Respiratory Virus Co-infection Research Articles

SARS-CoV-2 and Respiratory Syncytial Virus Coinfection in Hospitalized Pediatric Patients.

In this study, children under 24 months of age hospitalized with respiratory compromise due to COVID-19 were retrospectively analyzed according to the event of coinfection with respiratory syncytial virus. Of 32 patients, 18.7% had coinfection and these had a significantly longer length of stay. There were no differences regarding need for intensive care, mechanical ventilation or mortality rates.

COVID-19 and respiratory tract viral co-infections: Choosing the screening method

COVID-19 and respiratory tract viral co-infections: Choosing the screening method

Prevalence of Co-infection at the Time of Hospital Admission in COVID-19 Patients, A Multicenter Study.

BackgroundBacterial infections may complicate viral pneumonias. Recent reports suggest that bacterial co-infection at time of presentation is uncommon in coronavirus disease 2019 (COVID-19); however, estimates were based on microbiology tests alone. We sought to develop and apply consensus definitions, incorporating clinical criteria to better understand the rate of co-infections and antibiotic use in COVID-19.MethodsA total of 1016 adult patients admitted to 5 hospitals in the Johns Hopkins Health System between March 1, 2020, and May 31, 2020, with COVID-19 were evaluated. Adjudication of co-infection using definitions developed by a multidisciplinary team for this study was performed. Both respiratory and common nonrespiratory co-infections were assessed. The definition of bacterial community-acquired pneumonia (bCAP) included proven (clinical, laboratory, and radiographic criteria plus microbiologic diagnosis), probable (clinical, laboratory, and radiographic criteria without microbiologic diagnosis), and possible (not all clinical, laboratory, and radiographic criteria met) categories. Clinical characteristics and antimicrobial use were assessed in the context of the consensus definitions.ResultsBacterial respiratory co-infections were infrequent (1.2%); 1 patient had proven bCAP, and 11 (1.1%) had probable bCAP. Two patients (0.2%) had viral respiratory co-infections. Although 69% of patients received antibiotics for pneumonia, the majority were stopped within 48 hours in patients with possible or no evidence of bCAP. The most common nonrespiratory infection was urinary tract infection (present in 3% of the cohort).ConclusionsUsing multidisciplinary consensus definitions, proven or probable bCAP was uncommon in adults hospitalized due to COVID-19, as were other nonrespiratory bacterial infections. Empiric antibiotic use was high, highlighting the need to enhance antibiotic stewardship in the treatment of viral pneumonias.

Gene editing and RNAi approaches for COVID-19 diagnostics and therapeutics.

The novel coronavirus pneumonia (COVID-19) is a highly infectious acute respiratory disease caused by Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV-2) (Prec Clin Med 2020;3:9–13, Lancet 2020;395:497–506, N. Engl J Med 2020a;382:1199–207, Nature 2020;579:270–3). SARS-CoV-2 surveillance is essential to controlling widespread transmission. However, there are several challenges associated with the diagnostic of the COVID-19 during the current outbreak (Liu and Li (2019), Nature 2020;579:265–9, N. Engl J Med 2020;382:727–33). Firstly, the high number of cases overwhelms diagnostic test capacity and proposes the need for a rapid solution for sample processing (Science 2018;360:444–8). Secondly, SARS-CoV-2 is closely related to other important coronavirus species and subspecies, so detection assays can give false-positive results if they are not efficiently specific to SARS-CoV-2. Thirdly, patients with suspected SARS-CoV-2 infection sometimes have a different respiratory viral infection or co-infections with SARS-CoV-2 and other respiratory viruses (MedRxiv 2020a;1–18). Confirmation of the COVID-19 is performed mainly by virus isolation followed by RT-PCR and sequencing (N. Engl J Med 2020;382:727–33, MedRxiv 2020a, Turkish J Biol 2020;44:192–202). The emergence and outbreak of the novel coronavirus highlighted the urgent need for new therapeutic technologies that are fast, precise, stable, easy to manufacture, and target-specific for surveillance and treatment. Molecular biology tools that include gene-editing approaches such as CRISPR-Cas12/13-based SHERLOCK, DETECTR, CARVER and PAC-MAN, antisense oligonucleotides, antisense peptide nucleic acids, ribozymes, aptamers, and RNAi silencing approaches produced with cutting-edge scientific advances compared to conventional diagnostic or treatment methods could be vital in COVID-19 and other future outbreaks. Thus, in this review, we will discuss potent the molecular biology approaches that can revolutionize diagnostic of viral infections and therapies to fight COVID-19 in a highly specific, stable, and efficient way.

12: Utility of Testing for Respiratory Viral Co-Infections With SARS-CoV-2 at Time of Initial Diagnosis

Copyright © 2020 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.

High burden of viral respiratory co-infections in a cohort of children with suspected pulmonary tuberculosis

BackgroundThe presentation of pulmonary tuberculosis (PTB) in young children is often clinically indistinguishable from other common respiratory illnesses, which are frequently infections of viral aetiology. As little is known about the role of viruses in children with PTB, we investigated the prevalence of respiratory viruses in children with suspected PTB at presentation and follow-up.MethodsIn an observational cohort study, children < 13 years were routinely investigated for suspected PTB in Cape Town, South Africa between December 2015 and September 2017 and followed up for 24 weeks. Nasopharyngeal aspirates (NPAs) were tested for respiratory viruses using multiplex PCR at enrolment, week 4 and 8.ResultsSeventy-three children were enrolled [median age 22.0 months; (interquartile range 10.0–48.0); 56.2% male and 17.8% HIV-infected. Anti-tuberculosis treatment was initiated in 54.8%; of these 50.0% had bacteriologically confirmed TB. At enrolment, ≥1 virus were detected in 95.9% (70/73) children; most commonly human rhinovirus (HRV) (74.0%). HRV was more frequently detected in TB cases (85%) compared to ill controls (60.6%) (p = 0.02). Multiple viruses were detected in 71.2% of all children; 80% of TB cases and 60.6% of ill controls (p = 0.07). At follow-up, ≥1 respiratory virus was detected in 92.2% (47/51) at week 4, and 94.2% (49/52) at week 8.ConclusionsWe found a high prevalence of viral respiratory co-infections in children investigated for PTB, irrespective of final PTB diagnosis, which remained high during follow up. Future work should include investigating the whole respiratory ecosystem in combination with pathogen- specific immune responses.

Does respiratory co-infection facilitate dispersal of SARS-CoV-2? investigation of a super-spreading event in an open-space office

BackgroundSuper-spreaders are individuals infecting disproportionately large numbers of contacts. They probably play a crucial role in the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We describe a super-spreading event within a team working in an open-space office and investigate factors potentially having facilitated SARS-CoV-2 transmission.MethodsIn this retrospective cohort study, semi-structured telephone interviews with all team members were carried out to identify symptoms, contacts, and adherence to basic hygiene measures. During site visits, we gathered information about workplace and seating arrangements. The secondary attack rate in office and households was calculated. Potential respiratory viral co-infections were assessed by multiplex PCR. SARS-CoV-2 whole-genome sequencing was performed using a tiled-amplicon sequencing approach.ResultsOf 13 team members, 11 fell ill with Coronavirus disease 2019 (COVID-19). Due to the sequence of events and full genome sequence data, one person was considered the index case for this outbreak, directly infecting 67 to 83% of the teammates. All team members reported repetitive close contacts among themselves during joint computer work, team meetings and a “Happy Birthday” serenade. Two individuals shared nuts and dates. The arrangement of the office and meeting rooms precluded sufficient adherence to physical distancing. The index case and a further individual were diagnosed with an adenovirus serotype 4 co-infection.ConclusionWe identified several environmental and behavioral factors that probably have facilitated the transmission of SARS-CoV-2. The relevance of the adenovirus co-infection remains unclear and merits further investigation.

Severity of influenza virus and respiratory syncytial virus coinfections in hospitalized adult patients

Abstract Background With the introduction of molecular diagnostic techniques over the past decades, different kinds of viral pathogens in the same sample are detected simultaneously more frequently. Nevertheless, influenza virus (Flu) and respiratory syncytial virus (RSV) coinfection in adults was reported only occasionally. Moreover, the clinical implications of Flu/RSV coinfection in the respiratory tract of adults remain unclear. Methods This retrospective study analyzed adult patients with acute respiratory infection from January 2017 to June 2019 in China-Japan Friendship Hospital. Results A total of 574, 235 and 113 patients were positive for influenza A-only (FA-only), influenza B-only (FB-only) and RSV-only in influenza seasons (from Nov 2017 to Mar 2018 and from Nov 2018 to Mar 2019), respectively. Of these, 19 cases were coinfected by Flu and RSV and admitted to this hospital. Compared with 809 Flu-only infected patients and 113 RSV-only infected patients, both the rates of intensive care unit(ICU) admission and use of invasive mechanical ventilation in Flu/RSV coinfected patients were higher (ICU admission: 47.4% vs. 20.1%, P=0.004; 47.4% vs. 22.1%, P=0.020; invasive mechanical ventilation: 47.4% vs.13.2%, P Conclusion The findings of this study suggest that coinfection of Flu/RSV in adults is associated with a high adverse outcome. Thus, Flu/RSV coinfections should be increasingly appreciated and given appropriate management.

Risk factors for the development of post-infectious bronchiolitis obliterans after Mycoplasma pneumoniae pneumonia in the era of increasing macrolide resistance

BackgroundThe prevalence of macrolide-resistant Mycoplasma pneumoniae (MP) pneumonia has been rapidly increased. MP pneumonia is a risk factor for the development of post-infectious bronchiolitis obliterans (PIBO). The aim of the present study was to identify the risk factors for the development of PIBO after MP pneumonia in the era of increasing macrolide resistance of MP. Materials and methodsThis retrospective study enrolled 150 children with a mean age of 6.0 years admitted to the hospital due to MP pneumonia between May 2019 and February 2020 at a tertiary hospital. The clinical, radiologic, and laboratory data were obtained using retrospective chart review. ResultsEighteen children (12%) were diagnosed with PIBO after MP pneumonia. PIBO was diagnosed after a mean duration of 100.0 days (range, 6–268 days) from symptom onset. The respiratory virus co-infection (adjusted odds ratio [aOR], 4.069; 95% confidence interval [95% CI], 1.224–13.523), adenovirus co-infection (aOR, 5.607; 95% CI, 1.801–17.454), longer duration between symptom onset and admission (aOR, 1.150; 95% CI, 1.020–1.298), higher levels of serum lactate dehydrogenase (LDH) at the time of admission (aOR, 1.001; 95% CI, 1.000–1.003), and poor response to stepwise treatment increased the risk for development of PIBO after MP pneumonia. However, macrolide resistance of MP was not associated with development of PIBO after MP pneumonia. ConclusionThe present study suggests that respiratory virus co-infection, including adenovirus, poor response to the treatment of MP pneumonia, and higher levels of serum LDH, but not macrolide resistance of MP, are risk factors of PIBO after MP pneumonia.

Clinical Impact of Combined Viral and Bacterial Infection in Pediatric Mycoplasmal Community-Acquired Pneumonia in Western China

Community-acquired pneumonia (CAP) refers to an infection contracted outside the hospital that leads to lung parenchyma inflammation. The clinical characteristics of Mycoplasma pneumoniae (M. pneumoniae) infection in CAP patients were rarely reported. The aim of this study was to describe the clinical characteristic and the impact of co-infections of M. pneumoniae with viral and bacterial pathogens in hospitalized children with CAP in Liuzhou, China. This study retrospects children diagnosed with CAP due to M. pneumoniae infection at a tertiary maternal and child health care hospital. Data related to co-infection pathogens, demographics, clinical characteristics, and hospitalization cost were collected from the electronic medical system in this hospital. A total of 983 children were diagnosed with mycoplasmal CAP in 2017. Among them, 18.2% had a bacterial-M. pneumoniae co-infection and 11.3% had a viral-M. pneumoniae co-infection. The highest infection rate of M. pneumoniae was 19.1% in February and March, while the highest rates of bacterial-M. pneumoniae and viral-M. pneumoniae co-infections were 3.6% in December and 2.3% in January, respectively. The prevalence of coughing and wheezing had significant differences between the bacterial- or viral-M. pneumoniae co-infections and the mono-infection groups. Furthermore, the chest X-ray progression, pleural effusions, respiratory failure, and ventilation rates were higher in the respiratory viral- and bacterial-M. pneumoniae co-infection groups than in the mono-infection group. Children with a bacterial or respiratory viral co-infection had a longer hospitalization and spent more on treatment fees than those with a M. pneumoniae mono-infection (P value &lt;0.001). We conclude that children with mycoplasmal CAP, either with a bacterial or viral co-infection, who show signs of coughing and wheezing and have a radiographic progression, will have a severe disease progression and should be specifically treated and managed.

High incidence and characteristic of PRRSV and resistant bacterial Co-Infection in pig farms

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and resistant bacterial co-infection is a serious threat to pig farms. This study was aimed to determine the characteristics of the co-infection of PRRSV with resistant bacterial strains in pig farms. The presence of the PRRSV orf5 gene was confirmed by RT-PCR from 395 samples. Bacterial strains were isolated from PRRSV positive samples. Antimicrobial drug susceptibility was determined by the Kirby-Bauer method. Resistant genes were determined by PCR amplification and sequencing. The whole genome of carbapenems resistant E.coli was sequenced and analyse. A total of 75 samples were PRRSV positive, and 45 different orf5 sequences were finally determined. Phylogenetic analysis showed that 45 sequences are clustered into four groups, including JXA1-like, NADC30-like, GD-QY2-like, and CH-1a-like viruses. Twenty-one samples were identified with PRRSV and amoxicillin resistance bacterial co-infection, and 23 were found with amoxicillin resistance (including 15 Escherichia coli, 3 Klebsiella pneumoniae, 2 Haemophilus parasuis, 1 Actinobacillus pleuropneumoniae, 1 Pasteurella multocida, and 1 Proteus mirabilis). All bacterial strains were resistant to the most commonantibiotics and were carriers of a large number of resistance genes. Whole-genome sequencing of E. coli ScEc7 yielded 113 scaffolds of genome DNA, one IncX3 plasmid pScEc7-NDM-5 (46,161 bp) and one IncF plasmid pScEc7-CTX-M (129,978 bp). It carries19 resistance genes, 8 virulence factors, and several mobile genetic elements. The results obtained let us to concluded that: (1) Co-infection is common in pig farms. (2) The orf5 gene continues to undergo its sequences divergence. (3) The bacterial carrying diverse resistance genes were resistant to most of the commonly used antibiotics. (4) Carbapenems resistant isolate has a large number of resistance genes, virulence factors, and MGEs. Therefore, continuous study of the characteristic of PRRSV and resistant bacterial co-infection is necessary for healthy pig aquaculture.

Derivation and Validation of a Predictive Score for Disease Worsening in Patients with COVID-19.

The prospective observational cohort study COMPASS-COVID-19 aimed to develop a risk assessment model for early identification of hospitalized COVID-19 patients at risk for worsening disease. Patients with confirmed COVID-19 ( n = 430) hospitalized between March 18 and April 21, 2020 were divided in derivation ( n = 310) and validation ( n = 120) cohorts. Two groups became evident: (1) good prognosis group (G-group) with patients hospitalized at the conventional COVID-19 ward and (2) Worsening disease group (W-group) with patients admitted to the intensive care unit (ICU) from the emergency departments. The study end point was disease worsening (acute respiratory failure, shock, myocardial dysfunction, bacterial or viral coinfections, and acute kidney injury) requiring ICU admission. All patients were routinely evaluated for full blood count, prothrombin time, fibrinogen, D-dimers, antithrombin (AT), and protein C activity. Data from the first hospitalization day at the conventional ward or the ICU were analyzed. Cardiovascular risk factors and comorbidities were routinely registered. Obesity, hypertension, diabetes and male gender, increased fibrinogen and D-dimers, thrombocytopenia, AT deficiency, lymphopenia, and an International Society on Thrombosis and Haemostasis (ISTH) score for compensated disseminated intravascular coagulation score (cDIC-ISTH) ≥ 5 were significant risk factors for worsening disease. The COMPASS-COVID-19 score was derived from multivariate analyses and includes obesity, gender, hemoglobin, lymphocyte, and the cDIC-ISTH score (including platelet count, prothrombin time, D-dimers, AT, and protein C levels). The score has a very good discriminating capacity to stratify patients at high and low risk for worsening disease, with an area under the receiver operating characteristic curve value of 0.77, a sensitivity of 81%, and a specificity of 60%. Application of the COMPASS-COVID-19 score at the validation cohort showed 96% sensitivity. The COMPASS-COVID-19 score is an accurate clinical decision-making tool for an easy identification of COVID-19 patients being at high risk for disease worsening.

Presumed respiratory syncytial virus and severe acute respiratory syndrome coronavirus-2 co-infection in a critically ill infant: Diagnostic uncertainty and emergency management.

Presumed respiratory syncytial virus and severe acute respiratory syndrome coronavirus-2 co-infection in a critically ill infant: Diagnostic uncertainty and emergency management.

Respiratory viral coinfection in a birth cohort of infants in rural Nepal.

BackgroundAcute respiratory illnesses are a leading cause of global morbidity and mortality in children. Coinfection with multiple respiratory viruses is common. Although the effects of each virus have been studied individually, the impacts of coinfection on disease severity are less understood.MethodsA secondary analysis was performed of a maternal influenza vaccine trial conducted between 2011 and 2014 in Nepal. Prospective weekly household‐based active surveillance of infants was conducted from birth to 180 days of age. Mid‐nasal swabs were collected and tested for respiratory syncytial virus (RSV), rhinovirus, influenza, human metapneumovirus (HMPV), coronavirus, parainfluenza (HPIV), and bocavirus by RT‐PCR. Coinfection was defined as the presence of two or more respiratory viruses detected as part of the same illness episode.ResultsOf 1730 infants with a respiratory illness, 327 (19%) had at least two respiratory viruses detected in their primary illness episode. Of 113 infants with influenza, 23 (20%) had coinfection. Of 214 infants with RSV, 87 (41%) had coinfection. The cohort of infants with coinfection had increased occurrence of fever lasting ≥ 4 days (OR 1.4, 95% CI: 1.1, 2.0), and so did the subset of coinfected infants with influenza (OR 5.8, 95% CI: 1.8, 18.7). Coinfection was not associated with seeking further care (OR 1.1, 95% CI: 0.8, 1.5) or pneumonia (OR 1.2, 95% CI: 0.96, 1.6).ConclusionA high proportion of infants had multiple viruses detected. Coinfection was associated with greater odds of fever lasting for four or more days, but not with increased illness severity by other measures.

Dynamics and predisposition of respiratory viral co-infections in children and adults

ObjectivesThe epidemiology of respiratory co-infection pairings is poorly understood. Here we assess the dynamics of respiratory viral co-infections in children and adults and determine predisposition for or against specific viral pairings. MethodsOver five respiratory seasons from 30 November 2013 through 6 June 2018, the mono-infection and co-infection prevalence of 13 viral pathogens was tabulated at The Cleveland Clinic. Employing a model to proportionally distribute viral pairs using individual virus co-infection rate with prevalence patterns of concurrent co-circulating viruses, we compared predicted occurrence with observed occurrence of 132 viral pairing permutations using binomial analysis. ResultsOf 30 535 respiratory samples, 9843 (32.2%) were positive for at least one virus and 1018 (10.8%) of these were co-infected. Co-infected samples predominantly originated from children. Co-infection rate in paediatric population was 35.0% (2068/5906), compared with only 5.8% (270/4591) in adults. Adenovirus C (ADVC) had the highest co-infection rate (426/623, 68.3%) while influenza virus B had the lowest (55/546, 10.0%). ADVC–rhinovirus (HRV), respiratory syncytial virus A (RSVA)–HRV and RSVB–HRV pairings occurred at significantly higher frequencies than predicted by the proportional distribution model (p < 0.05). Additionally, several viral pairings had fewer co-infections than predicted by our model: notably metapneumovirus (hMPV)–parainfluenza virus 3, hMPV–RSVA and RSVA–RSVB. ConclusionsThis is one of the largest studies on respiratory viral co-infections in children and adults. Co-infections are substantially more common in children, especially under 5 years of age, and the most frequent pairings occurred at a higher frequency than would be expected by random. Specific pairings occur at altered rates compared with those predicted by proportional distribution, suggesting either direct or indirect interactions result between specific viral pathogens.

Assessment of immunodeficiency scoring index performance in enterovirus/rhinovirus respiratory infection after allogeneic hematopoietic stem cell transplantation.

Enterovirus/rhinoviruses (EvRh) are the most common cause of respiratory virus infections in recipients of allogeneic stem cell transplantation (allo-HSCT). We sought to analyze the value of the immunodeficiency scoring index (ISI) in predicting lower respiratory tract disease (LRTD) progression and mortality in a prospective cohort of consecutive adult (>16years) allo-HSCT recipients with EvRh infection from December 1 2013 to December 1 2019 at two Spanish transplant centers. We included 234 allo-HSCT recipients with 383 EvRh episodes. Out of 383 EvRh episodes, 98 (25%) had LRTD. Multivariate logistic regression analysis identified three independent factors associated with LRTD progression: Ig G<400mg/dL, community-acquired respiratory virus (CARV) co-infection and high-risk ISI. Inclusion of Ig G levels and CARV co-infection in the ISI improved its performance by significantly increasing the area under the receiver operator characteristic curve (AUROC) from 0.643 to 0.734 (P=.03). Likewise, the two conditions identified by multivariate analyses as associated with higher probability of mortality were high-risk ISI and EvRh infection within 6months after transplant. Our findings confirm the value of high-risk ISI in predicting both probability of EvRh LRTD and 3-month overall mortality. We also demonstrate that the original ISI could be adapted to other CARV types by including additional variables to improve its performance.

Pathology and Pathogenesis of SARS-CoV-2 Associated with Fatal Coronavirus Disease, United States.

An ongoing pandemic of coronavirus disease (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Characterization of the histopathology and cellular localization of SARS-CoV-2 in the tissues of patients with fatal COVID-19 is critical to further understand its pathogenesis and transmission and for public health prevention measures. We report clinicopathologic, immunohistochemical, and electron microscopic findings in tissues from 8 fatal laboratory-confirmed cases of SARS-CoV-2 infection in the United States. All cases except 1 were in residents of long-term care facilities. In these patients, SARS-CoV-2 infected epithelium of the upper and lower airways with diffuse alveolar damage as the predominant pulmonary pathology. SARS-CoV-2 was detectable by immunohistochemistry and electron microscopy in conducting airways, pneumocytes, alveolar macrophages, and a hilar lymph node but was not identified in other extrapulmonary tissues. Respiratory viral co-infections were identified in 3 cases; 3 cases had evidence of bacterial co-infection.

Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area

There is limited information describing the presenting characteristics and outcomes of US patients requiring hospitalization for coronavirus disease 2019 (COVID-19). To describe the clinical characteristics and outcomes of patients with COVID-19 hospitalized in a US health care system. Case series of patients with COVID-19 admitted to 12 hospitals in New York City, Long Island, and Westchester County, New York, within the Northwell Health system. The study included all sequentially hospitalized patients between March 1, 2020, and April 4, 2020, inclusive of these dates. Confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by positive result on polymerase chain reaction testing of a nasopharyngeal sample among patients requiring admission. Clinical outcomes during hospitalization, such as invasive mechanical ventilation, kidney replacement therapy, and death. Demographics, baseline comorbidities, presenting vital signs, and test results were also collected. A total of 5700 patients were included (median age, 63 years [interquartile range {IQR}, 52-75; range, 0-107 years]; 39.7% female). The most common comorbidities were hypertension (3026; 56.6%), obesity (1737; 41.7%), and diabetes (1808; 33.8%). At triage, 30.7% of patients were febrile, 17.3% had a respiratory rate greater than 24 breaths/min, and 27.8% received supplemental oxygen. The rate of respiratory virus co-infection was 2.1%. Outcomes were assessed for 2634 patients who were discharged or had died at the study end point. During hospitalization, 373 patients (14.2%) (median age, 68 years [IQR, 56-78]; 33.5% female) were treated in the intensive care unit care, 320 (12.2%) received invasive mechanical ventilation, 81 (3.2%) were treated with kidney replacement therapy, and 553 (21%) died. As of April 4, 2020, for patients requiring mechanical ventilation (n = 1151, 20.2%), 38 (3.3%) were discharged alive, 282 (24.5%) died, and 831 (72.2%) remained in hospital. The median postdischarge follow-up time was 4.4 days (IQR, 2.2-9.3). A total of 45 patients (2.2%) were readmitted during the study period. The median time to readmission was 3 days (IQR, 1.0-4.5) for readmitted patients. Among the 3066 patients who remained hospitalized at the final study follow-up date (median age, 65 years [IQR, 54-75]), the median follow-up at time of censoring was 4.5 days (IQR, 2.4-8.1). This case series provides characteristics and early outcomes of sequentially hospitalized patients with confirmed COVID-19 in the New York City area.

RETRACTED: Co infection of respiratory syncytial viruses (RSV) and Streptococcus pneumonia modulates pathogenesis and dependent of serotype and phase variant

Streptococcus pneumoniae (pneumococcus) is touted to be the generally found pathogen in patients with respiratory issues and there is an epidemiologic linkage present between Respiratory syncytial virus (RSV). This study aim at investigating the interaction between RSV and two serotypes of S. pneumoniae using a distinct animal model and a well-established colonizing pneumococcal strain. Phase variants phenotype of each strain was determined under oblique light. Co infection model was developed using BALB/c mice housed in a BSL-2 facility. Coinfection experiments were performed and number of bacterial colonies was quantified and phase determination was evaluated. RSV was detected in sample through real-time quantitative PCR. Adherence assays were performed to determine adherence of Spn strains and its knock out ΔNanA to nasopharyngeal carcinoma (NPC) epithelial CNE3 cell line. The biofilm viability was determined and phase composition was counted using plate count. Neuraminidase activity was measured in fluorometircassessed using 2'-(4-methylumbelliferyl)-α-D-N-acetylneuraminic acid (MUAN) as substrate as described in earlier literature. The GraphPad Software version 5.01 i.e., GraphPad Prism was used to conduct the statistical analysis. The extent of bacterial colonization was increased significantly (p<0.05), when the mice were co infected. Nasal epithelium remained intact in mock sample with features of a thick mucociliary border. A small percentage of pneumococci exhibit phase variation between opaque phase and transparent phase. The percentage adherent of both phase were not found to be varying significantly within serotype but it was seen that nonpathogenic type 27 was more adherent. Biofilm formation was selectively more for transparent phase from a mixed-phase inoculum. Adherence of both phase variant of S. pneumoniae to nasopharyngeal epithelial cells 2h post infection expressed as the percentage of adherent bacteria relative to the inoculum. In absence of viral infection, the nasal colonization of the opaque and the transparent variant was increased many folds, which was a significant differences. The extent of nasal colonization by the ΔNanA mutant strain were significantly reduced post-bacterial infection for both type of wild-type (P<0.05). The findings explore insights into the interactions occurring between S. pneumoniae and RSV during respiratory infections and pneumococcal acquisition, indicate that pneumococcal serotypes have different ability to cause infection as well as co infections and potentially follow an unappreciated mechanism. Much more research work is needed to further understand the minutiae of this interaction within co-infection process.

Respiratory Virus Co-infection in Acute Respiratory Infections in Children.

Purpose of ReviewThis investigation aims to understand the role and burden of viral co-infections for acute respiratory illnesses in children. Co-infection can be either viral-viral or viral-bacterial and with new technology there is more information on the role they play on the health of children.Recent FindingsWith the proliferation of multiplex PCR for rapid diagnosis of multiple viruses as well as innovations on identification of bacterial infections, research has been attempting to discover how these co-infections affect each other and the host. Studies are aiming to discern if the epidemiology of viruses seen at a population level is related to the interaction between different viruses on a host level. Studies are also attempting to discover the burden of morbidity and mortality of these viral-viral co-infections on the pediatric population. It is also becoming important to understand the interplay of certain viruses with specific bacteria and understanding the impact of viral-bacterial co-infections.SummaryRSV continues to contribute to a large burden of disease for pediatric patients with acute respiratory illnesses. However, recent literature suggests that viral-viral co-infections do not add to this burden and might, in some cases, be protective of severe disease. Viral-bacterial co-infections, on the other hand, are most likely adding to the burden of morbidity in pediatric patients because of the synergistic way they can infect the nasopharyngeal space. Future research needs to focus on confirming these conclusions as it could affect hospital cohorting, role of molecular testing, and therapeutic interventions.