequent, respectively. Interestingly, nearly half of our positive cases (47.2%) were identified by coronaviruses (ОС43, Е229, NL63, and HKUI), followed by influenza A virus (25.4%). However, for more comprehensive results, we recommend using greater sample size.

The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract

OBJECTIVES

The respiratory tract is the portal of entry for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a variety of respiratory pathogens other than SARS-CoV-2 have been associated with severe cases of COVID-19 disease, the dynamics of the upper respiratory microbiota during disease the course of disease, and how they impact disease manifestation, remain uncertain.

METHODS

We collected 349 longitudinal upper respiratory samples from a cohort of 65 COVID-19 patients (cohort 1), 28 samples from 28 recovered COVID-19 patients (cohort 2), and 59 samples from 59 healthy controls (cohort 3). All COVID-19 patients originated from the earliest stage of the epidemic in Wuhan. Based on a modified clinical scale, the disease course was divided into five clinical disease phases (pseudotimes): "Healthy" (pseudotime 0), "Incremental" (pseudotime 1), "Critical" (pseudotime 2), "Complicated" (pseudotime 3), "Convalescent" (pseudotime 4), and "Long-term follow-up" (pseudotime 5). Using meta-transcriptomics, we investigated the features and dynamics of transcriptionally active microbes in the upper respiratory tract (URT) over the course of COVID-19 disease, as well as its association with disease progression and clinical outcomes.

RESULTS

Our results revealed that the URT microbiome exhibits substantial heterogeneity during disease course. Two clusters of microbial communities characterized by low alpha diversity and enrichment for multiple pathogens or potential pathobionts (including Acinetobacter and Candida) were associated with disease progression and a worse clinical outcome. We also identified a series of microbial indicators that classified disease progression into more severe stages. Longitudinal analysis revealed that although the microbiome exhibited complex and changing patterns during COVID-19, a restoration of URT microbiomes from early dysbiosis toward more diverse status in later disease stages was observed in most patients. In addition, a group of potential pathobionts were strongly associated with the concentration of inflammatory indicators and mortality.

CONCLUSION

This study revealed strong links between URT microbiome dynamics and disease progression and clinical outcomes in COVID-19, implying that the treatment of severe disease should consider the full spectrum of microbial pathogens present.

Pediatric COVID-19: clinical and epidemiological data of 1303 cases in a general hospital in Brazil

OBJECTIVE

This study aimed to describe the clinical characteristics of the pediatric population with COVID-19 in an Emergency Department (ED) of a Brazilian general hospital.

METHODS

Epidemiological and clinical data of patients younger than 20 years old were collected from patients' medical records from February 2020 to July 2021. Most of the epidemiological data described pertains to hospitalized patients. We also reviewed coinfections, treatment, and outcomes and compared the first and second waves of COVID-19.

RESULTS

We identified a total of 1303 episodes of SARS-CoV-2 infection. The median time from symptom onset to diagnosis was three days. Symptoms were present in 92.3% of the patients. The most common symptoms were fever (45.2%), nasal congestion/discharge (44.2%), and cough (39.4%). Chest radiography and tomography were performed in 7.7 and 3.3% of cases, with abnormal findings in 29.7 and 53.4%, respectively. Hospital admissions occurred in 3.5% of patients, mainly in the presence of comorbidities, in children under five years old and in those who presented to the ED during the first wave of COVID-19. Coinfection with a viral agent was identified in 20% of the 71 cases tested in this study, and a positive rapid test for Streptococcus pyogenes was found in 8% of the 174 cases tested, with no impact of these coinfections on hospitalization.

CONCLUSIONS

We found that COVID-19 was a mild disease in most children in our study population, with most hospitalizations and readmissions occurring during the first wave of COVID-19.

Investigation of etiology of community-acquired pneumonia in hospitalized patients in a tertiary hospital of São Paulo City, Brazil

BACKGROUND

Community-Acquired Pneumonia (CAP) is the primary cause of hospitalization in the United States and the third leading cause of death in Brazil. The gold standard for diagnosing the etiology of CAP includes blood culture, Gram-stained sputum, and sputum culture. However, these methods have low sensitivity. No studies investigating the etiology of CAP have been conducted in Brazil in the last 20-years, and the empirical choice of antimicrobials is mainly based on the IDSA guidelines. This is the first national study with this aim, and as a result, there's potential for the Brazilian consensus to be impacted and possibly modify its guidelines rather than adhering strictly to the IDSA's recommendations.

METHODS

The aim of this study is to identify the main microorganisms implicated in CAP by employing a multiplex Polymerase Chain Reaction (mPCR) at the foremost public hospital in Brazil. All patients who were admitted to the emergency department and diagnosed with severe CAP underwent an mPCR panel using nasopharyngeal and oropharyngeal swabs, with the aim of detecting 13 bacterial and 21 viral pathogens.

RESULTS

A total of 169 patients were enrolled in the study. The mPCR panel identified an etiological agent in 61.5% of patients, with viruses being the most common (42.01%), led by Rhinovirus, followed by Influenza and Coronavirus (non-SARS-CoV-2). Bacterial agents were identified in 34.91% of patients, with S. pneumoniae being the most common, followed by H. influenzae, M. catarrhalis, and S. aureus. Additionally, we found that the prescription for 92.3% of patients could be modified, with most changes involving de-escalation of antibiotics and antiviral therapy.

CONCLUSION

Our study revealed different etiological causes of CAP than those suggested by the Brazilian guidelines. Using molecular diagnostic tests, we were able to optimize treatment by using fewer antibiotics.

Investigation of microbial coinfection in 453 septic COVID-19 patients admitted to hospital; a retrospective study

Aim

We evaluated the rate of COVID-19 microbial coinfection in an Iranian population.

Methods

In this single-center, retrospective observational study, we evaluated 453 septic COVID-19 patients for possible coinfection in an Iranian hospital.

Results

Overall, 211 (46.57%) cases died due to COVID-19 complications. Positive respiratory secretion and blood cultures were reported in 99 (21.9%) and 19 (4.2%) cases. Klebsiella species were the most commonly isolated microorganisms in respiratory (n = 50, 50.5%) and blood (n = 10, 52.6%) specimens. After adjustment for underlying disorders, positive respiratory microbial cultures significantly increase the odds of developing death, intubation, and ICU admission and negatively impact healthy discharge (P < 0.05).

Conclusion

Coinfections with bacteria and fungi independently contribute to poor outcomes in septic COVID-19 patients.

The Fallacy of a Single Diagnosis

BACKGROUND

Diagnostic reasoning requires clinicians to think through complex uncertainties. We tested the possibility of a bias toward an available single diagnosis in uncertain cases.

DESIGN

We developed 5 different surveys providing a succinct description of a hypothetical individual patient scenaric. Each scenario was formulated in 2 versions randomized to participants, with the versions differing only in whether an alternative diagnosis was present or absent. The 5 scenarios were designed as separate tests of robustness using diverse cases, including a cautious scenario, a risky scenario, a sophisticated scenario, a validation scenario, and a comparative scenario (each survey containing only 1 version of 1 scenario). Participants included community members (n = 1104) and health care professionals (n = 200) who judged the chances of COVID infection in an individual patient.

RESULTS

The first scenario described a cautious patient and found a 47% reduction in the estimated odds of COVID when a flu diagnosis was present compared with absent (odds ratio = 0.53, 95% confidence interval 0.30 to 0.94, P = 0.003). The second scenario described a less cautious patient and found a 70% reduction in the estimated odds of COVID in the presence of a flu diagnosis (odds ratio = 0.30, 95% confidence interval 0.13 to 0.70, P < 0.001). The third was a more sophisticated scenario presented to medical professionals and found a 73% reduction in the estimated odds of COVID in the presence of a mononucleosis diagnosis (odds ratio = 0.27, 95% confidence interval 0.10 to 0.75, P < 0.001). Two further scenarios-avoiding mention of population norms-replicated the results.

LIMITATIONS

Brief hypothetical scenarios may overestimate the extent of bias in more complicated medical situations.

CONCLUSIONS

These results demonstrate that an available simple diagnosis can lead individuals toward premature closure and a failure to fully consider additional severe diseases.

HIGHLIGHTS

Occum's razor has been debated for centuries yet rarely subjected to experimental testing for evidence-based medicine.This article offers direct evidence that people favor an available simple diagnosis, thereby neglecting to consider additional serious diseases.The bias can lead individuals to mistakenly lower their judged likelihood of COVID or another disease when an alternate diagnosis is present.This misconception over the laws of probability appears in judgments by community members and by health care workers.The pitfall in reasoning extends to high-risk cases and is not easily attributed to information, incentives, or random chance.

SARS-CoV-2 Related Viral Respiratory Co-Infections: A Narrative Review

Background

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the new coronavirus originating from Wuhan, China, responsible for the illness known as coronavirus disease 2019 (COVID-19). Early experience and the recent literature have shown that co-infection of SARS-CoV-2 with another respiratory virus might occur. Similar symptoms of acute respiratory infections (ARIs) and COVID-19 represent a challenge for diagnostic and therapeutic efficacy and may modify COVID-19 outcomes.

Materials and Methods

We reviewed the literature on the epidemic pattern and major learning points on important aspects of SARS-CoV-2-related viral respiratory co-infections during the COVID-19 pandemic. Databases such as PubMed, Scopus, Science Direct, and Google Scholar were used to conduct a comprehensive search.

Results

The circulation of respiratory viruses changed as the COVID-19 epidemic continues. Phenomena like viral interference, resource competition, and differences in virus-host range might explain why simultaneous viral respiratory infections have seemed to vanish with the spread of SARS-CoV-2.

Conclusion

Key research to be conducted during this pandemic should include the simultaneous screening of other respiratory pathogens with many available commercial platforms for transmission containment and appropriate clinical management.

Bacterial coinfection and antibiotic resistance in hospitalized COVID-19 patients: a systematic review and meta-analysis

Background

There were a few studies on bacterial coinfection in hospitalized COVID-19 patients worldwide. This systematic review aimed to provide the pooled prevalence of bacterial coinfection from published studies from 2020 to 2022.

Methods

Three databases were used to search the studies, and 49 studies from 2,451 identified studies involving 212,605 COVID-19 patients were included in this review.

Results

The random-effects inverse-variance model determined that the pooled prevalence of bacterial coinfection in hospitalized COVID-19 patients was 26.84% (95% CI [23.85-29.83]). The pooled prevalence of isolated bacteria for Acinetobacter baumannii was 23.25% (95% CI [19.27-27.24]), Escherichia coli was 10.51% (95% CI [8.90-12.12]), Klebsiella pneumoniae was 15.24% (95% CI [7.84-22.64]), Pseudomonas aeruginosa was 11.09% (95% CI [8.92-13.27]) and Staphylococcus aureus (11.59% (95% CI [9.71-13.46])). Meanwhile, the pooled prevalence of antibiotic-resistant bacteria for extended-spectrum beta-lactamases producing Enterobacteriaceae was 15.24% (95% CI [7.84-22.64]) followed by carbapenem-resistant Acinetobacter baumannii (14.55% (95% CI [9.59-19.52%])), carbapenem-resistant Pseudomonas aeruginosa (6.95% (95% CI [2.61-11.29])), methicillin-resistant Staphylococcus aureus (5.05% (95% CI [3.49-6.60])), carbapenem-resistant Enterobacteriaceae (4.95% (95% CI [3.10-6.79])), and vancomycin-resistant Enterococcus (1.26% (95% CI [0.46-2.05])).

Conclusion

All the prevalences were considered as low. However, effective management and prevention of the infection should be considered since these coinfections have a bad impact on the morbidity and mortality of patients.

Viral Coinfections in Hospitalized Coronavirus Disease 2019 Patients Recruited to the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK Study

Background

We conducted this study to assess the prevalence of viral coinfection in a well characterized cohort of hospitalized coronavirus disease 2019 (COVID-19) patients and to investigate the impact of coinfection on disease severity.

Methods

Multiplex real-time polymerase chain reaction testing for endemic respiratory viruses was performed on upper respiratory tract samples from 1002 patients with COVID-19, aged <1 year to 102 years old, recruited to the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK study. Comprehensive demographic, clinical, and outcome data were collected prospectively up to 28 days post discharge.

Results

A coinfecting virus was detected in 20 (2.0%) participants. Multivariable analysis revealed no significant risk factors for coinfection, although this may be due to rarity of coinfection. Likewise, ordinal logistic regression analysis did not demonstrate a significant association between coinfection and increased disease severity.

Conclusions

Viral coinfection was rare among hospitalized COVID-19 patients in the United Kingdom during the first 18 months of the pandemic. With unbiased prospective sampling, we found no evidence of an association between viral coinfection and disease severity. Public health interventions disrupted normal seasonal transmission of respiratory viruses; relaxation of these measures mean it will be important to monitor the prevalence and impact of respiratory viral coinfections going forward.

Distribution of Viral Respiratory Infections during the COVID-19 Pandemic Using the FilmArray Respiratory Panel

This study was conducted to evaluate the distribution of respiratory viral pathogens in the emergency department during the coronavirus disease 2019 (COVID-19) pandemic. Between May 2020 and September 2022, patients aged between 0.1 and 98 years arrived at the emergency department of Asia University Hospital, and samples from nasopharyngeal swabs were tested by the FilmArrayTM Respiratory Panel (RP). SARS-CoV-2 positivity was subsequently retested by the cobas Liat system. There were 804 patients for whom the FilmArrayTM RP was tested, and 225 (27.9%) of them had positive results for respiratory viruses. Rhinovirus/enterovirus was the most commonly detected pathogen, with 170 (61.8%) cases, followed by adenovirus with 38 (13.8%), SARS-CoV-2 with 16 (5.8%) cases, and coronavirus 229E, with 16 (5.8%) cases. SARS-CoV-2 PCR results were positive in 16 (5.8%) cases, and there were two coinfections of SARS-CoV-2 with adenovirus and rhinovirus/enterovirus. A total of 43 (5.3%) patients were coinfected; the most coinfection was adenovirus plus rhinovirus/enterovirus, which was detectable in 18 (41.9%) cases. No atypical pathogens were found in this study. Intriguingly, our results showed that there was prefect agreement between the detection of SARS-CoV-2 conducted with the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test and the FilmArrayTM RP. Therefore, the FilmArrayTM RP assay is a reliable and feasible method for the detection of SARS-CoV-2. In summary, FilmArrayTM RP significantly broadens our capability to detect multiple respiratory infections due to viruses and atypical bacteria. It provides a prompt evaluation of pathogens to enhance patient care and clinical selection strategies in emergency departments during the COVID-19 pandemic.

Disulfiram alleviates acute lung injury and related intestinal mucosal barrier impairment by targeting GSDMD-dependent pyroptosis

BACKGROUND

Pyroptosis was implicated in acute lung injury (ALI). Disulfiram is reported as an effective pyroptosis inhibitor by inhibiting gasdermin D(GSDMD). However, the function of pyroptosis executor GSDMD and treatment of disulfiramon on ALI, especially whether it was involved in ALI-associated intestinal mucosal barrier impairment remains unclear. This study aims to explore the role of pyroptosis and disulfiram' treatment on ALI and related intestinal mucosal barrier impairment.

METHODS

First, we established lipopolysaccharide (LPS)-induced ALI models in wild-type and Gsdmd knockout (Gsdmd^-/-), to detect the effect of pyroptosis on ALI-related intestinal mucosal barrier impairment. Furthermore, we used wild-type mice treated with disulfiram to investigate the treatment of disulfiram on ALI and related intestinal mucosal barrier impairment.

RESULTS

The data showed that GSDMD-mediated pyroptosis was activated in both lung and intestinal mucosa tissues in LPS-induced ALI, and deficiency of Gsdmd ameliorated LPS-induced ALI and related intestinal mucosal barrier damage. We also disclosed that disulfiram inhibited the pyroptosis level, and alleviated ALI and related intestinal mucosal barrier impairment induced by LPS.

CONCLUSION

These findings suggested the role of GSDMD-mediated pyroptosis and the potential application treatment of disulfiram in ALI and related intestinal mucosal barrier damage.

The Menace of Candida auris Epidemic Amidst the COVID-19 Pandemic: A Systematic Review

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the causative agent for the Coronavirus Disease 2019 (COVID-19) pandemic, has sparked a medical emergency worldwide. With the rise in COVID-19 infections and an eventual increase in hospitalized critically ill patients, a trend of bacterial, fungal, and viral superinfection has been noted. One important agent of co-infection identified is Candida auris. Due to its multidrug-resistant nature and easy transmissibility, C. auris is difficult to manage in COVID-positive patients. Patients with comorbidities, immunosuppressive states, intubated and on ventilators are more likely to contract the fungal infection. Therefore, it is essential to the first screen, diagnose, and isolate patients with C. auris infection and manage and treat them while preventing the spread of the disease. Failure to recognize and prevent its spread may lead to an eventual epidemic or even a pandemic during the current COVID-pandemic, which the exhausted healthcare system can most definitely not handle. This systematic review investigates the prevalence of C. auris, its pathophysiology, diagnosis, prevention, and treatment during the COVID-19 pandemic.

Bacterial Co-Infection in Patients with COVID-19 Hospitalized (ICU and Not ICU): Review and Meta-Analysis

The prevalence of patients hospitalized in ICUs with COVID-19 and co-infected by pathogenic bacteria is relevant in this study, considering the integrality of treatment. This systematic review assesses the prevalence of co-infection in patients admitted to ICUs with SARS-CoV-2 infection, using the PRISMA guidelines. We examined the results of the PubMed, Embase, and SciELO databases, searching for published English literature from December 2019 to December 2021. A total of 542 rec ords were identified, but only 38 were eligible and, and of these only 10 were included. The tabulated studies represented a sample group of 1394 co-infected patients. In total, 35%/138 of the patients were co-infected with Enterobacter spp., 27% (17/63) were co-infected with methicillin-sensitive Staphylococ cus aureus, 21% (84/404) were co-infected with Klebsiella spp., 16% (47/678) of patients were co-infected with coagulase-negative Staphylococcus, 13% (10/80) co-infected with Escherichia coli (ESBL), and 3% (30/1030) of patients were co-infected with Pseudomonas aeruginosa. The most common co-infections were related to blood flow; although in the urinary and respiratory tracts of patients Streptococcus pneumoniae was found in 57% (12/21) of patients, coagulase negative Staphylococcus in 44% (7/16) of patients, and Escherichia coli was found in 37% (11/29) of patients. The present research demonstrated that co-infections caused by bacteria in patients with COVID-19 are a concern.

Respiratory etiological surveillance among quarantined patients with suspected lower respiratory tract infection at a medical center in southern Taiwan during COVID-19 pandemic

Background

A comprehensive study of respiratory pathogens was conducted in an area with a low prevalence of COVID-19 among the adults quarantined at a tertiary hospital.

Methods

From March to May 2020, 201 patients suspected lower respiratory tract infection (LRTI) were surveyed for etiologies by multiplex polymerase chain reaction (PCR: FilmArray TM Respiratory Panel) test combination with cultural method, viral antigen detection and serologic surveys.

Results

Total 201 patients tested with FilmArray TM Respiratory Panel were enrolled, of which 68.2% had sputum bacterial culture, 86.1% had pneumococcus and Legionella urine antigen test. Their median age was 72.0 year-old with multiple comorbidities, and 11.4% were nursing home residents. Bacteria accounted for 59.7% of identified pathogens. Atypical pathogens were identified in 31.3% of total pathogens, of which viruses accounted for 23.9%. In comparison to patients with bacterial infection, patients with atypical pathogens were younger (median= 77.2 vs 67.1, years, P = 0.017) and had shorter length of hospital (8.0 vs 4.5, days, P = 0.007).

Conclusions

Patients with LRTI caused by atypical pathogens was indistinguishable from those with bacterial pathogens by clinical manifestations or biomarkers. Multiplex PCR providing rapid diagnosis of atypical pathogens enhance patient care and decision making when rate of sputum culture sampling was low in quarantine ward during pandemic.

Co-infection of SARS-CoV-2 with other viral respiratory pathogens in Yogyakarta, Indonesia: A cross-sectional study

Background

Growing evidence shows that viral co-infection is found repeatedly in patients with Coronavirus Disease–2019 (COVID-19). This is the first report of SARS-CoV-2 co-infection with viral respiratory pathogens in Indonesia.

Methods

Over a one month period of April to May 2020, SARS-CoV-2 positive nasopharyngeal swabs in our COVID-19 referral laboratory in Yogyakarta, Indonesia, were tested for viral respiratory pathogens by real-time, reverse transcription polymerase chain reaction (RT-PCR). Proportion of co-infection reported in percentage.

Results

Fifty-nine samples were positive for other viral respiratory pathogens among a total of 125 samples. Influenza A virus was detected in 32 samples, Influenza B in 16 samples, Human metapneumovirus in 1 sample, and adenovirus in 10 samples. We did not detect any co-infection with respiratory syncytial virus. Nine (7.2%) patients had co-infection with more than two viruses.

Conclusion

Viral co-infection with SARS-CoV-2 is common. These results will provide a helpful reference for diagnosis and clinical treatment of patients with COVID-19.

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Viral co-infection with SARS-CoV-2 is common.

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Co-infection by two viral respiratory pathogens is prevalent.

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Pandemic transmission control may also impact in other viral respiratory infections.

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Early identification of co-infection is necessary, given differences in treatment.

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Simple laboratory diagnosis algorithm may be applied to screen viral co-infection.

Viral Etiological Agent(s) of Respiratory Tract Infections in Symptomatic Individuals during the Second Wave of COVID-19 Pandemic: A Single Drive-Thru Mobile Collection Site Study

One of the tools to contain the SARS-CoV-2 pandemic was to increase the number of performed tests and to improve the access to diagnostics. To this effect, mobile collection sites (MCSs) were established. This study was performed on samples collected at the MCS between November 2020 and March 2021. We aimed to confirm/exclude SARS-CoV-2, differentiate SARS-CoV-2 variants, and detect other respiratory pathogens. SARS-CoV-2 and other respiratory viruses were identified by RT-qPCRs. A total of 876 (46.35%) SARS-CoV-2 positive specimens in the diagnostic tests were identified. The wild-type variant was determined in 667 (76.14%) samples; the remaining 209 (23.86%) samples specimens were identified as Alpha variant. A total of 51 (5.6%) non-SARS-CoV-2 cases were detected in retrospective studies. These accounted for 33 cases of mono-infection including rhinovirus (RV), human adenovirus (HAdV), human metapneumovirus (HMPV), enterovirus (EV), and influenza virus, and 18 cases of co-infection (SARS-CoV-2 with RV or HAdV or HMPV, and RV with EV). Our research shows that the results obtained from the MCS have value in epidemiological studies, reflecting national trends on a micro scale. Although the spread of COVID-19 is a major public health concern, SARS-CoV-2 is not the only pathogen responsible for respiratory infections.

Respiratory viral infections other than SARS CoV-2 among the North Indian patients presenting with acute respiratory illness during the first COVID-19 wave

Acute respiratory infections due to viral or bacterial etiology can cause 60 deaths per one lakh population. Viral etiology is more common as compared to bacterial, but lack of definite diagnosis leads to increased usage of empirical antibiotics. During the first wave of the COVID-19 pandemic, there was a need to identify co-infections especially in severe acute respiratory illness (SARI) patients to identify it as one of the cofactors for increased severity of illness and to identify the causative agents in COVID-19 negative individuals. The SARS CoV-2 real time PCR was carried out using ICMR approved kits and the other respiratory viruses were detected using the multiplex commercially available real time  kit. A total of 186 patients presenting with either SARI (89.8%) or influenza like illness (10.2%) were included in the study. Out of these, 43 (23.1%) were positive for SARS CoV-2 RNA and 2 (4.6%) patients with SARI showed concomitant infection with either human rhinovirus or human respiratory syncytial virus . Out of 143 patients negative for SARS CoV-2, 35 (24.5%) were positive for one or more microbial infections and 28 (19.6%) infected with other respiratory viral infection most common being human rhinovirus. The results suggest that viral coinfections are significantly higher among COVID-19 negative individuals (24.5% vs 4.6%) presenting with respiratory illness as compared to COVID-19 positive individuals possibly due to viral interference and competitive advantage of SARS-CoV-2 in modulating the host immunity. Further detailed research is required for the understanding of mechanisms of viral co-infection.

Prevalence and Clinical Impact of Coinfection in Patients with Coronavirus Disease 2019 in Korea

Coinfection rates with other pathogens in coronavirus disease 2019 (COVID-19) varied during the pandemic. We assessed the latest prevalence of coinfection with viruses, bacteria, and fungi in COVID-19 patients for more than one year and its impact on mortality. A total of 436 samples were collected between August 2020 and October 2021. Multiplex real-time PCR, culture, and antimicrobial susceptibility testing were performed to detect pathogens. The coinfection rate of respiratory viruses in COVID-19 patients was 1.4%. Meanwhile, the rates of bacteria and fungi were 52.6% and 10.5% in hospitalized COVID-19 patients, respectively. Respiratory syncytial virus, rhinovirus, Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans were the most commonly detected pathogens. Ninety percent of isolated A. baumannii was non-susceptible to carbapenem. Based on a multivariate analysis, coinfection (odds ratio [OR] = 6.095), older age (OR = 1.089), and elevated lactate dehydrogenase (OR = 1.006) were risk factors for mortality as a critical outcome. In particular, coinfection with bacteria (OR = 11.250), resistant pathogens (OR = 11.667), and infection with multiple pathogens (OR = 10.667) were significantly related to death. Screening and monitoring of coinfection in COVID-19 patients, especially for hospitalized patients during the pandemic, are beneficial for better management and survival.

Simultaneous Detection of Multiple Respiratory Viruses Among SARS-CoV-2-positive and negative Patients by Multiplex TaqMan One-step Real-time PCR

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has clinical manifestations similar to other common respiratory viral infections. There are limited data on the frequency of viral respiratory coinfection among patients infected with SARS-CoV-2 in Iran. Objectives: This cross-sectional study investigated the prevalence of multiple respiratory viruses among SARS-CoV-2-positive and negative patients during the coronavirus disease 2019 (COVID-19) pandemic in Iran. Methods: We included oropharyngeal/nasopharyngeal swab specimens of patients suspected of COVID-19 from December 2020 to March 2021. A reliable multiplex TaqMan one-step real-time PCR method was employed to detect 17 viral respiratory pathogens simultaneously. Descriptive analyses were performed to characterize the specimens concerning age, gender, clinical manifestations, and underlying disease. Results: Multiple respiratory viruses with a frequency of 18.78% were detected in 197 studied patients. Human metapneumovirus was the most prevalent pathogen detected in both SARS-CoV-2-positive (n = 7, 7.7%) and negative (n = 7, 6.6%) patients. Moreover, the frequency rate of viral infection was almost the same in both SARS-CoV-2-positive (18.68%) and negative (18.86%) patients. Altogether, there were no differences in baseline demographic characteristics such as age, sex, clinical symptoms, and comorbidities between the two groups (P > 0.05). Conclusions: The data presented here expand our understanding of the epidemiology of multiple types of viral respiratory pathogens in suspected COVID-19 patients. Therefore, simultaneous screening of other viral respiratory pathogens will be helpful for clinicians and researchers interested in the control of viral respiratory tract infections.

Incidence and Outcome of Coinfections with SARS-CoV-2 and Rhinovirus

Background: We aimed to compare the clinical severity in patients who were coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinovirus or monoinfected with a single one of these viruses. Methods: The study period ranged from 1 March 2020 to 28 February 2021 (one year). SARS-CoV-2 and other respiratory viruses were identified by real-time reverse-transcription-PCR as part of the routine work at Marseille University hospitals. Bacterial and fungal infections were detected by standard methods. Clinical data were retrospectively collected from medical files. This study was approved by the ethical committee of our institute. Results: A total of 6034/15,157 (40%) tested patients were positive for at least one respiratory virus. Ninety-three (4.3%) SARS-CoV-2-infected patients were coinfected with another respiratory virus, with rhinovirus being the most frequent (62/93, 67%). Patients coinfected with SARS-CoV-2 and rhinovirus were significantly more likely to report a cough than those with SARS-CoV-2 monoinfection (62% vs. 31%; p = 0.0008). In addition, they were also significantly more likely to report dyspnea than patients with rhinovirus monoinfection (45% vs. 36%; p = 0.02). They were also more likely to be transferred to an intensive care unit and to die than patients with rhinovirus monoinfection (16% vs. 5% and 7% vs. 2%, respectively) but these differences were not statistically significant. Conclusions: A close surveillance and investigation of the co-incidence and interactions of SARS-CoV-2 and other respiratory viruses is needed. The possible higher risk of increased clinical severity in SARS-CoV-2-positive patients coinfected with rhinovirus warrants further large scale studies.

Clinical and laboratory characteristics of children with SARS-CoV-2 infection

We describe the demographic, clinical, radiological, and laboratory findings of 422 children (0-18 year-of-age) suspected of having severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection admitted to a pediatric emergency department between March 23, and July 23, 2020. We compared the characteristics of SARS-CoV-2-positive patients to SARS-CoV-2-negative patients. SARS-CoV-2 infection was confirmed in 78 (18.4%). Fever (51.2%) and cough (43.5%) were the most commonly reported signs in the SARS-CoV-2-positive patients. Isolated rhinorrhea (7.2%) was reported only in the SARS-CoV-2-negative group (p = .0014). Patients with SARS-CoV-2 infection were classified according to severity, with the percentages of asymptomatic, mild, moderate, severe, and critical cases determined to be 29.5%, 56.4%, 12.9%, 1.2%, and 0%, respectively. Of the 422 children, 128 (30.3%) underwent nasopharyngeal polymerase chain reaction testing for other respiratory viral pathogens; 21 (16.4%) were infected with viral pathogens other than SARS-CoV-2. Only one patient (4.7%) with confirmed coronavirus disease 2019 (COVID-19) disease was coinfected with respiratory syncytial virus and rhinovirus. The results indicate lower median white blood cell, neutrophil, and lymphocyte counts, lower lactate dehydrogenase, d-dimer, and procalcitonin levels in the SARS-CoV-2-positive group (p ≤ .001). Our findings confirm that COVID-19 in children has a mild presentation. In our cohort, no patient with SARS-CoV-2 infection had isolated rhinorrhea.

Respiratory Pathogen Coinfections in SARS-CoV-2-Positive Patients in Southeastern Wisconsin: A Retrospective Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.

Evaluation of a multiplex PCR screening approach to identify community-acquired bacterial co-infections in COVID-19: a multicenter prospective cohort study of the German competence network of community-acquired pneumonia (CAPNETZ)

Purpose

Thorough knowledge of the nature and frequency of co-infections is essential to optimize treatment strategies and risk assessment in cases of coronavirus disease 2019 (COVID-19). This study aimed to evaluate the multiplex polymerase chain reaction (PCR) screening approach for community-acquired bacterial pathogens (CABPs) at hospital admission, which could facilitate identification of bacterial co-infections in hospitalized COVID-19 patients.

Methods

Clinical data and biomaterials from 200 hospitalized COVID-19 patients from the observational cohort of the Competence Network for community-acquired pneumonia (CAPNETZ) prospectively recruited between March 17, 2020, and March 12, 2021 in 12 centers in Germany and Switzerland, were included in this study. Nasopharyngeal swab samples were analyzed on hospital admission using multiplex real-time reverse transcription (RT)-PCR for a broad range of CABPs.

Results

In total of 200 patients Staphylococcus aureus (27.0%), Haemophilus influenzae (13.5%), Streptococcus pneumoniae (5.5%), Moraxella catarrhalis (2.5%), and Legionella pneumophila (1.5%) were the most frequently detected bacterial pathogens. PCR detection of bacterial pathogens correlated with purulent sputum, and showed no correlation with ICU admission, mortality, and inflammation markers. Although patients who received antimicrobial treatment were more often admitted to the ICU and had a higher mortality rate, PCR pathogen detection was not significantly related to antimicrobial treatment.

Conclusion

General CABP screening using multiplex PCR with nasopharyngeal swabs may not facilitate prediction or identification of bacterial co-infections in the early phase of COVID-19-related hospitalization. Most patients with positive PCR results appear to be colonized rather than infected at that time, questioning the value of routine antibiotic treatment on admission in COVID-19 patients.

Supplementary Information

The online version contains supplementary material available at 10.1007/s15010-021-01720-8.

A systematic review on SARS-CoV-2-associated fungal coinfections

A severe pandemic of Coronavirus Disease (COVID‐19) has been sweeping the globe since 2019, and this time, it did not stop, with frequent mutations transforming into virulent strains, for instance, B.1.1.7, B.1.351, and B.1.427. In recent months, a fungal infection, mucormycosis has emerged with more fatal responses and significantly increased mortality rate. To measure the severity and potential alternative approaches against black fungus coinfection in COVID‐19 patients, PubMed, Google Scholar, World Health Organization (WHO) newsletters, and other online resources, based on the cases reported and retrospective observational analysis were searched from the years 2015–2021. The studies reporting mucormycosis with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) coinfection and/or demonstrating potential risk factors, such as a history of diabetes mellitus or suppressed immune system were included, and reports published in non‐English language were excluded. More than 20 case reports and observational studies on black fungus coinfection in COVID‐19 patients were eligible for inclusion. The results indicated that diabetes mellitus, hyperglycemic, and immunocompromised COVID‐19 patients with mucormycosis were at a higher risk. We found that it was prudent to assess the potential risk factors and severity of invasive mycosis via standardized diagnostic and clinical settings. Large‐scale studies need to be conducted to identify early biomarkers and optimization of diagnostic methods has to be established per population and geographical variation. This will not only help clinicians around the world to detect the coinfection in time but also will prepare them for future outbreaks of other potential pandemics.

Observational studies and case reports of Post‐COVID black fungus co‐infection highlighted in review.

Along with risk factors, radiological interventions of black fungus co‐infection in COVID‐19 patients and challenges for accurate diagnosis were elaborated.

The review discusses interconnection between fungus and SARS‐CoV‐2 co‐infection of mechanism to identify potential biomarkers.

Our conclusion will contribute to motivate researchers to design follow‐up plans for black fungus infection in COVID‐19.

Distribution of spreading viruses during COVID-19 pandemic: Effect of mitigation strategies

Background

The study aimed to evaluate the distribution of circulating respiratory viral pathogens other than severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) during the first year of the coronavirus disease-2019 (COVID-19) pandemic with especially focusing on the effects of the national-based mitigation strategies.

Methods

This single-center study was conducted between March 11, 2020-March 11, 2021. All children who were tested by polymerase chain reaction on nasopharyngeal swabs for SARS-CoV-2 and other common respiratory viral pathogens were included in the study.

Results

A total of 995 children with suspected COVID-19 admitted to the study center. Of these, 513 patients who were tested by polymerase chain reaction for both SARS-CoV-2 and common respiratory viral pathogens were included in the final analysis. Two hundred ninety-five patients were (57.5%) male. The median age was 3 years of age (27 days-17 years). A total of 321 viral pathogens identified in 310 (n: 310/513, 60.4%) patients, and 11 of them (n: 11/310, 3.5%) had co-detection with more than 1 virus. The most common detected virus was rhinovirus (n: 156/513, 30.4%), and SARS-CoV-2 (n: 122/513, 23.8%) followed by respiratory syncytial virus (n: 18/513, 3.5%). The influenza virus was detected in 2 patients (0.4%). A total of 193 patients were negative for both SARS-CoV-2 and other pathogens.

Conclusions

There is a decline in the frequency of all viral pathogens like SARS-CoV-2 in correlation with the national-based mitigation strategies against COVID-19 during the pandemic.

Co-infection of SARS-CoV-2 and influenza viruses: A systematic review and meta-analysis

We conducted this meta-analysis to determine the proportion of co-infection with influenza viruses in SARS-CoV-2 positive patients and to investigate the severity of COVID-19 in these patients. We included studies with SARS-CoV-2 infection confirmed by qRT-PCR and influenza virus infection (A and/or B) by nucleic acid tests. The proportion of co-infection was compared between children and adults, and between critically ill or deceased patients compared to overall patients. Fifty-four articles were included. The overall proportion of co-infection was 0.7%, 95%CI = [0.4 – 1.3]. Most influenza co-infections were due to the influenza A virus (74.4%). The proportion of co-infection with influenza viruses among children (3.2%, 95% CI = [0.9 – 10.9]) was significantly higher than that in adult patients (0.3%, 95% CI = [0.1 – 1.2]), p-value <0.01. The proportion of co-infection with influenza viruses among critically ill patients tended to be higher than that in overall patients (2.2%, 95% CI = [0.3 – 22.4] versus 0.6%, 95% CI = [0.3 – 1.2], respectively, p-value = 0.22). Screening for pathogens in co-infection, particularly influenza viruses in patients infected with SARS-CoV-2, is necessary. This warrants close surveillance and investigation of the co-incidences and interactions of SARS-CoV-2 and other respiratory viruses, which is facilitated by the expansion of syndromic diagnosis approaches through the use of multiplex PCR assays.

One Year on: An Overview of Singapore's Response to COVID-19-What We Did, How We Fared, How We Can Move Forward

Background—One year has passed since the first COVID-19 case in Singapore. This scoping review commemorates Singaporean researchers that have expanded the knowledge on this novel virus. We aim to provide an overview of healthcare-related articles published in peer-reviewed journals, authored by the Singapore research community about COVID-19 during the first year of the pandemic. Methods—This was reported using the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) protocol. It included healthcare-related articles about COVID-19 published between 23 January 2020 and 22 January 2021 with a Singapore-affiliated author. MEDLINE, Embase, Scopus, Web of Science, CINAHL, PsycINFO, Google Scholar, and local journals were searched. The articles were screened independently by two reviewers. Results—The review included 504 articles. Most of the articles narrated the changes to hospital practice (210), while articles on COVID-19 pathology (94) formed most of the non-narrative papers. Publications on public health (61) and the indirect impacts to clinical outcomes (45) were other major themes explored by the research community. The remaining articles detailed the psychological impact of the pandemic (35), adaptations of medical education (30), and narratives of events (14). Conclusion—Amidst a resurgence of community cases involving variant COVID-19 strains, the resources from the research community will provide valuable guidance to navigate these uncertain times.

Major Insights in Dynamics of Host Response to SARS-CoV-2: Impacts and Challenges

The coronavirus disease 2019 (COVID-19), a pandemic declared by the World Health Organization on March 11, 2020, is caused by the infection of highly transmissible species of a novel coronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). As of July 25, 2021, there are 194,372,584 cases and 4,167,937 deaths with high variability in clinical manifestations, disease burden, and post-disease complications among different people around the globe. Overall, COVID-19 is manifested as mild to moderate in almost 90% of the cases and only the rest 10% of the cases need hospitalization. However, patients with older age and those having different comorbidities have made worst the pandemic scenario. The variability of pathological consequences and clinical manifestations of COVID-19 is associated with differential host-SARS-CoV-2 interactions, which are influenced by the factors that originated from the SARS-CoV-2 and the host. These factors usually include the genomic attributes and virulent factors of the SARS-CoV-2, the burden of coinfection with other viruses and bacteria, age and gender of the individuals, different comorbidities, immune suppressions/deficiency, genotypes of major histocompatibility complex, and blood group antigens and antibodies. We herein retrieved and reviewed literatures from PubMed, Scopus, and Google relevant to clinical complications and pathogenesis of COVID-19 among people of different age, sex, and geographical locations; genomic characteristics of SARS-CoV-2 including its variants, host response under different variables, and comorbidities to summarize the dynamics of the host response to SARS-CoV-2 infection; and host response toward approved vaccines and treatment strategies against COVID-19. After reviewing a large number of published articles covering different aspects of host response to SARS-CoV-2, it is clear that one aspect from one region is not working with the scenario same to others, as studies have been done separately with a very small number of cases from a particular area/region of a country. Importantly, to combat such a pandemic as COVID-19, a conclusive understanding of the disease dynamics is required. This review emphasizes on the identification of the factors influencing the dynamics of host responses to SARS-CoV-2 and offers a future perspective to explore the molecular insights of COVID-19.

The Positive Rhinovirus/Enterovirus Detection and SARS-CoV-2 Persistence beyond the Acute Infection Phase: An Intra-Household Surveillance Study

We aimed to assess the duration of nasopharyngeal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA persistence in adults self-confined at home after acute infection; and to identify the associations of SARS-CoV-2 persistence with respiratory virus co-detection and infection transmission. A cross-sectional intra-household study was conducted in metropolitan Barcelona (Spain) during the time period of April to June 2020. Every adult who was the first family member reported as SARS-CoV-2-positive by reverse transcription polymerase chain reaction (RT-PCR) as well as their household child contacts had nasopharyngeal swabs tested by a targeted SARS-CoV-2 RT-PCR and a multiplex viral respiratory panel after a 15 day minimum time lag. Four-hundred and four households (404 adults and 708 children) were enrolled. SARS-CoV-2 RNA was detected in 137 (33.9%) adults and 84 (11.9%) children. Rhinovirus/Enterovirus (RV/EV) was commonly found (83.3%) in co-infection with SARS-CoV-2 in adults. The mean duration of SARS-CoV-2 RNA presence in adults’ nasopharynx was 52 days (range 26–83 days). The persistence of SARS-CoV-2 was significantly associated with RV/EV co-infection (adjusted odds ratio (aOR) 9.31; 95% CI 2.57–33.80) and SARS-CoV-2 detection in child contacts (aOR 2.08; 95% CI 1.24–3.51). Prolonged nasopharyngeal SARS-CoV-2 RNA persistence beyond the acute infection phase was frequent in adults quarantined at home during the first epidemic wave; which was associated with RV/EV co-infection and could enhance intra-household infection transmission.

Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology

This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.

Coinfections with Bacteria, Fungi, and Respiratory Viruses in Patients with SARS-CoV-2: A Systematic Review and Meta-Analysis

Background: Coinfection with bacteria, fungi, and respiratory viruses in SARS-CoV-2 is of particular importance due to the possibility of increased morbidity and mortality. In this meta-analysis, we calculated the prevalence of such coinfections. Methods: Electronic databases were searched from 1 December 2019 to 31 March 2021. Effect sizes of prevalence were pooled with 95% confidence intervals (CIs). To minimize heterogeneity, we performed sub-group analyses. Results: Of the 6189 papers that were identified, 72 articles were included in the systematic review (40 case series and 32 cohort studies) and 68 articles (38 case series and 30 cohort studies) were included in the meta-analysis. Of the 31,953 SARS-CoV-2 patients included in the meta-analysis, the overall pooled proportion who had a laboratory-confirmed bacterial infection was 15.9% (95% CI 13.6–18.2, n = 1940, 49 studies, I² = 99%, p < 0.00001), while 3.7% (95% CI 2.6–4.8, n = 177, 16 studies, I² = 93%, p < 0.00001) had fungal infections and 6.6% (95% CI 5.5–7.6, n = 737, 44 studies, I² = 96%, p < 0.00001) had other respiratory viruses. SARS-CoV-2 patients in the ICU had higher co-infections compared to ICU and non-ICU patients as follows: bacterial (22.2%, 95% CI 16.1–28.4, I² = 88% versus 14.8%, 95% CI 12.4–17.3, I² = 99%), and fungal (9.6%, 95% CI 6.8–12.4, I² = 74% versus 2.7%, 95% CI 0.0–3.8, I² = 95%); however, there was an identical other respiratory viral co-infection proportion between all SARS-CoV-2 patients [(ICU and non-ICU) and the ICU only] (6.6%, 95% CI 0.0–11.3, I² = 58% versus 6.6%, 95% CI 5.5–7.7, I² = 96%). Funnel plots for possible publication bias for the pooled effect sizes of the prevalence of coinfections was asymmetrical on visual inspection, and Egger’s tests confirmed asymmetry (p values < 0.05). Conclusion: Bacterial co-infection is relatively high in hospitalized patients with SARS-CoV-2, with little evidence of S. aureus playing a major role. Knowledge of the prevalence and type of co-infections in SARS-CoV-2 patients may have diagnostic and management implications.

Viral coinfections in COVID-19

The most consequential challenge raised by coinfection is perhaps the inappropriate generation of recombinant viruses through the exchange of genetic material among different strains. These genetically similar viruses can interfere with the replication process of each other and even compete for the metabolites required for the maintenance of the replication cycle. Due to the similarity in clinical symptoms of most viral respiratory tract infections, and their coincidence with COVID-19, caused by SARS-CoV-2, it is recommended to develop a comprehensive diagnostic panel for detection of respiratory and nonrespiratory viruses through the evaluation of patient samples. Given the resulting changes in blood markers, such as coagulation factors and white blood cell count following virus infection, these markers can be of diagnostic value in the detection of mixed infection in individuals already diagnosed with a certain viral illness. In this review, we seek to investigate the coinfection of SARS-CoV-2 with other respiratory and nonrespiratory viruses to provide novel insights into the development of highly sensitive diagnostics and effective treatment modalities.

Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis

INTRODUCTION

The recovery of other pathogens in patients with SARS-CoV-2 infection has been reported, either at the time of a SARS-CoV-2 infection diagnosis (co-infection) or subsequently (superinfection). However, data on the prevalence, microbiology, and outcomes of co-infection and superinfection are limited. The purpose of this study was to examine the occurrence of co-infections and superinfections and their outcomes among patients with SARS-CoV-2 infection.

PATIENTS AND METHODS

We searched literature databases for studies published from October 1, 2019, through February 8, 2021. We included studies that reported clinical features and outcomes of co-infection or superinfection of SARS-CoV-2 and other pathogens in hospitalized and non-hospitalized patients. We followed PRISMA guidelines, and we registered the protocol with PROSPERO as: CRD42020189763.

RESULTS

Of 6639 articles screened, 118 were included in the random effects meta-analysis. The pooled prevalence of co-infection was 19% (95% confidence interval [CI]: 14%-25%, I2 = 98%) and that of superinfection was 24% (95% CI: 19%-30%). Pooled prevalence of pathogen type stratified by co- or superinfection were: viral co-infections, 10% (95% CI: 6%-14%); viral superinfections, 4% (95% CI: 0%-10%); bacterial co-infections, 8% (95% CI: 5%-11%); bacterial superinfections, 20% (95% CI: 13%-28%); fungal co-infections, 4% (95% CI: 2%-7%); and fungal superinfections, 8% (95% CI: 4%-13%). Patients with a co-infection or superinfection had higher odds of dying than those who only had SARS-CoV-2 infection (odds ratio = 3.31, 95% CI: 1.82-5.99). Compared to those with co-infections, patients with superinfections had a higher prevalence of mechanical ventilation (45% [95% CI: 33%-58%] vs. 10% [95% CI: 5%-16%]), but patients with co-infections had a greater average length of hospital stay than those with superinfections (mean = 29.0 days, standard deviation [SD] = 6.7 vs. mean = 16 days, SD = 6.2, respectively).

CONCLUSIONS

Our study showed that as many as 19% of patients with COVID-19 have co-infections and 24% have superinfections. The presence of either co-infection or superinfection was associated with poor outcomes, including increased mortality. Our findings support the need for diagnostic testing to identify and treat co-occurring respiratory infections among patients with SARS-CoV-2 infection.

Containment of COVID-19 and reduction in healthcare-associated respiratory viral infections through a multi-tiered infection control strategy

BACKGROUND

During the ongoing COVID-19 pandemic, healthcare-associated transmission of respiratory viral infections (RVI) is a concern. To reduce the impact of SARS-CoV-2 and other respiratory viruses on patients and healthcare workers (HCWs) we devised and evaluated a multi-tiered infection control strategy with the goal of preventing nosocomial transmission of SARS-CoV2 and other RVIs across a large healthcare campus.

METHODS

From January-June 2020, a multi-tiered infection control strategy was implemented across a healthcare campus in Singapore, comprising the largest acute tertiary hospital as well as four other subspecialty centres, with more than 10,000 HCWs. Drawing on our institution's experience with an outbreak of Severe Acute Respiratory Syndrome (SARS) in 2003, this strategy included improved patient segregation and distancing, and heightened infection prevention and control (IPC) measures including universal masking. All symptomatic patients were tested for COVID-19 and common RVIs.

RESULTS

A total of 16,162 admissions campus-wide were screened; 7.1% (1155/16,162) tested positive for COVID-19. Less than 5% of COVID-19 cases (39/1155) were initially detected outside of isolation wards in multi-bedded cohorted wards. Improved distancing and enhanced IPC measures successfully mitigated onward spread even amongst COVID-19 cases detected outside of isolation. COVID-19 rates amongst HCWs were kept low (0.13%, 17/13,066) and reflected community acquisition rather than nosocomial spread. Rates of healthcare-associated-RVI amongst inpatients fell to zero and this decrease was sustained even after the lifting of visitor restrictions.

CONCLUSION

This multi-tiered infection control strategies can be implemented at-scale to successfully mitigate healthcare-associated transmission of respiratory viral pathogens.

The Complexity of Co-Infections in the Era of COVID-19

The current frequency of COVID-19 in a pandemic era ensures that co-infections with a variety of co-pathogens will occur. Generally, there is a low rate of bonafide co-infections in early COVID-19 pulmonary infection as currently appreciated. Reports of high co-infection rates must be tempered by limitations in current diagnostic methods since amplification technologies do not necessarily confirm live pathogen and may be subject to considerable laboratory variation. Some laboratory methods may not exclude commensal microbes. Concurrent serodiagnoses have long been of concern for accuracy in these contexts. Presumed virus co-infections are not specific to COVID-19. The association of influenza viruses and SARS-CoV-2 in co-infection has been considerably variable during influenza season. Other respiratory virus co-infections have generally occurred in less than 10% of COVID-19 patients. Early COVID-19 disease is more commonly associated with bacterial co-pathogens that typically represent usual respiratory micro-organisms. Late infections, especially among severe clinical presentations, are more likely to be associated with nosocomial or opportunistic pathogens given the influence of treatments that can include antibiotics, antivirals, immunomodulating agents, blood products, immunotherapy, steroids, and invasive procedures. As anticipated, hospital care carries risk for multi-resistant bacteria. Overall, co-pathogen identification is linked with longer hospital stay, greater patient complexity, and adverse outcomes. As for other viral infections, a general reduction in the use of empiric antibiotic treatment is warranted. Further insight into co-infections with COVID-19 will contribute overall to effective antimicrobial therapies and disease control.

Reduction in asthma admissions during the COVID-19 pandemic: consequence of public health measures in Singapore

We read with interest the study by Izquierdoet al. [1] that reported a lower proportion of patients with concurrent asthma and coronavirus disease 2019 (COVID-19), compared to other chronic diseases. During the ongoing pandemic, various studies have also observed a lower occurrence of persons with asthma amongst hospitalised COVID-19 cases [2, 3]. Several hypotheses have been postulated to account for these observations, including lower susceptibility to COVID-19 amongst patients with asthma [2, 3] and a remission in rates of common circulating respiratory viral infections (RVIs) [4]. RVIs are potential triggers of asthma exacerbations and may cause a loss of asthma control [5]. During the COVID-19 pandemic, community-wide public health measures introduced to reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as universal masking and social distancing, may reduce community transmission of common RVIs [4], potentially decreasing the frequency and severity of asthma exacerbations and hence reducing hospitalisations. However, patients may demonstrate a higher threshold to seek care due to fear of nosocomial transmission during the pandemic. Significant community transmission of SARS-CoV-2 may thus confound causal interpretation of trends in asthma hospitalisations. While the ongoing pandemic provides a rare opportunity to ascertain the impact of public health measures on hospitalisations for asthma exacerbations, such observations are only possible in areas that have mitigated community transmission and maintained public health interventions over a sustained duration.

A sustained reduction in asthma admissions with PCR-proven respiratory viral infections coincided with the widespread adoption of public health measures, including social distancing and wearing of face coverings, during a pandemichttps://bit.ly/2Kug9iw

Unintended consequences of infection prevention and control measures during COVID-19 pandemic

BACKGROUND

In the current COVID-19 pandemic, aggressive Infection Prevention and Control (IPC) measures have been adopted to prevent health care-associated transmission of COVID-19. We evaluated the impact of a multimodal IPC strategy originally designed for the containment of COVID-19 on the rates of other hospital-acquired-infections (HAIs).

METHODOLOGY

From February-August 2020, a multimodal IPC strategy was implemented across a large health care campus in Singapore, comprising improved segregation of patients with respiratory symptoms, universal masking and heightened adherence to Standard Precautions. The following rates of HAI were compared pre- and postpandemic: health care-associated respiratory-viral-infection (HA-RVI), methicillin-resistant Staphylococcus aureus, and CP-CRE acquisition rates, health care-facility-associated C difficile infections and device-associated HAIs.

RESULTS

Enhanced IPC measures introduced to contain COVID-19 had the unintended positive consequence of containing HA-RVI. The cumulative incidence of HA-RVI decreased from 9.69 cases per 10,000 patient-days to 0.83 cases per 10,000 patient-days (incidence-rate-ratio = 0.08; 95% confidence interval [CI] = 0.05-0.13, P< .05). Hospital-wide MRSA acquisition rates declined significantly during the pandemic (incidence-rate-ratio = 0.54, 95% CI = 0.46-0.64, P< .05), together with central-line-associated-bloodstream infection rates (incidence-rate-ratio = 0.24, 95% CI = 0.07-0.57, P< .05); likely due to increased compliance with Standard Precautions. Despite the disruption caused by the pandemic, there was no increase in CP-CRE acquisition, and rates of other HAIs remained stable.

CONCLUSIONS

Multimodal IPC strategies can be implemented at scale to successfully mitigate health care-associated transmission of RVIs. Good adherence to personal-protective-equipment and hand hygiene kept other HAI rates stable even during an ongoing pandemic where respiratory infections were prioritized for interventions.

If Not COVID-19 What Is It? Analysis of COVID-19 versus Common Respiratory Viruses among Symptomatic Health Care Workers in a Tertiary Infectious Disease Referral Hospital in Manila, Philippines

The COVID-19 global pandemic is entering its second year. In this short report we present additional results as a supplement to our previous paper on COVID-19 and common respiratory virus screening for healthcare workers (HCWs) in a tertiary infectious disease referral hospital in Manila, Philippines. We sought to understand what etiologic agents could explain the upper/lower respiratory tract infection-like (URTI/LRTI-like) symptoms exhibited by 88% of the 324 HCWs tested. Among the patients who had URTI/LRTI-like symptoms, only seven (2%) were positive for COVID-19, while 38 (13%) of the symptomatic participants were identified positive for another viral etiologic agent. Rhinovirus was the most common infection, with 21 (9%) of the symptomatic participants positive for rhinovirus. Based on these results, testing symptomatic HCWs for common respiratory illnesses in addition to COVID-19 should be considered during this time of global pandemic.

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

Accumulating evidence supports the high prevalence of co-infections among Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients, and their potential to worsen the clinical outcome of COVID-19. However, there are few data on Southern Hemisphere populations, and most studies to date have investigated a narrow spectrum of viruses using targeted qRT-PCR. Here we assessed respiratory viral co-infections among SARS-CoV-2 patients in Australia, through respiratory virome characterization. Nasopharyngeal swabs of 92 SARS-CoV-2-positive cases were sequenced using pan-viral hybrid-capture and the Twist Respiratory Virus Panel. In total, 8% of cases were co-infected, with rhinovirus (6%) or influenzavirus (2%). Twist capture also achieved near-complete sequencing (> 90% coverage, > tenfold depth) of the SARS-CoV-2 genome in 95% of specimens with Ct < 30. Our results highlight the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture, for SARS-CoV-2 whole-genome sequencing without amplicon generation and the simultaneous identification of viral co-infections with ease.

Respiratory co-infections with COVID-19 in the Veterans Health Administration, 2020

Reporting of Coronavirus disease 2019 (COVID-19) co-infections with other respiratory pathogens has varied. We evaluated 825,280 molecular and/or viral culture respiratory assays within the Veterans Health Administration from September 29, 2019 to May 31, 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in 10,222 of 174,746 (5.8%) individuals. 30,063 (17.2%) of 174,746 individuals tested for SARS-CoV-2 had additional respiratory pathogen testing; co-infection was identified in 56 of 3757 (1.5%) individuals positive for SARS-CoV-2. Among those negative for SARS-CoV-2, 1022 of 26,306 (3.9%) were positive for at least 1 respiratory pathogen. Compared to COVID-19 mono-infection, individuals with COVID-19 co-infection had lower odds of being female. Compared to non-COVID-19 respiratory pathogen infection, individuals with COVID-19 co-infection had lower odds of being female, were hospitalized more frequently, had higher odds of death, and were younger at death. Our findings suggest COVID-19 co-infections were rare; however, not all COVID-19 patients were concurrently tested for other respiratory pathogens and seasonal decreases in other respiratory pathogens were occurring as COVID-19 emerged.

Clinical characteristics of COVID-19 patients hospitalized at Clinique Ngaliema, a public hospital in Kinshasa, in the Democratic Republic of Congo: A retrospective cohort study

OBJECTIVES

To describe the clinical characteristics of patients infected with SARS-CoV-2 at Clinique Ngaliema, a public hospital, in Kinshasa, in the Democratic Republic of Congo (DRC).

METHODS

This retrospective study analyzed medical records including socio-demographics, past medical history, clinical manifestation, comorbidities, laboratory data, treatment and disease outcome of 160 hospitalized COVID-19 patients, with confirmed result of SARS-CoV-2 viral infection.

RESULTS

The median age of patients was 54 years (IQR: 38-64), and there was no significant gender difference (51% of male). The most common comorbidities were hypertension (55 [34%]), diabetes (31 [19%]) and obesity (13 [8%]). Fever (93 [58%]), cough (92 [57%]), fatigue (87 [54%]), shortness of breath (72 [45%]) and myalgia (33 [21%]) were the most common symptoms, upon admission. Patients were categorized into mild (92 [57%]), moderate (19 [12%]) and severe (49 [31%]). Severe patients were older and were more likely to have comorbidities, compared to mild ones. The majority of patients (92% [147 of 160]) patients received hydroxychloroquine or chloroquine phosphate. Regression model revealed that older age, lower SpO2, higher heart rate and elevated AST at admission were all risk factors associated with in-hospital death. The prevalence of COVID-19 and malaria co-infection was 0.63% and 70 (44%) of all patients received antimalarial treatment before hospitalization.

CONCLUSION

Our findings indicated that the epidemiological and clinical feature of COVID-19 patients in Kinshasa are broadly similar to previous reports from other settings. Older age, lower SpO2, tachycardia, and elevated AST could help to identify patients at higher risk of death at an early stage of the illness. Plasmodium spp co-infection was not common in hospitalized COVID-19 patients.

Co-infection of SARS-CoV-2 with Chlamydia or Mycoplasma pneumoniae: a case series and review of the literature

INTRODUCTION

The novel coronavirus SARS-CoV-2 has spread all over the world causing a global pandemic and representing a great medical challenge. Nowadays, there is limited knowledge on the rate of co-infections with other respiratory pathogens, with viral co-infection being the most representative agents. Co-infection with Mycoplasma pneumoniae has been described both in adults and pediatrics whereas only two cases of Chlamydia pneumoniae have been reported in a large US study so far.

METHODS

In the present report, we describe a series of seven patients where co-infection with C. pneumoniae (n = 5) or M. pneumoniae (n = 2) and SARS-CoV-2 was detected in a large teaching hospital in Rome.

RESULTS AND CONCLUSION

An extensive review of the updated literature regarding the co-infection between SARS-CoV-2 and these atypical pathogens is also performed.

COVID-19: A Rural US Emergency Department Perspective

Several aspects led to the poor control of the coronavirus disease 2019 (COVID-19) outbreak in the US from a rural emergency department (ED) perspective. These include US residents’ attitude towards political involvement in health and civil rights; lack of enough testing kits and rapid test results, or not available at all; and personal protective equipment (PPE) shortages. These obstacles related to medical supplies and resources, and lack of coordinated approach to the pandemic in the US, are important information for retrospective disaster research to understand study limitations, extrapolate accurate and valid data, and for other countries to understand how and why the US had higher numbers of COVID-19 cases and deaths compared to other countries.

Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19

Objectives

This study was performed during the early outbreak period of coronavirus disease 2019 (COVID-19) and the seasonal epidemics of other respiratory viral infections, in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses. It also compared the diagnostic performances of upper respiratory tract (URT) and lower respiratory tract (LRT) samples for SARS-CoV-2 infection.

Methods

From 25 January to 29 March 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were simultaneously tested for SARS-CoV-2 and other respiratory viruses.

Results

A total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age 50 (range, 1–103) years. Twenty-one (1.5%) patients were positive for both SARS-CoV-2 and other respiratory viruses. The detection rate of SARS-CoV-2 was significantly higher in LRT than in URT (53.6% vs. 13.4%; p < 0.0001). The analysis of paired samples from 117 (8.2%) patients showed that SARS-CoV-2 load was lower in URT than in LRT samples in 65% of cases.

Conclusion

The detection of other respiratory viruses in patients during this epidemic period could not rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increased the accuracy of diagnosis of COVID-19.

Children were less frequently infected with SARS-CoV-2 than adults during 2020 COVID-19 pandemic in Warsaw, Poland

Clinical data suggest that during the current COVID-19 pandemic, children are less prone than adults to SARS-CoV-2 infection. Our purpose was to determine the frequency of SARS-CoV-2 in children vs. adults during the 2020 pandemic in Warsaw, Poland, and to investigate whether RSV and/or influenza A/B infections were associated with SARS-CoV-2 infections. We present results of RT-PCR tests for SARS-CoV-2 performed in Warsaw, Poland. Some of the pediatric subjects were also PCR-tested for RSV, and A and B influenza. We compared the test results from the four groups of symptomatic and asymptomatic subjects: 459 symptomatic pediatric patients (children 0–18 years old), 1774 symptomatic adults, 445 asymptomatic children, and 239 asymptomatic adults. 3.26% (15/459) of symptomatic pediatric patients were positive for SARS-CoV-2 in contrast to 5.58% (99/1774) of symptomatic adults (p = 0.0448). There were no SARS-CoV-2 positive cases in the group of asymptomatic children (0/445) and two positive cases in the group of asymptomatic adults (2/239), i.e., 0.83%. In the group of symptomatic pediatric patients, 17.14% (6/35) (p = 0.0002) were positive for RSV, 8.16% (4/49) were positive for influenza A, and 2.04% (1/49), thus 10.20% (5/49) (p = 0.0176) for influenza A/B. Children were less prone to SARS-CoV-2 infection than the adults during the COVID-19 pandemic in Warsaw. Higher percentage of symptomatic children was infected with RSV or influenza A/B than with SARS-CoV-2. This suggests a necessity for the testing for all these viruses for an early identification and isolation of SARS-CoV-2-positive patients for an ensuing 2020 autumn return of COVID-19.