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BACKGROUND: The U.S. mpox outbreak in 2022 introduced new and exacerbated existing challenges that disproportionately stigmatize gay, bisexual, and other sexual minoritized men (GBSMM). This study contextualizes the perceptions, susceptibility, and lived experiences of the mpox outbreak among GBSMM in the U.S. using an intersectional framework. METHODS: Between September 2022 to February 2023, we conducted 33 semi-structured qualitative interviews with purposively sampled GBSMM in the Northeast and the South region of the United States on various aspects related to their experience during the mpox outbreak. RESULTS: We identified four themes: (1) understanding and conceptualizations of mpox, (2) mpox vaccine availability and accessibility, (3) mpox vaccine hesitancy and mistrust, and (4) call to action and recommendations. GBSMM collectively discussed the elevated mpox stigmatization and homophobic discourse from mainstream social media and news outlets. GBSMM also discussed the lack of availability of mpox vaccines, unclear procedures to receive the vaccine, and continued mistrust in government, non-government, and other institutions of health that were complicit in anti-LGBTQ + narratives related to mpox. However, they expressed that these challenges may be addressed through more LGTBQ + representation and leveraging ways to empower these communities. CONCLUSION: GBSMM have mpox experiences that are distinct and multifaceted. Effectively addressing mpox and mitigating public health emergencies for GBSMM requires prioritizing destigmatizing communication channels and vaccine distribution strategies by centering their stories and lived experiences to advance health equity.
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Brotes de Enfermedades , Homosexualidad Masculina , Mpox , Investigación Cualitativa , Minorías Sexuales y de Género , Adolescente , Adulto , Humanos , Masculino , Adulto Joven , Brotes de Enfermedades/prevención & control , Homosexualidad Masculina/psicología , Homosexualidad Masculina/estadística & datos numéricos , Entrevistas como Asunto , Minorías Sexuales y de Género/psicología , Estados UnidosRESUMEN
BACKGROUND: Sexual minority cisgender men and transgender (SMMT) individuals, particularly emerging adults (aged 18-34 years), often report hazardous drinking. Given that alcohol use increases the likelihood of HIV risk behaviors, and HIV disproportionately affects SMMT individuals, there is a need to test interventions that reduce hazardous alcohol use and subsequent HIV risk behaviors among this population. Ecological momentary interventions (EMIs), which use mobile phones to deliver risk reduction messages based on current location and behaviors, can help to address triggers that lead to drinking in real time. OBJECTIVE: This study will test an EMI that uses motivational interviewing (MI), smartphone surveys, mobile breathalyzers, and location tracking to provide real-time messaging that addresses triggers for drinking when SMMT individuals visit locations associated with hazardous alcohol use. In addition, the intervention will deliver harm reduction messaging if individuals report engaging in alcohol use. METHODS: We will conduct a 3-arm randomized controlled trial (N=405 HIV-negative SMMT individuals; n=135, 33% per arm) comparing the following conditions: (1) Tracking and Reducing Alcohol Consumption (a smartphone-delivered 4-session MI intervention), (2) Tracking and Reducing Alcohol Consumption and Environmental Risk (an EMI combining MI with real-time messaging based on geographic locations that are triggers to drinking), and (3) a smartphone-based alcohol monitoring-only control group. Breathalyzer results and daily self-reports will be used to assess the primary and secondary outcomes of drinking days, drinks per drinking day, binge drinking episodes, and HIV risk behaviors. Additional assessments at baseline, 3 months, 6 months, and 9 months will evaluate exploratory long-term outcomes. RESULTS: The study is part of a 5-year research project funded in August 2022 by the National Institute on Alcohol Abuse and Alcoholism. The first 1.5 years of the study will be dedicated to planning and development activities, including formative research, app design and testing, and message design and testing. The subsequent 3.5 years will see the study complete participant recruitment, data collection, analyses, report writing, and dissemination. We expect to complete all study data collection in or before January 2027. CONCLUSIONS: This study will provide novel evidence about the relative efficacy of using a smartphone-delivered MI intervention and real-time messaging to address triggers for hazardous alcohol use and sexual risk behaviors. The EMI approach, which incorporates location-based preventive messaging and behavior surveys, may help to better understand the complexity of daily stressors among SMMT individuals and their impact on hazardous alcohol use and HIV risk behaviors. The tailoring of this intervention toward SMMT individuals helps to address their underrepresentation in existing alcohol use research and will be promising for informing where structural alcohol use prevention and treatment interventions are needed to support SMMT individuals. TRIAL REGISTRATION: ClinicalTrials.gov NCT05576350; https://www.clinicaltrials.gov/study/NCT05576350. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/55166.
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Respiratory syncytial virus (RSV) is a common cause of respiratory infections, causing significant morbidity and mortality, especially in young children. Why RSV infection in children is more severe as compared to healthy adults is not fully understood. In the present study, we infect both pediatric and adult human nose organoid-air liquid interface (HNO-ALIs) cell lines with two contemporary RSV isolates and demonstrate how they differ in virus replication, induction of the epithelial cytokine response, cell injury, and remodeling. Pediatric HNO-ALIs were more susceptible to early RSV replication, elicited a greater overall cytokine response, demonstrated enhanced mucous production, and manifested greater cellular damage compared to their adult counterparts. Adult HNO-ALIs displayed enhanced mucus production and robust cytokine response that was well controlled by superior regulatory cytokine response and possibly resulted in lower cellular damage than in pediatric lines. Taken together, our data suggest substantial differences in how pediatric and adult upper respiratory tract epithelium responds to RSV infection. These differences in epithelial cellular response can lead to poor mucociliary clearance and predispose infants to a worse respiratory outcome of RSV infection.
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Background: Respiratory viral infections are common in febrile infants ≤90 days. However, the detection of viruses other than enterovirus in the blood and cerebrospinal fluid (CSF) of young infants is not well defined. We sought to quantify the occurrence of respiratory viruses in the blood and CSF of febrile infants ≤90 days. Methods: We conducted a nested cohort study examining plasma and CSF samples from febrile infants 15-90 days via rtPCR. The samples were tested for respiratory viruses (respiratory syncytial virus, influenza, enterovirus, parechovirus, adenovirus, bocavirus). Clinical and laboratory data were also collected to determine the presence of serious bacterial infections (SBI). Results: Twenty-four percent (30 of 126) of infants had plasma/CSF specimens positive for a respiratory virus. Enterovirus and parechovirus were the most commonly detected respiratory viruses. Viral positivity was highest in plasma samples at 25% (27 of 107) compared with CSF samples at 15% (nine of 62). SBIs (specifically urinary tract infections) were less common in infants with a sample positive for a respiratory virus compared to those without a virus detected (3% vs. 26%, p = 0.008). Conclusions: Our findings support the use of molecular diagnostics to include the identification of parechovirus in addition to enterovirus in febrile infants ≤90 days. Additionally, these data support the utilization of blood specimens to diagnose enterovirus and parechovirus infections in febrile infants ≤90 days.
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Infecciones por Enterovirus , Enterovirus , Infecciones por Picornaviridae , Virus Sincitial Respiratorio Humano , Virus , Lactante , Humanos , Estudios de Cohortes , Virus/genética , Infecciones por Enterovirus/epidemiología , Enterovirus/genética , Antígenos Virales , Fiebre/diagnóstico , Infecciones por Picornaviridae/epidemiologíaRESUMEN
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
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Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
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BACKGROUND: Studies suggest infants may be at increased risk of severe coronavirus disease 2019 (COVID-19) relative to older children, but few data exist regarding the incidence of COVID-19 episodes and associated risk factors. We estimate incidence rates and describe characteristics associated with medically attended COVID-19 episodes among infants younger than 6 months of age. METHODS: We analyzed electronic medical record data from a cohort of infants born March 1, 2020-February 28, 2021. Data from 3 health care delivery systems included demographic characteristics, maternal and infant outpatient visit and hospitalization diagnoses and severe acute respiratory syndrome coronavirus syndrome 2 (SARS-CoV-2) test results. Medically attended COVID-19 episodes were defined by positive SARS-CoV-2 clinical tests and/or COVID-19 diagnosis codes during medical care visits. Unadjusted and site-adjusted incidence rates by infant month of age, low and high SARS-CoV-2 circulation periods and maternal COVID-19 diagnosis were calculated. RESULTS: Among 18,192 infants <6 months of age whose mothers received prenatal care within the 3 systems, 173 (1.0%) had medically attended COVID-19 episodes. Incidence rates were highest among infants under 1 month of age (2.0 per 1000 person-weeks) and 1 month (2.0 per 1000 person-weeks) compared with older infants. Incidence rates were also higher for infants born to women with postpartum COVID-19 compared with women without known COVID-19 and women diagnosed with COVID-19 during pregnancy. CONCLUSIONS: Infants of women with postpartum COVID-19 had a higher risk of medically attended COVID-19 than infants born to mothers who were diagnosed during pregnancy or never diagnosed underscoring the importance of COVID-19 prevention measures for their household members and caregivers to prevent infections in infants.
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COVID-19 , Complicaciones Infecciosas del Embarazo , Embarazo , Niño , Lactante , Humanos , Femenino , Adolescente , Recién Nacido , COVID-19/epidemiología , Incidencia , SARS-CoV-2 , Prueba de COVID-19 , Factores de Riesgo , Complicaciones Infecciosas del Embarazo/prevención & controlRESUMEN
BACKGROUND: Identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during peripartum hospitalizations is important to guide care, implement prevention measures, and understand infection burden. METHODS: This cross-sectional analysis used electronic health record data from hospitalizations during which pregnancies ended (peripartum hospitalizations) among a cohort of pregnant persons at 3 US integrated healthcare networks (sites 1-3). Maternal demographic, medical encounter, SARS-CoV-2 testing, and pregnancy and neonatal outcome information was extracted for persons with estimated delivery and pregnancy end dates during March 2020-February 2021 and ≥1 antenatal care record. Site-stratified multivariable logistic regression was used to identify factors associated with testing and compare pregnancy and neonatal outcomes among persons tested. RESULTS: Among 17 858 pregnant persons, 10 863 (60.8%) had peripartum SARS-CoV-2 testing; 222/10 683 (2.0%) had positive results. Testing prevalence varied by site and was lower during March-May 2020. Factors associated with higher peripartum SARS-CoV-2 testing odds were Asian race (adjusted odds ratio [aOR]: 1.36; 95% confidence interval [CI]: 1.03-1.79; referent: White) (site 1), Hispanic or Latino ethnicity (aOR: 1.33; 95% CI: 1.08-1.64) (site 2), peripartum Medicaid coverage (aOR: 1.33; 95% CI: 1.06-1.66) (site 1), and preterm hospitalization (aOR: 1.69; 95% CI: 1.19-2.39 [site 1]; aOR: 1.39; 95% CI: 1.03-1.88 [site 2]). CONCLUSIONS: Findings highlight potential disparities in SARS-CoV-2 peripartum testing by demographic and pregnancy characteristics. Testing practice variations should be considered when interpreting studies relying on convenience samples of pregnant persons testing positive for SARS-CoV-2. Efforts to address testing differences between groups could improve equitable testing practices and care for pregnant persons with SARS-CoV-2 infections.
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COVID-19 , Complicaciones Infecciosas del Embarazo , Recién Nacido , Femenino , Embarazo , Humanos , SARS-CoV-2 , COVID-19/diagnóstico , COVID-19/epidemiología , Prueba de COVID-19 , Estudios Transversales , Periodo Periparto , Complicaciones Infecciosas del Embarazo/diagnóstico , Complicaciones Infecciosas del Embarazo/epidemiología , HospitalizaciónRESUMEN
Background: Coronavirus-2019 (COVID-19) is known to affect the heart and is associated with a pro-inflammatory state. Most studies to date have focused on clinically sick subjects. Here, we report cardiac and proinflammatory biomarkers levels in ambulatory young adults with asymptomatic or mild COVID-19 infection compared to those without infection 4-8 weeks after severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) testing. Methods: 131 asymptomatic or mildly symptomatic subjects were enrolled following testing for SARS-COV-2. Fifty subjects tested negative, and 81 subjects tested positive. Serum samples were collected for measurement of C-reactive protein, ferritin, interleukin-6, NT-pro-B-type natriuretic peptide, and cardiac troponin 28-55 days after SARS-COV-2 RT-PCR testing. Results: Biomarker levels trended higher in SARS-COV-2-positive vs negative subjects, but differences in biomarker levels or proportion of subjects with elevated biomarkers were not statistically significant with respect to SARS-COV-2 status. Among individuals with ≥ 1 comorbidity, odds of elevated CRP were greater compared to individuals without any comorbidities (odds ratio [OR] = 2.90); this effect size was increased 1.4-fold among SARS-COV-2-positive subjects (OR = 4.03). Similarly, NT-pro-BNP was associated with CVD, with the strongest association in COVID-positive individuals (OR = 16.9). Conclusions: In a relatively young, healthy adult population, mild COVID-19 infection was associated with mild elevations in cardiac and proinflammatory biomarkers within 4-8 weeks of mild or asymptomatic COVID-19 infection in individuals with preexisting comorbidities, but not among individuals without comorbidities. For the general population of young adults, we did not find evidence of elevation of cardiac or proinflammatory biomarkers 4-8 weeks after COVID-19 infection.Clinical Perspective: This is a characterization of cardiac and proinflammatory biomarkers in ambulatory subjects following asymptomatic or mild COVID-19 infection. Young, ambulatory individuals did not have cardiac and proinflammatory biomarker elevation 4-8 weeks after mild COVID-19 infection. However, COVID-19 infection was associated with biomarker elevations in select individuals with comorbidities.Clinical study number: H-47423.
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Influenza testing and case-confirmation rates in pregnant populations have not been reported during the coronavirus disease 2019 (COVID-19) pandemic. Using electronic medical record data from a cohort of nearly 20,000 pregnancies in the United States, this retrospective cohort study examines the frequency of acute respiratory or febrile illness encounters, influenza testing, and influenza positivity during the 2020-2021 influenza season, which occurred during the COVID-19 pandemic, compared with the 2019-2020 influenza season, which largely did not. The ratios of influenza tests to acute respiratory or febrile illness visits were similar in the 2019-2020 and 2020-2021 influenza seasons (approximately 1:8 and 1:9, respectively) but were low and varied by study site. Although influenza testing in pregnant patients continued in the 2020-2021 season, when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulation was widespread in the United States, no cases of influenza were identified in our study cohort.
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COVID-19 , Gripe Humana , Humanos , Embarazo , Femenino , Estados Unidos/epidemiología , Gripe Humana/diagnóstico , Gripe Humana/epidemiología , Pandemias , Estaciones del Año , SARS-CoV-2 , COVID-19/epidemiología , Estudios RetrospectivosRESUMEN
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019 in Wuhan, China, and then rapidly spread causing an unprecedented pandemic. A robust serological assay is needed to evaluate vaccine candidates and better understand the epidemiology of coronavirus disease (COVID-19). Methods: We used the full-length spike (S) protein of SARS-CoV-2 for the development of qualitative and quantitative IgG and IgA anti-S enzyme linked immunosorbent assays (ELISA). A total of 320 sera used for assay development were comprised of pandemic sera from SARS-CoV-2 infected adults (n=51) and pre-pandemic sera (n=269) including sera from endemic human coronavirus infected adults. Reverse cumulative curves and diagnostic test statistics were evaluated to define the optimal serum dilution and OD cutoff value for IgG anti-S and IgA anti-S ELISAs. The IgG and IgA anti-S, and three functional antibodies (ACE-2 receptor blocking antibody, lentipseudovirus-S neutralizing antibody, and SARS-CoV-2 neutralizing antibody) were measured using additional SARS-CoV-2 PCR positive sera (n=76) and surveillance sera (n=25). Lastly, the IgG and IgA anti-S levels were compared in different demographic groups. Results: The optimal serum dilution for the qualitative IgG anti-S ELISA was at 1:1024 yielding a 99.6% specificity, 92.2% sensitivity, 92.9% positive predictive value (PPV), and 99.6% negative predictive value (NPV) at a SARS-CoV-2 seroprevalence of 5%. The optimal serum dilution for the qualitative IgA anti-S ELISA was at 1:128 yielding a 98.9% specificity, 76.5% sensitivity, 78.3% PPV, and 98.8% NPV at the same seroprevalence. Significant correlations were demonstrated between the IgG and IgA (r=0.833 for concentrations, r=0.840 for titers) as well as between IgG and three functional antibodies (r=0.811-0.924 for concentrations, r=0.795-0.917 for titers). The IgG and IgA anti-S levels were significantly higher in males than females (p<0.05), and in adults with moderate/severe symptoms than in adults with mild/moderate symptoms (p<0.001). Conclusion: We developed a highly specific and sensitive IgG anti-S ELISA assay to SARS-CoV-2 using full length S protein. The IgG anti-S antibody level was strongly associated with IgA and functional antibody levels in adults with SARS-CoV-2 infection. Gender and disease severity, rather than age, play an important role in antibody levels.
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Anticuerpos Antivirales/inmunología , COVID-19/inmunología , Inmunoglobulina A/inmunología , Inmunoglobulina G/inmunología , SARS-CoV-2/inmunología , Adulto , COVID-19/diagnóstico , Prueba Serológica para COVID-19 , Femenino , Células HEK293 , HumanosRESUMEN
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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COVID-19/patología , SARS-CoV-2/genética , Análisis de Secuencia de ADN/métodos , COVID-19/virología , ADN Complementario/química , ADN Complementario/metabolismo , Frecuencia de los Genes , Variación Genética , Genoma Viral , Humanos , Sistemas de Lectura Abierta/genética , ARN Viral/genética , ARN Viral/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa , SARS-CoV-2/aislamiento & purificación , Carga ViralRESUMEN
Since the start of the SARS-CoV-2 pandemic, it has been difficult to differentiate between SARS-CoV-2 re-infection and prolonged RNA shedding. In this report, we identified patients with positive RT-PCR results for SARS-CoV-2 ≥70 days apart. Clinical and laboratory data were collected and criteria were applied to discern whether the presentation was consistent with SARS-CoV-2 re-infection or prolonged viral RNA shedding. Eleven individuals met the initial testing criteria, of which, seven met at least one criteria for re-infection and four were consistent with prolonged RNA shedding. These data demonstrate the need for criteria to differentiate SARS-CoV-2 re-infection from prolonged RNA shedding.
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COVID-19 , SARS-CoV-2 , Humanos , Pandemias , ARN Viral/genética , Reinfección , Esparcimiento de VirusRESUMEN
BACKGROUND: During the coronavirus disease 2019 pandemic, a minority of index cases are associated with a majority of secondary cases suggesting that superspreaders could drive the pandemic. We identified a phenotype in individuals with extremely high viral load who could act as superspreaders. METHODS: Data were analyzed from individuals tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from 18 March through 15 August 2020. Outcomes were compared using contingency table and quantile regression to test the equality of medians between the pandemic waves and by viral load groups. RESULTS: Of the 11 564 samples tested, 1319 (11.4%) were positive for SARS-CoV-2. An increase in weekly median viral load occurred in the second wave of the SARS-CoV2 pandemic. This population was more likely to be women, outpatients, and symptomatic and to have an extremely high or high viral load. In patients with multiple reverse-transcription polymerase chain reaction-positive test results, the durations of viral shedding were comparable between individuals with asymptomatic/mild and mild/moderate illness severity. CONCLUSIONS: We detected a small group of individuals with extremely high SARS-CoV-2 viral loads and mild illness. We believe that these individuals' characteristics could be consistent with the superspreader phenomenon and that greater awareness of the social dynamics of these individuals is needed to understand the spread of SARS-CoV-2.
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COVID-19/epidemiología , COVID-19/virología , Fenotipo , SARS-CoV-2 , Carga Viral/tendencias , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , COVID-19/diagnóstico , Prueba de Ácido Nucleico para COVID-19 , Femenino , Humanos , Masculino , Persona de Mediana Edad , ARN Viral/aislamiento & purificación , Texas/epidemiología , Esparcimiento de Virus , Adulto JovenRESUMEN
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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BACKGROUND: Molecular diagnostic methods enhance the sensitivity and broaden the spectrum of detectable respiratory viruses in febrile infants ≤90 days of life. We describe the occurrence of respiratory viruses in this population, as well as the rates of serious bacterial infection (SBI) and respiratory viral coinfection with regard to viral characteristics. METHODS: This was a prospective observational cohort study performed in the emergency department that included previously healthy febrile infants ≤90 days of life. Clinical and historical characteristics were documented, and a respiratory nasal wash specimen was obtained from each patient. This sample was tested for 17 common respiratory pathogens, and a chart review was conducted to ascertain whether the infant was diagnosed with an SBI. RESULTS: In a 12-month period, 67% of the 104 recruited febrile infants were positive for a respiratory virus. The most commonly detected viruses were rhinovirus, respiratory syncytial virus, enterovirus and influenza. The rate of respiratory viral and SBI coinfection was 9% overall, and infants with either a systemic respiratory virus or negative viral testing were 3 times more likely to have an SBI than those with viruses typically restricted to the respiratory mucosa (95% confidence interval: 1.1, 9.7). CONCLUSIONS: Respiratory viruses are readily detectable via nasopharyngeal wash in febrile infants ≤90 days of life. With the enhanced sensitivity of molecular respiratory diagnostics, rates of coinfection of respiratory viruses and SBI may be higher than previously thought. Further investigation utilizing molecular diagnostics is needed to guide usage in febrile infants ≤90 days.
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Infecciones Bacterianas/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Virosis/complicaciones , Bacterias/aislamiento & purificación , Infecciones Bacterianas/microbiología , Coinfección/epidemiología , Coinfección/microbiología , Coinfección/virología , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Estudios Prospectivos , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Medición de Riesgo , Virosis/virología , Virus/clasificación , Virus/aislamiento & purificaciónRESUMEN
PURPOSE: Respiratory syncytial virus (RSV) and influenza are important viral pathogens worldwide. Children, in particular, bear considerable burdens of morbidity and mortality associated with these viruses. There are limited therapeutic options for children infected with RSV or influenza. This review focuses on therapeutics for RSV and influenza that are currently under clinical investigation. METHODS: This study used a systematic approach to identify prospective therapeutics in clinical trials and briefly reviewed those that are currently available for use in adults and children. FINDINGS: Overall, we found 14 investigational drugs currently in clinical trials for RSV and 20 investigation drugs currently in clinical trials for influenza. These candidates range in development from Phase I to Phase III clinical trials. IMPLICATIONS: Both RSV and influenza are targets for active therapeutic research, and promising candidates for both viruses are currently in clinical development.