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1.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-332884

ABSTRACT

Prolonged infections in immunocompromised individuals may be a source for novel SARS-CoV-2 variants, particularly when both the immune system and antiviral therapy fail to clear the infection, thereby promoting adaptation. Here we describe an approximately 16-month case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual's virus was resistant to this antibody via a globally unique Spike amino acid variant (E484T) that evolved from E484A earlier in infection. With the emergence and spread of the Omicron Variant of Concern, which also contains Spike E484A, E484T may arise again as an antibody-resistant derivative of E484A.

3.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-331701

ABSTRACT

Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings and detected 106 SARS-CoV-2 positive samples, demonstrating SARS-CoV-2 can be detected in air collected from daily and weekly sampling intervals. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection in the community. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air surveillance is a scalable, cost-effective, and high throughput alternative to individual testing for detecting respiratory pathogens in congregate settings.

4.
Disaster Med Public Health Prep ; : 1-8, 2022 Mar 07.
Article in English | MEDLINE | ID: covidwho-1730191

ABSTRACT

OBJECTIVE: Respiratory illnesses, including coronavirus disease 2019 (COVID-19), have resulted in millions of deaths globally. Guidance on mask-wearing in community settings has been inconsistent. This review examined the effectiveness of mask-wearing on respiratory virus transmission in community settings. METHODS: A search was conducted for English language reports of randomized controlled trials of mask-wearing in the community and effect on laboratory-confirmed respiratory infections or influenza-like illness. Investigators abstracted study characteristics and assessed bias. Meta-analysis was conducted to calculate pooled risk estimates. RESULTS: Eleven studies were included. In 7 studies that evaluated influenza-like illness symptoms as an outcome (3029 participants), this study found mask-wearing associated with a decreased risk of influenza-like illness (overall risk ratio [RR], 0.83; 95% confidence interval [CI], 0.71 to 0.96). Studies examining laboratory-confirmed respiratory infections as an outcome (10,531 participants) showed no statistically significant association between mask-wearing and infections (RR, 1.04; 95% CI, 0.60-1.80). However, masking combined with enhanced hand hygiene was associated with a decreased risk for both influenza-like illness symptoms (RR, 0.88; 95% CI, 0.51-1.51) and laboratory-confirmed respiratory infection (RR, 0.79; 95% CI, 0.52-1.18). CONCLUSIONS: Masking in community settings decreases transmission of influenza-like illness. Mask-wearing combined with enhanced hand hygiene reduces transmission of influenza-like illness and laboratory-confirmed respiratory infection.

5.
JAMA Intern Med ; 182(2): 153-162, 2022 02 01.
Article in English | MEDLINE | ID: covidwho-1598451

ABSTRACT

Importance: Persons with immune dysfunction have a higher risk for severe COVID-19 outcomes. However, these patients were largely excluded from SARS-CoV-2 vaccine clinical trials, creating a large evidence gap. Objective: To identify the incidence rate and incidence rate ratio (IRR) for COVID-19 breakthrough infection after SARS-CoV-2 vaccination among persons with or without immune dysfunction. Design, Setting, and Participants: This retrospective cohort study analyzed data from the National COVID Cohort Collaborative (N3C), a partnership that developed a secure, centralized electronic medical record-based repository of COVID-19 clinical data from academic medical centers across the US. Persons who received at least 1 dose of a SARS-CoV-2 vaccine between December 10, 2020, and September 16, 2021, were included in the sample. Main Outcomes and Measures: Vaccination, COVID-19 diagnosis, immune dysfunction diagnoses (ie, HIV infection, multiple sclerosis, rheumatoid arthritis, solid organ transplant, and bone marrow transplantation), other comorbid conditions, and demographic data were accessed through the N3C Data Enclave. Breakthrough infection was defined as a COVID-19 infection that was contracted on or after the 14th day of vaccination, and the risk after full or partial vaccination was assessed for patients with or without immune dysfunction using Poisson regression with robust SEs. Poisson regression models were controlled for a study period (before or after [pre- or post-Delta variant] June 20, 2021), full vaccination status, COVID-19 infection before vaccination, demographic characteristics, geographic location, and comorbidity burden. Results: A total of 664 722 patients in the N3C sample were included. These patients had a median (IQR) age of 51 (34-66) years and were predominantly women (n = 378 307 [56.9%]). Overall, the incidence rate for COVID-19 breakthrough infection was 5.0 per 1000 person-months among fully vaccinated persons but was higher after the Delta variant became the dominant SARS-CoV-2 strain (incidence rate before vs after June 20, 2021, 2.2 [95% CI, 2.2-2.2] vs 7.3 [95% CI, 7.3-7.4] per 1000 person-months). Compared with partial vaccination, full vaccination was associated with a 28% reduced risk for breakthrough infection (adjusted IRR [AIRR], 0.72; 95% CI, 0.68-0.76). People with a breakthrough infection after full vaccination were more likely to be older and women. People with HIV infection (AIRR, 1.33; 95% CI, 1.18-1.49), rheumatoid arthritis (AIRR, 1.20; 95% CI, 1.09-1.32), and solid organ transplant (AIRR, 2.16; 95% CI, 1.96-2.38) had a higher rate of breakthrough infection. Conclusions and Relevance: This cohort study found that full vaccination was associated with reduced risk of COVID-19 breakthrough infection, regardless of the immune status of patients. Despite full vaccination, persons with immune dysfunction had substantially higher risk for COVID-19 breakthrough infection than those without such a condition. For persons with immune dysfunction, continued use of nonpharmaceutical interventions (eg, mask wearing) and alternative vaccine strategies (eg, additional doses or immunogenicity testing) are recommended even after full vaccination.


Subject(s)
COVID-19 Testing/statistics & numerical data , COVID-19/diagnosis , COVID-19/epidemiology , Health Status , Vaccination/statistics & numerical data , Adult , Aged , COVID-19 Vaccines , Cohort Studies , Female , Humans , Incidence , Male , Middle Aged , Retrospective Studies , Risk Factors , SARS-CoV-2/isolation & purification , Sex Distribution
6.
Infect Control Hosp Epidemiol ; 43(1): 109-113, 2022 01.
Article in English | MEDLINE | ID: covidwho-1586124

Subject(s)
COVID-19 , Humans , SARS-CoV-2
7.
Clin Infect Dis ; 73(11): e3974-e3976, 2021 12 06.
Article in English | MEDLINE | ID: covidwho-1559856

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) asymptomatic infections may play a critical role in disease transmission. We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at 2 hospital systems in 2 counties in Wisconsin. The SARS-CoV-2 prevalence was 1% or lower at both systems despite the higher incidence of coronavirus disease 2019 (COVID-19) in Milwaukee County.


Subject(s)
COVID-19 , SARS-CoV-2 , Asymptomatic Infections/epidemiology , Humans , Prevalence , Wisconsin/epidemiology
8.
Am J Infect Control ; 50(4): 459-461, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1549624

ABSTRACT

Preventing transmission of COVID-19 between healthcare workers is essential to optimize patient, employee, and organizational outcomes. We used a systems engineering approach to analyze contact tracing interviews from a cluster of COVID-19 at our healthcare institution and identified modifiable and non-modifiable causes of transmission. Similar work system analyses may be useful to institutions in identifying multiple factors contributing to infection clusters among healthcare workers, and in developing layered infection prevention methods to further reduce transmission.


Subject(s)
COVID-19 , SARS-CoV-2 , Health Personnel , Humans , Infectious Disease Transmission, Patient-to-Professional , Systems Analysis
9.
Non-conventional in English | [Unspecified Source], Grey literature | ID: grc-750514

ABSTRACT

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.

10.
N Engl J Med ; 385(25): e90, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-1434203

ABSTRACT

BACKGROUND: The prioritization of U.S. health care personnel for early receipt of messenger RNA (mRNA) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (Covid-19), allowed for the evaluation of the effectiveness of these new vaccines in a real-world setting. METHODS: We conducted a test-negative case-control study involving health care personnel across 25 U.S. states. Cases were defined on the basis of a positive polymerase-chain-reaction (PCR) or antigen-based test for SARS-CoV-2 and at least one Covid-19-like symptom. Controls were defined on the basis of a negative PCR test for SARS-CoV-2, regardless of symptoms, and were matched to cases according to the week of the test date and site. Using conditional logistic regression with adjustment for age, race and ethnic group, underlying conditions, and exposures to persons with Covid-19, we estimated vaccine effectiveness for partial vaccination (assessed 14 days after receipt of the first dose through 6 days after receipt of the second dose) and complete vaccination (assessed ≥7 days after receipt of the second dose). RESULTS: The study included 1482 case participants and 3449 control participants. Vaccine effectiveness for partial vaccination was 77.6% (95% confidence interval [CI], 70.9 to 82.7) with the BNT162b2 vaccine (Pfizer-BioNTech) and 88.9% (95% CI, 78.7 to 94.2) with the mRNA-1273 vaccine (Moderna); for complete vaccination, vaccine effectiveness was 88.8% (95% CI, 84.6 to 91.8) and 96.3% (95% CI, 91.3 to 98.4), respectively. Vaccine effectiveness was similar in subgroups defined according to age (<50 years or ≥50 years), race and ethnic group, presence of underlying conditions, and level of patient contact. Estimates of vaccine effectiveness were lower during weeks 9 through 14 than during weeks 3 through 8 after receipt of the second dose, but confidence intervals overlapped widely. CONCLUSIONS: The BNT162b2 and mRNA-1273 vaccines were highly effective under real-world conditions in preventing symptomatic Covid-19 in health care personnel, including those at risk for severe Covid-19 and those in racial and ethnic groups that have been disproportionately affected by the pandemic. (Funded by the Centers for Disease Control and Prevention.).


Subject(s)
COVID-19/prevention & control , Health Personnel , /administration & dosage , Adolescent , Adult , Aged , COVID-19/diagnosis , COVID-19/ethnology , COVID-19 Serological Testing , Case-Control Studies , Female , Humans , Immunization, Secondary , Male , Middle Aged , Polymerase Chain Reaction , United States
11.
Clin Infect Dis ; 73(6): e1329-e1336, 2021 09 15.
Article in English | MEDLINE | ID: covidwho-1411883

ABSTRACT

BACKGROUND: Healthcare personnel (HCP) are at increased risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We posit that current infection control guidelines generally protect HCP from SARS-CoV-2 infection in a healthcare setting. METHODS: In this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in HCP at a major academic medical institution in the Upper Midwest of the United States between 25 March and 27 December 2020. We obtained limited epidemiological data through informal interviews and review of the electronic health record and combined this information with healthcare-associated viral sequences and viral sequences collected in the broader community to infer the most likely source of infection in HCP. RESULTS: We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or coworker (55 of 95 [57.9%]) and were genetically similar to viruses circulating concurrently in the community. We found that 10.5% of HCP infections (10 of 95) could be traced to a coworker. Strikingly, only 4.2% (4 of 95) could be traced to a patient source. CONCLUSIONS: Infections among HCP add further strain to the healthcare system and put patients, HCP, and communities at risk. We found no evidence for healthcare-associated transmission in the majority of HCP infections evaluated. Although we cannot rule out the possibility of cryptic healthcare-associated transmission, it appears that HCP most commonly become infected with SARS-CoV-2 via community exposure. This emphasizes the ongoing importance of mask wearing, physical distancing, robust testing programs, and rapid distribution of vaccines.


Subject(s)
COVID-19 , SARS-CoV-2 , Delivery of Health Care , Health Personnel , Humans , Retrospective Studies , United States/epidemiology
12.
Future Microbiol ; 16: 119-130, 2021 01.
Article in English | MEDLINE | ID: covidwho-1389070

ABSTRACT

A review of nasal sprays and gargles with antiviral properties suggests that a number of commonly used antiseptics including povidone-iodine, Listerine®, iota-carrageenan and chlorhexidine should be studied in clinical trials to mitigate both the progression and transmission of SARS-CoV-2. Several of these antiseptics have demonstrated the ability to cut the viral load of SARS-CoV-2 by 3-4 log10 in 15-30 s in vitro. In addition, hypertonic saline targets viral replication by increasing hypochlorous acid inside the cell. A number of clinical trials are in process to study these interventions both for prevention of transmission, prophylaxis after exposure, and to diminish progression by reduction of viral load in the early stages of infection.


Subject(s)
Anti-Infective Agents, Local/administration & dosage , Anti-Infective Agents, Local/therapeutic use , COVID-19/prevention & control , SARS-CoV-2/drug effects , COVID-19/transmission , Carrageenan/therapeutic use , Chlorhexidine/therapeutic use , Drug Combinations , Hydrogen Peroxide/therapeutic use , Nasal Sprays , Oils, Volatile/therapeutic use , Povidone-Iodine/therapeutic use , Salicylates/therapeutic use , Terpenes/therapeutic use , Viral Load/drug effects
13.
PLoS One ; 16(7): e0254456, 2021.
Article in English | MEDLINE | ID: covidwho-1309962

ABSTRACT

INTRODUCTION: Vaccination programs aim to control the COVID-19 pandemic. However, the relative impacts of vaccine coverage, effectiveness, and capacity in the context of nonpharmaceutical interventions such as mask use and physical distancing on the spread of SARS-CoV-2 are unclear. Our objective was to examine the impact of vaccination on the control of SARS-CoV-2 using our previously developed agent-based simulation model. METHODS: We applied our agent-based model to replicate COVID-19-related events in 1) Dane County, Wisconsin; 2) Milwaukee metropolitan area, Wisconsin; 3) New York City (NYC). We evaluated the impact of vaccination considering the proportion of the population vaccinated, probability that a vaccinated individual gains immunity, vaccination capacity, and adherence to nonpharmaceutical interventions. We estimated the timing of pandemic control, defined as the date after which only a small number of new cases occur. RESULTS: The timing of pandemic control depends highly on vaccination coverage, effectiveness, and adherence to nonpharmaceutical interventions. In Dane County and Milwaukee, if 50% of the population is vaccinated with a daily vaccination capacity of 0.25% of the population, vaccine effectiveness of 90%, and the adherence to nonpharmaceutical interventions is 60%, controlled spread could be achieved by June 2021 versus October 2021 in Dane County and November 2021 in Milwaukee without vaccine. DISCUSSION: In controlling the spread of SARS-CoV-2, the impact of vaccination varies widely depending not only on effectiveness and coverage, but also concurrent adherence to nonpharmaceutical interventions.


Subject(s)
COVID-19 Vaccines/therapeutic use , COVID-19/prevention & control , Patient Compliance/statistics & numerical data , Vaccination Coverage/statistics & numerical data , Computer Simulation , Humans , Masks , Physical Distancing , Respiratory Protective Devices/statistics & numerical data , United States , Urban Health
14.
Am J Infect Control ; 49(6): 775-783, 2021 06.
Article in English | MEDLINE | ID: covidwho-1300594

ABSTRACT

BACKGROUND: Daily use of chlorhexidine gluconate (CHG) has been shown to reduce risk of healthcare-associated infections. We aimed to assess moving CHG bathing into routine practice using a human factors approach. We evaluated implementation in non-intensive care unit (ICU) settings in the Veterans Health Administration. METHODS: Our multiple case study approach included non-ICU units from 4 Veterans Health Administration settings. Guided by the Systems Engineering Initiative for Patient Safety, we conducted focus groups and interviews to capture barriers and facilitators to daily CHG bathing. We measured compliance using observations and skin CHG concentrations. RESULTS: Barriers to daily CHG include time, concern of increasing antibiotic resistance, workflow and product concerns. Facilitators include engagement of champions and unit shared responsibility. We found shortfalls in patient education, hand hygiene and CHG use on tubes and drains. CHG skin concentration levels were highest among patients from spinal cord injury units. These units applied antiseptic using 2% CHG impregnated wipes vs 4% CHG solution/soap. DISCUSSION: Non-ICUs implementing CHG bathing must consider human factors and work system barriers to ensure uptake and sustained practice change. CONCLUSIONS: Well-planned rollouts and a unit culture promoting shared responsibility are key to compliance with daily CHG bathing. Successful implementation requires attention to staff education and measurement of compliance.


Subject(s)
Anti-Infective Agents, Local , Cross Infection , Baths , Chlorhexidine/analogs & derivatives , Cross Infection/prevention & control , Ergonomics , Humans , Intensive Care Units
15.
Mayo Clin Proc ; 96(9): 2312-2322, 2021 09.
Article in English | MEDLINE | ID: covidwho-1294050

ABSTRACT

OBJECTIVE: To identify significant factors that help predict whether health care personnel (HCP) will test positive for severe acute respiratory coronavirus 2 (SARS-CoV-2). PATIENTS AND METHODS: We conducted a prospective cohort study among 7015 symptomatic HCP from March 25, 2020, through November 11, 2020. We analyzed the associations between health care role, contact history, symptoms, and a positive nasopharyngeal swab SARS-CoV-2 polymerase chain reaction test results, using univariate and multivariable modelling. RESULTS: Of the symptomatic HCP, 624 (8.9%) were positive over the study period. On multivariable analysis, having a health care role other than physician or advanced practice provider, contact with family or community member with known or suspected coronavirus disease 2019 (COVID-19), and seven individual symptoms (cough, anosmia, ageusia, fever, myalgia, chills, and headache) were significantly associated with higher adjusted odds ratios for testing positive for SARS-CoV-2. For each increase in symptom number, the odds of testing positive nearly doubled (odds ratio, 1.93; 95% CI, 1.82 to 2.07, P<.001). CONCLUSION: Symptomatic HCP have higher adjusted odds of testing positive for SARS-CoV-2 based on three distinct factors: (1) nonphysician/advanced practice provider role, (2) contact with a family or community member with suspected or known COVID-19, and (3) specific symptoms and symptom number. Differences among health care roles, which persisted after controlling for contacts, may reflect the influence of social determinants. Contacts with COVID-19-positive patients and/or HCP were not associated with higher odds of testing positive, supporting current infection control efforts. Targeted symptom and contact questionnaires may streamline symptomatic HCP testing for COVID-19.


Subject(s)
Antibodies, Viral/analysis , COVID-19 Testing/methods , COVID-19/epidemiology , Health Personnel/statistics & numerical data , Pandemics , SARS-CoV-2/immunology , Follow-Up Studies , Humans , Prospective Studies
16.
BMJ Open ; 11(6): e046480, 2021 06 29.
Article in English | MEDLINE | ID: covidwho-1288391

ABSTRACT

INTRODUCTION: Clostridioides difficile infection (CDI) is one of the most common healthcare-associated infections in the USA, having high incidence in intensive care units (ICU). Antibiotic use increases risk of CDI, with fluoroquinolones (FQs) particularly implicated. In healthcare settings, antibiotic stewardship (AS) and infection control interventions are effective in CDI control, but there is little evidence regarding the most effective AS interventions. Preprescription authorisation (PPA) restricting FQs is a potentially promising AS intervention to reduce CDI. The FQ Restriction for the Prevention of CDI (FIRST) trial will evaluate the effectiveness of an FQ PPA intervention in reducing CDI rates in adult ICUs compared with preintervention care, and evaluate implementation effectiveness using a human-factors and systems engineering model. METHODS AND ANALYSIS: This is a multisite, stepped-wedge, cluster, effectiveness-implementation clinical trial. The trial will take place in 12 adult medical-surgical ICUs with ≥10 beds, using Epic as electronic health record (EHR) and pre-existing AS programmes. Sites will receive facilitated implementation support over the 15-month trial period, succeeded by 9 months of follow-up. The intervention comprises a clinical decision support system for FQ PPA, integrated into the site EHRs. Each ICU will be considered a single site and all ICU admissions included in the analysis. Clinical data will be extracted from EHRs throughout the trial and compared with the corresponding pretrial period, which will constitute the baseline for statistical analysis. Outcomes will include ICU-onset CDI rates, FQ days of therapy (DOT), alternative antibiotic DOT, average length of stay and hospital mortality. The study team will also collect implementation data to assess implementation effectiveness using the Systems Engineering Initiative for Patient Safety model. ETHICS AND DISSEMINATION: The trial was approved by the Institutional Review Board at the University of Wisconsin-Madison (2018-0852-CP015). Results will be made available to participating sites, funders, infectious disease societies, critical care societies and other researchers. TRIAL REGISTRATION NUMBER: NCT03848689.


Subject(s)
Clostridioides difficile , Clostridium Infections , Adult , Clostridioides , Clostridium Infections/drug therapy , Clostridium Infections/epidemiology , Clostridium Infections/prevention & control , Fluoroquinolones/therapeutic use , Humans , Intensive Care Units
17.
MMWR Morb Mortal Wkly Rep ; 70(20): 753-758, 2021 May 21.
Article in English | MEDLINE | ID: covidwho-1237005

ABSTRACT

Throughout the COVID-19 pandemic, health care personnel (HCP) have been at high risk for exposure to SARS-CoV-2, the virus that causes COVID-19, through patient interactions and community exposure (1). The Advisory Committee on Immunization Practices recommended prioritization of HCP for COVID-19 vaccination to maintain provision of critical services and reduce spread of infection in health care settings (2). Early distribution of two mRNA COVID-19 vaccines (Pfizer-BioNTech and Moderna) to HCP allowed assessment of the effectiveness of these vaccines in a real-world setting. A test-negative case-control study is underway to evaluate mRNA COVID-19 vaccine effectiveness (VE) against symptomatic illness among HCP at 33 U.S. sites across 25 U.S. states. Interim analyses indicated that the VE of a single dose (measured 14 days after the first dose through 6 days after the second dose) was 82% (95% confidence interval [CI] = 74%-87%), adjusted for age, race/ethnicity, and underlying medical conditions. The adjusted VE of 2 doses (measured ≥7 days after the second dose) was 94% (95% CI = 87%-97%). VE of partial (1-dose) and complete (2-dose) vaccination in this population is comparable to that reported from clinical trials and recent observational studies, supporting the effectiveness of mRNA COVID-19 vaccines against symptomatic disease in adults, with strong 2-dose protection.


Subject(s)
COVID-19 Vaccines/immunology , COVID-19/prevention & control , Health Personnel/statistics & numerical data , Occupational Diseases/prevention & control , Adult , Aged , COVID-19/epidemiology , COVID-19 Testing , COVID-19 Vaccines/administration & dosage , Case-Control Studies , Female , Humans , Immunization Schedule , Male , Middle Aged , Occupational Diseases/epidemiology , United States/epidemiology , Young Adult
18.
PLoS One ; 16(5): e0251170, 2021.
Article in English | MEDLINE | ID: covidwho-1218426

ABSTRACT

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.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Superinfection/epidemiology , Bacterial Infections/epidemiology , Bacterial Infections/mortality , Bacterial Infections/therapy , COVID-19/mortality , COVID-19/therapy , Coinfection/mortality , Coinfection/therapy , Hospitalization , Humans , Mycoses/epidemiology , Mycoses/mortality , Mycoses/therapy , Prevalence , SARS-CoV-2/isolation & purification , Superinfection/mortality , Superinfection/therapy , Treatment Outcome , Virus Diseases/epidemiology , Virus Diseases/mortality , Virus Diseases/therapy
20.
Ann Intern Med ; 174(1): 50-57, 2021 01.
Article in English | MEDLINE | ID: covidwho-1067967

ABSTRACT

BACKGROUND: Across the United States, various social distancing measures were implemented to control the spread of coronavirus disease 2019 (COVID-19). However, the effectiveness of such measures for specific regions with varying population demographic characteristics and different levels of adherence to social distancing is uncertain. OBJECTIVE: To determine the effect of social distancing measures in unique regions. DESIGN: An agent-based simulation model. SETTING: Agent-based model applied to Dane County, Wisconsin; the Milwaukee metropolitan (metro) area; and New York City (NYC). PATIENTS: Synthetic population at different ages. INTERVENTION: Different times for implementing and easing social distancing measures at different levels of adherence. MEASUREMENTS: The model represented the social network and interactions among persons in a region, considering population demographic characteristics, limited testing availability, "imported" infections, asymptomatic disease transmission, and age-specific adherence to social distancing measures. The primary outcome was the total number of confirmed COVID-19 cases. RESULTS: The timing of and adherence to social distancing had a major effect on COVID-19 occurrence. In NYC, implementing social distancing measures 1 week earlier would have reduced the total number of confirmed cases from 203 261 to 41 366 as of 31 May 2020, whereas a 1-week delay could have increased the number of confirmed cases to 1 407 600. A delay in implementation had a differential effect on the number of cases in the Milwaukee metro area versus Dane County, indicating that the effect of social distancing measures varies even within the same state. LIMITATION: The effect of weather conditions on transmission dynamics was not considered. CONCLUSION: The timing of implementing and easing social distancing measures has major effects on the number of COVID-19 cases. PRIMARY FUNDING SOURCE: National Institute of Allergy and Infectious Diseases.


Subject(s)
COVID-19/prevention & control , Cooperative Behavior , Physical Distancing , COVID-19/epidemiology , Computer Simulation , Humans , New York City/epidemiology , SARS-CoV-2 , United States/epidemiology , Wisconsin/epidemiology
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