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Chwa JS, Shin Y, Lee Y, Fabrizio T, Congrave-Wilson Z, Cheng WA, Jumarang J, Kim M, Webby R, Bender JM, Pannaraj PS. SARS-CoV-2 Variants May Affect Saliva RT-PCR Assay Sensitivity. J Appl Lab Med 2024:jfae095. [PMID: 39246012 DOI: 10.1093/jalm/jfae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/09/2024] [Indexed: 09/10/2024]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants demonstrate predilection for different regions of the respiratory tract. While saliva-based reverse transcription-polymerase chain reaction (RT-PCR) testing is a convenient, cost-effective alternative to nasopharyngeal swabs (NPS), few studies to date have investigated whether saliva sensitivity differs across variants of concern. METHODS SARS-CoV-2 RT-PCR was performed on paired NPS and saliva specimens collected from individuals with acute coronavirus disease 2019 (COVID-19) symptoms or exposure to a COVID-19 household contact. Viral genome sequencing of NPS specimens and Los Angeles County surveillance data were used to determine the variant of infection. Saliva sensitivity was calculated using NPS-positive RT-PCR as the reference standard. Factors contributing to the likelihood of saliva SARS-CoV-2 RT-PCR positivity were evaluated with univariate and multivariable analyses. RESULTS Between June 2020 and December 2022, 548 saliva samples paired with SARS-CoV-2 positive NPS samples were tested by RT-PCR. Overall, saliva sensitivity for SARS-CoV-2 detection was 61.7% (95% CI, 57.6%-65.7%). Sensitivity was highest with Delta infection (79.6%) compared to pre-Delta (58.5%) and Omicron (61.5%) (P = 0.003 and 0.01, respectively). Saliva sensitivity was higher in symptomatic individuals across all variants compared to asymptomatic cases [pre-Delta 80.6% vs 48.3% (P < 0.001), Delta 100% vs 72.5% (P = 0.03), Omicron 78.7% vs 51.2% (P < 0.001)]. Infection with Delta, symptoms, and high NPS viral load were independently associated with 2.99-, 3.45-, and 4.0-fold higher odds of SARS-CoV-2 detection by saliva-based RT-PCR (P = 0.004, <0.001, and <0.001), respectively. CONCLUSIONS As new variants emerge, evaluating saliva-based testing approaches may be crucial to ensure effective virus detection.
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Affiliation(s)
- Jason S Chwa
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Yunho Shin
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Yesun Lee
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Thomas Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Zion Congrave-Wilson
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Wesley A Cheng
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Jaycee Jumarang
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Minjun Kim
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Richard Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Jeffrey M Bender
- Department of Pediatrics, City of Hope Comprehensive Cancer Center, Duarte, California, United States
| | - Pia S Pannaraj
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
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Jirmanus LZ, Valenti RM, Griest Schwartzman EA, Simon-Ortiz SA, Frey LI, Friedman SR, Fullilove MT. Too Many Deaths, Too Many Left Behind: A People's External Review of the U.S. Centers for Disease Control and Prevention's COVID-19 Pandemic Response. AJPM FOCUS 2024; 3:100207. [PMID: 38770235 PMCID: PMC11103433 DOI: 10.1016/j.focus.2024.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The U.S. population has suffered worse health consequences owing to COVID-19 than comparable wealthy nations. COVID-19 had caused more than 1.1 million deaths in the U.S. as of May 2023 and contributed to a 3-year decline in life expectancy. A coalition of public health workers and community activists launched an external review of the Centers for Disease Control and Prevention's pandemic management from January 2021 to May 2023. The authors used a modified Delphi process to identify core pandemic management areas, which formed the basis for a survey and literature review. Their analysis yields 3 overarching shortcomings of the Centers for Disease Control and Prevention's pandemic management: (1) Centers for Disease Control and Prevention leadership downplays the serious impacts and aerosol transmission risks of COVID-19, (2) Centers for Disease Control and Prevention leadership has aligned public guidance with commercial and political interests over scientific evidence, and (3) Centers for Disease Control and Prevention guidance focuses on individual choice rather than emphasizing prevention and equity. Instead, the agency must partner with communities most impacted by the pandemic and encourage people to protect one another using layered protections to decrease COVID-19 transmission. Because emerging variants can already evade existing vaccines and treatments and Long COVID can be disabling and lacks definitive treatment, multifaceted, sustainable approaches to the COVID-19 pandemic are essential to protect people, the economy, and future generations.
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Affiliation(s)
- Lara Z. Jirmanus
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- People's CDC, Boston, Massachusetts
| | | | | | | | | | - Samuel R. Friedman
- People's CDC, Boston, Massachusetts
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- Center for Drug Use and HIV/HCV Research, NYU Grossman School of Public Health, New York, New York
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Vicentini C, Russotto A, Bussolino R, Castagnotto M, Gastaldo C, Bresciano L, Bazzolo S, Gamba D, Corcione S, De Rosa FG, D'Ancona F, Zotti CM. Impact of COVID-19 on healthcare-associated infections and antimicrobial use in Italy, 2022. J Hosp Infect 2024; 149:14-21. [PMID: 38677480 DOI: 10.1016/j.jhin.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND It is unknown whether COVID-19 patients are at higher risk due to demographic and clinical characteristics associated with higher COVID-19 infection risk and severity of infection, or due to the disease and its management. AIM To assess the impact of COVID-19 on healthcare-associated infection (HAI) transmission and antimicrobial use (AMU) prevalence during the later stages of the pandemic. METHODS A point-prevalence survey (PPS) was conducted among 325 acute care hospitals of 19 out of 21 Regions of Italy, during November 2022. Non-COVID-19 patients were matched to COVID-19 patients according to age, sex, and severity of underlying conditions. HAI and AMU prevalence were calculated as the percentage of patients with at least one HAI or prescribed at least one antimicrobial over all included patients, respectively. FINDINGS In total, 60,403 patients were included, 1897 (3.14%) of which were classified as COVID-19 patients. Crude HAI prevalence was significantly higher among COVID-19 patients compared to non-COVID-19 patients (9.54% vs 8.01%; prevalence rate ratio (PRR): 1.19; 95% confidence interval (CI): 1.04-1.38; P < 0.05), and remained higher in the matched sample; however, statistical significance was not maintained (odds ratio (OR): 1.25; 95% CI: 0.99-1.59; P = 0.067). AMU prevalence was significantly higher among COVID-19 patients prior to matching (46.39% vs 41.52%; PRR: 1.21; 95% CI: 1.11-1.32; P < 0.001), and significantly lower after matching (OR: 0.77; 95% CI: 0.66-0.89; P < 0.001). CONCLUSION COVID-19 patients could be at higher HAI risk due to underlying clinical conditions and the intensity of healthcare needs. Further efforts should be dedicated to antimicrobial stewardship among COVID-19 patients.
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Affiliation(s)
- C Vicentini
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy.
| | - A Russotto
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - R Bussolino
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - M Castagnotto
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - C Gastaldo
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - L Bresciano
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - S Bazzolo
- Department of Environment, Land and Infrastructure Engineering (DIATI), Politecnico of Turin, Turin, Italy
| | - D Gamba
- Department of Surgical Sciences, University of Turin, Turin, Italy
| | - S Corcione
- Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - F G De Rosa
- Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - F D'Ancona
- Epidemiology, Biostatistics and Mathematical Modeling Unit (EPI), Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - C M Zotti
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
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4
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Wei J, Lu C, Ding Y, Lu Y, Yang X, Zhang X, Tang G. Gustatory dysfunction and long COVID in Chinese patients with COVID-19: A 6-month follow-up study. Oral Dis 2024. [PMID: 38654678 DOI: 10.1111/odi.14958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/20/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
AIMS To evaluate long COVID of gustatory dysfunction and the associated risk factors regarding onset and recovery in Chinese patients. METHODS We conducted a cross-sectional study of patients with SARS-CoV-2 Omicron infection at Changxing Mobile Cabin Hospital in Shanghai, China, from March to May 2022. A prospective follow-up of patients with gustatory dysfunction was conducted at 6 months after discharge. RESULTS In total, 18.48% (241/1304) reported gustatory dysfunction. The 6-month follow-up response rate was 89.63% (216/241) and 74.02% recovered their taste sense within 1-3 weeks. A total of 20.37% of patients (44/216) presented with long COVID. Symptoms persisted for 12 patients (5.56%) after 6 months. Having multiple taste impairments (OR, 2.364; 95% CI, 1.286-4.348; p = 0.006) was associated with a higher risk of gustatory dysfunction with long COVID. Having received a COVID-19 vaccine booster was positively associated with taste sensation recovery (HR, 1.344; 95% CI, 1.012-1.785; p = 0.041). CONCLUSIONS About 20.37% of patients with COVID-19 might develop long COVID of gustatory dysfunction and 5.56% with persisting changes in their sense of taste. Most patients recovered taste sensations within 1-3 weeks after COVID-19 symptom onset and receiving a booster shot of the COVID-19 vaccine presented a protective effect on the taste sensation recovery.
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Affiliation(s)
- Jie Wei
- Department of Stomatology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenghui Lu
- Department of Stomatology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Affiliated Stomatological Hospital of Guilin Medical University, Guilin, China
| | - Yan Ding
- Department of Stomatology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongjian Lu
- Department of Stomatology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Yang
- Department of Stomatology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi Zhang
- Clinical Research Unit, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoyao Tang
- Department of Stomatology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Al Hossain F, Tonmoy MTH, Nuvvula S, Chapman BP, Gupta RK, Lover AA, Dinglasan RR, Carreiro S, Rahman T. Syndromic surveillance of population-level COVID-19 burden with cough monitoring in a hospital emergency waiting room. Front Public Health 2024; 12:1279392. [PMID: 38605877 PMCID: PMC11007176 DOI: 10.3389/fpubh.2024.1279392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Syndromic surveillance is an effective tool for enabling the timely detection of infectious disease outbreaks and facilitating the implementation of effective mitigation strategies by public health authorities. While various information sources are currently utilized to collect syndromic signal data for analysis, the aggregated measurement of cough, an important symptom for many illnesses, is not widely employed as a syndromic signal. With recent advancements in ubiquitous sensing technologies, it becomes feasible to continuously measure population-level cough incidence in a contactless, unobtrusive, and automated manner. In this work, we demonstrate the utility of monitoring aggregated cough count as a syndromic indicator to estimate COVID-19 cases. In our study, we deployed a sensor-based platform (Syndromic Logger) in the emergency room of a large hospital. The platform captured syndromic signals from audio, thermal imaging, and radar, while the ground truth data were collected from the hospital's electronic health record. Our analysis revealed a significant correlation between the aggregated cough count and positive COVID-19 cases in the hospital (Pearson correlation of 0.40, p-value < 0.001). Notably, this correlation was higher than that observed with the number of individuals presenting with fever (ρ = 0.22, p = 0.04), a widely used syndromic signal and screening tool for such diseases. Furthermore, we demonstrate how the data obtained from our Syndromic Logger platform could be leveraged to estimate various COVID-19-related statistics using multiple modeling approaches. Aggregated cough counts and other data, such as people density collected from our platform, can be utilized to predict COVID-19 patient visits related metrics in a hospital waiting room, and SHAP and Gini feature importance-based metrics showed cough count as the important feature for these prediction models. Furthermore, we have shown that predictions based on cough counting outperform models based on fever detection (e.g., temperatures over 39°C), which require more intrusive engagement with the population. Our findings highlight that incorporating cough-counting based signals into syndromic surveillance systems can significantly enhance overall resilience against future public health challenges, such as emerging disease outbreaks or pandemics.
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Affiliation(s)
- Forsad Al Hossain
- Manning College of Information and Computer Sciences, University of Massachusetts-Amherst, Amherst, MA, United States
| | - M. Tanjid Hasan Tonmoy
- Halıcıoǧlu Data Science Institute, University of California, San Diego, San Diego, CA, United States
| | - Sri Nuvvula
- Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA, United States
| | - Brittany P. Chapman
- Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA, United States
| | - Rajesh K. Gupta
- Halıcıoǧlu Data Science Institute, University of California, San Diego, San Diego, CA, United States
| | - Andrew A. Lover
- School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA, United States
| | - Rhoel R. Dinglasan
- Infectious Diseases and Immunology, University of Florida, Gainesville, FL, United States
| | - Stephanie Carreiro
- Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA, United States
| | - Tauhidur Rahman
- Halıcıoǧlu Data Science Institute, University of California, San Diego, San Diego, CA, United States
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6
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Townsley H, Gahir J, Russell TW, Greenwood D, Carr EJ, Dyke M, Adams L, Miah M, Clayton B, Smith C, Miranda M, Mears HV, Bailey C, Black JRM, Fowler AS, Crawford M, Wilkinson K, Hutchinson M, Harvey R, O’Reilly N, Kelly G, Goldstone R, Beale R, Papineni P, Corrah T, Gilson R, Caidan S, Nicod J, Gamblin S, Kassiotis G, Libri V, Williams B, Gandhi S, Kucharski AJ, Swanton C, Bauer DLV, Wall EC. COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history. PLoS One 2024; 19:e0294897. [PMID: 38512960 PMCID: PMC10956747 DOI: 10.1371/journal.pone.0294897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/11/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND SARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). METHODS In a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive polymerase chain reaction (PCR) or lateral flow test, self-swabbed on alternate weekdays until day 10. We compared participant-reported symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 or BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR cycle threshold (Ct) as a proxy for viral load using Chi-squared (χ2) and Wilcoxon tests. RESULTS 563 infection episodes were reported among 491 participants. Across infection episodes, there was little variation in symptom burden (4 [IQR 3-5] symptoms) and duration (8 [IQR 6-11] days). Whilst symptom profiles differed among infections caused by Delta compared to Omicron sub-variants, symptom profiles were similar between Omicron sub-variants. Anosmia was reported more frequently in Delta infections after 2 doses compared with Omicron sub-variant infections after 3 doses, for example: 42% (25/60) of participants with Delta infection compared to 9% (6/67) with Omicron BA.4/5 (χ2 P < 0.001; OR 7.3 [95% CI 2.7-19.4]). Fever was less common with Delta (20/60 participants; 33%) than Omicron BA.4/5 (39/67; 58%; χ2 P = 0.008; OR 0.4 [CI 0.2-0.7]). Amongst infections with an Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. PCR Ct values were negatively associated with time since vaccination in participants infected with BA.1 (β = -0.05 (CI -0.10-0.01); P = 0.031); however, this trend was not observed in BA.2 or BA.4/5 infections. CONCLUSION Our study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults. TRIAL REGISTRATION NCT04750356.
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Affiliation(s)
- Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Joshua Gahir
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | - Matala Dyke
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Murad Miah
- The Francis Crick Institute, London, United Kingdom
| | | | - Callie Smith
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
| | - James R. M. Black
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | | | | | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Gavin Kelly
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, United Kingdom
| | - Richard Gilson
- Camden and North West London NHS Community Trust, London, United Kingdom
| | - Simon Caidan
- The Francis Crick Institute, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - George Kassiotis
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St Mary’s Hospital, Imperial College London, London, United Kingdom
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
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7
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Xu T, Chen Y, Zhan W, Chung KF, Qiu Z, Huang K, Chen R, Xie J, Wang G, Zhang M, Wang X, Yao H, Liao X, Zhang Y, Zhang G, Zhang W, Sun D, Zhu J, Jiang S, Feng J, Zhao J, Sun G, Huang H, Zhang J, Wang L, Wu F, Li S, Xu P, Chi C, Chen P, Jiang M, He W, Huang L, Luo W, Li S, Zhong N, Lai K. Profiles of Cough and Associated Risk Factors in Nonhospitalized Individuals With SARS-CoV-2 Omicron Variant Infection: Cross-Sectional Online Survey in China. JMIR Public Health Surveill 2024; 10:e47453. [PMID: 38315527 PMCID: PMC10877488 DOI: 10.2196/47453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/19/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Cough is a common symptom during and after COVID-19 infection; however, few studies have described the cough profiles of COVID-19. OBJECTIVE The aim of this study was to investigate the prevalence, severity, and associated risk factors of severe and persistent cough in individuals with COVID-19 during the latest wave of the Omicron variant in China. METHODS In this nationwide cross-sectional study, we collected information of the characteristics of cough from individuals with infection of the SARS-CoV-2 Omicron variant using an online questionnaire sent between December 31, 2022, and January 11, 2023. RESULTS There were 11,718 (n=7978, 68.1% female) nonhospitalized responders, with a median age of 37 (IQR 30-47) years who responded at a median of 16 (IQR 12-20) days from infection onset to the time of the survey. Cough was the most common symptom, occurring in 91.7% of participants, followed by fever, fatigue, and nasal congestion (68.8%-87.4%). The median cough visual analog scale (VAS) score was 70 (IQR 50-80) mm. Being female (odds ratio [OR] 1.31, 95% CI 1.20-1.43), having a COVID-19 vaccination history (OR 1.71, 95% CI 1.37-2.12), current smoking (OR 0.48, 95% CI 0.41-0.58), chronic cough (OR 2.04, 95% CI 1.69-2.45), coronary heart disease (OR 1.71, 95% CI 1.17-2.52), asthma (OR 1.22, 95% CI 1.02-1.46), and gastroesophageal reflux disease (GERD) (OR 1.21, 95% CI 1.01-1.45) were independent factors for severe cough (VAS>70, 37.4%). Among all respondents, 35.0% indicated having a productive cough, which was associated with risk factors of being female (OR 1.44, 95% CI 1.31-1.57), having asthma (OR 1.84, 95% CI 1.52-2.22), chronic cough (OR 1.44, 95% CI 1.19-1.74), and GERD (OR 1.22, 95% CI 1.01-1.47). Persistent cough (>3 weeks) occurred in 13.0% of individuals, which was associated with the risk factors of having diabetes (OR 2.24, 95% CI 1.30-3.85), asthma (OR 1.70, 95% CI 1.11-2.62), and chronic cough (OR 1.97, 95% CI 1.32-2.94). CONCLUSIONS Cough is the most common symptom in nonhospitalized individuals with Omicron SARS-CoV-2 variant infection. Being female, having asthma, chronic cough, GERD, coronary heart disease, diabetes, and a COVID-19 vaccination history emerged as independent factors associated with severe cough, productive cough, and persistent cough.
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Affiliation(s)
- Tingting Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuehan Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenzhi Zhan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kian Fan Chung
- Department of Respiratory Medicine, Royal Brompton and Harefield Hospital, London, United Kingdom
- Experimental Studies Unit, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Zhongmin Qiu
- Department of Pulmonary and Critical Care Medicine, School of Medicine, Tongji Hospital, Tongji University, Shanghai, China
| | - Kewu Huang
- Department of Pulmonary and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ruchong Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaxing Xie
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Gang Wang
- West China School of Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Min Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Xuefen Wang
- Department of Respiratory Medicine, The First Affliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongmei Yao
- Department of Respiratory Medicine, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Xiuqing Liao
- Department of Respiratory Medicine, Fuling Center Hospital of Chongqing, Chongqing, China
| | - Yunhui Zhang
- The First People's Hospital of Yunnan Province, Kunming, China
| | - Guojun Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dejun Sun
- Department of Pulmonary and Critical Care Medicine, the Inner Mongolia Autonomous Region People's Hospital, Hohhot, China
| | - Jia Zhu
- Department of Respiratory Medicine, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Shujuan Jiang
- Department of Pulmonary Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Juntao Feng
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Jianping Zhao
- Department of Respiratory Medicine, Tongji Hospital, Tongji Medical College of Hua Zhong University of Science and Technology, Wuhan, China
| | - Gengyun Sun
- Department of Respiratory Medicine, The First Affiliated Hospital of Medical University of Anhui, Hefei, China
| | - Huaqiong Huang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jianyong Zhang
- The Second Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Lingwei Wang
- Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Feng Wu
- Department of Pulmonary and Critical Care Medicine, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, China
| | - Suyun Li
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Pusheng Xu
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunhua Chi
- Department of Respiratory and Critical Care Medicine, Peking University First Hospital, Beijing, China
| | - Ping Chen
- General Hospital of Northern Theater Command, Shenyang, China
| | - Mei Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wen He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lianrong Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shiyue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kefang Lai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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8
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Kwok KO, Wei WI, Mcneil EB, Tang A, Tang JWT, Wong SYS, Yeoh EK. Comparative analysis of symptom profile and risk of death associated with infection by SARS-CoV-2 and its variants in Hong Kong. J Med Virol 2024; 96:e29326. [PMID: 38345166 DOI: 10.1002/jmv.29326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/19/2023] [Accepted: 12/07/2023] [Indexed: 02/15/2024]
Abstract
The recurrent multiwave nature of coronavirus disease 2019 (COVID-19) necessitates updating its symptomatology. We characterize the effect of variants on symptom presentation, identify the symptoms predictive and protective of death, and quantify the effect of vaccination on symptom development. With the COVID-19 cases reported up to August 25, 2022 in Hong Kong, an iterative multitier text-matching algorithm was developed to identify symptoms from free text. Multivariate regression was used to measure associations between variants, symptom development, death, and vaccination status. A least absolute shrinkage and selection operator technique was used to identify a parsimonious set of symptoms jointly associated with death. Overall, 70.9% (54 450/76 762) of cases were symptomatic with 102 symptoms identified. Intrinsically, the wild-type and delta variant caused similar symptoms among unvaccinated symptomatic cases, whereas the wild-type and omicron BA.2 subvariant had heterogeneous patterns, with seven symptoms (fatigue, fever, chest pain, runny nose, sputum production, nausea/vomiting, and sore throat) more frequent in the BA.2 cohort. With ≥2 vaccine doses, BA.2 was more likely than delta to cause fever among symptomatic cases. Fever, blocked nose, pneumonia, and shortness of breath remained jointly predictive of death among unvaccinated symptomatic elderly in the wild-type-to-omicron transition. Number of vaccine doses required for reducing occurrence varied by symptoms. We substantiate that omicron has a different clinical presentation compared to previous variants. Syndromic surveillance can be bettered with reduced reliance on symptom-based case identification, increased weighing on symptoms predictive of death in outcome prediction, individual-based risk assessment in care homes, and incorporating free-text symptom reporting.
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Affiliation(s)
- Kin On Kwok
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Hong Kong Institute of Asia-Pacific Studies, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wan In Wei
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Edward B Mcneil
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Arthur Tang
- School of Science, Engineering and Technology, RMIT University, Ho Chi Minh City, Vietnam
| | - Julian W-T Tang
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
- Department of Clinical Microbiology, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Samuel Y S Wong
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eng Kiong Yeoh
- Centre for Health Systems and Policy Research, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
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9
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Kang DH, Kim GHJ, Park SB, Lee SI, Koh JS, Brown MS, Abtin F, McNitt-Gray MF, Goldin JG, Lee JS. Quantitative Computed Tomography Lung COVID Scores with Laboratory Markers: Utilization to Predict Rapid Progression and Monitor Longitudinal Changes in Patients with Coronavirus 2019 (COVID-19) Pneumonia. Biomedicines 2024; 12:120. [PMID: 38255225 PMCID: PMC10813449 DOI: 10.3390/biomedicines12010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), is an ongoing issue in certain populations, presenting rapidly worsening pneumonia and persistent symptoms. This study aimed to test the predictability of rapid progression using radiographic scores and laboratory markers and present longitudinal changes. This retrospective study included 218 COVID-19 pneumonia patients admitted at the Chungnam National University Hospital. Rapid progression was defined as respiratory failure requiring mechanical ventilation within one week of hospitalization. Quantitative COVID (QCOVID) scores were derived from high-resolution computed tomography (CT) analyses: (1) ground glass opacity (QGGO), (2) mixed diseases (QMD), and (3) consolidation (QCON), and the sum, quantitative total lung diseases (QTLD). Laboratory data, including inflammatory markers, were obtained from electronic medical records. Rapid progression was observed in 9.6% of patients. All QCOVID scores predicted rapid progression, with QMD showing the best predictability (AUC = 0.813). In multivariate analyses, the QMD score and interleukin(IL)-6 level were important predictors for rapid progression (AUC = 0.864). With >2 months follow-up CT, remained lung lesions were observed in 21 subjects, even after several weeks of negative reverse transcription polymerase chain reaction test. AI-driven quantitative CT scores in conjugation with laboratory markers can be useful in predicting the rapid progression and monitoring of COVID-19.
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Affiliation(s)
- Da Hyun Kang
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; (D.H.K.); (S.-I.L.); (J.S.K.)
| | - Grace Hyun J. Kim
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA;
- Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90024, USA; (M.S.B.); (F.A.); (M.F.M.-G.)
| | - Sa-Beom Park
- Center of Biohealth Convergence and Open Sharing System, Hongik University, Seoul 04401, Republic of Korea;
| | - Song-I Lee
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; (D.H.K.); (S.-I.L.); (J.S.K.)
| | - Jeong Suk Koh
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea; (D.H.K.); (S.-I.L.); (J.S.K.)
| | - Matthew S. Brown
- Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90024, USA; (M.S.B.); (F.A.); (M.F.M.-G.)
| | - Fereidoun Abtin
- Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90024, USA; (M.S.B.); (F.A.); (M.F.M.-G.)
| | - Michael F. McNitt-Gray
- Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90024, USA; (M.S.B.); (F.A.); (M.F.M.-G.)
| | - Jonathan G. Goldin
- Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90024, USA; (M.S.B.); (F.A.); (M.F.M.-G.)
| | - Jeong Seok Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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10
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Chase JR, Bond L, Vail DJ, Sengthep M, Rodriguez A, Christianson J, Hudon SF, Oxford JT. Genomic Surveillance of SARS-CoV-2 Sequence Variants at Universities in Southwest Idaho. COVID 2024; 4:23-37. [PMID: 38549916 PMCID: PMC10977930 DOI: 10.3390/covid4010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2024]
Abstract
Although the impact of the SARS-CoV-2 pandemic on major metropolitan areas is broadly reported and readily available, regions with lower populations and more remote areas in the United States are understudied. The objective of this study is to determine the progression of SARS-CoV-2 sequence variants in a frontier and remote intermountain west state among university-associated communities. This study was conducted at two intermountain west universities from 2020 to 2022. Positive SARS-CoV-2 samples were confirmed by quantitative real-time reverse transcription-polymerase chain reaction and variants were identified by the next-generation sequencing of viral genomes. Positive results were obtained for 5355 samples, representing a positivity rate of 3.5% overall. The median age was 22 years. Viral genomic sequence data were analyzed for 1717 samples and phylogeny was presented. Associations between viral variants, age, sex, and reported symptoms among 1522 samples indicated a significant association between age and the Delta variant (B 1.167.2), consistent with the findings for other regions. An outbreak event of AY122 was detected August-October 2021. A 2-month delay was observed with respect to the timing of the first documented viral infection within this region compared to major metropolitan regions of the US.
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Affiliation(s)
- Jennifer R. Chase
- Biology Department, Northwest Nazarene University, Nampa, ID 83686, USA
| | - Laura Bond
- Biomolecular Research Center, Boise State University, Boise, ID 83725-1511, USA
| | - Daniel J. Vail
- Biomolecular Research Center, Boise State University, Boise, ID 83725-1511, USA
- Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Milan Sengthep
- Genetics and Infectious Disease Laboratory, Boise State University, Boise, ID 83725, USA
| | - Adriana Rodriguez
- Genetics and Infectious Disease Laboratory, Boise State University, Boise, ID 83725, USA
| | - Joe Christianson
- Genetics and Infectious Disease Laboratory, Boise State University, Boise, ID 83725, USA
- College of Medicine, Drexel University, 2900 W. Queen Lane, Philadelphia, PA 19129, USA
| | - Stephanie F. Hudon
- Genetics and Infectious Disease Laboratory, Boise State University, Boise, ID 83725, USA
| | - Julia Thom Oxford
- Biomolecular Research Center, Boise State University, Boise, ID 83725-1511, USA
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA
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11
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Liu W, Gong F, Zheng X, Pei L, Wang X, Yang S, Zhao S, Yang Z, Lin J, Jing F, Shang H, Bi Y, Wei D, Chen E, Chen Y. Factors associated with prolonged viral shedding of SARS-CoV-2 Omicron variant infection in Shanghai: A multicenter, retrospective, observational study. J Med Virol 2023; 95:e29342. [PMID: 38130170 DOI: 10.1002/jmv.29342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/06/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Shanghai has faced an unprecedented COVID-19 pandemic with the BA.2.2 strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron infection. Comprehensive insights into its epidemiology, clinical manifestations, and viral shedding dynamics are currently limited. This study encompasses 208373 COVID-19 patients that were infected with the Omicron BA.2.2 sub-lineage in Shanghai, China. Demographic information, clinical symptoms, vaccination status, isolation status, as well as viral shedding time (VST) were recorded. Among the COVID-19 patients included in this study, 187124 were asymptomatic and 21249 exhibited mild symptoms. The median VST was 8.3 days. The common clinical symptoms included fever, persistent cough, phlegm, sore throat, and gastrointestinal symptoms. Factors such as advanced age, presence of comorbidities, mild symptomatology, and delayed isolation correlated with extended VST. Conversely, female gender and administration of two or three vaccine doses correlated with a reduction in VST. This investigation offers an in-depth characterization and analytical perspective on Shanghai's recent COVID-19 surge. Prolonged viral shedding of SARS-CoV-2 was observed in elderly, male, symptomatic patients, and those with comorbidity. Female, individuals with two or three vaccine doses, as well as those isolated early, shows an effective reduced VST.
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Affiliation(s)
- Wenbin Liu
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangchen Gong
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangtao Zheng
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Pei
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaofeng Wang
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Song Yang
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanzhi Zhao
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhitao Yang
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingsheng Lin
- Department of Disciplinary Development and Planning, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Jing
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hanbing Shang
- Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Erzhen Chen
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Chen
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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Torabi SH, Riahi SM, Ebrahimzadeh A, Salmani F. Changes in symptoms and characteristics of COVID-19 patients across different variants: two years study using neural network analysis. BMC Infect Dis 2023; 23:838. [PMID: 38017395 PMCID: PMC10683353 DOI: 10.1186/s12879-023-08813-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Considering the fact that COVID-19 has undergone various changes over time, its symptoms have also varied. The aim of this study is to describe and compare the changes in personal characteristics, symptoms, and underlying conditions of individuals infected with different strains of COVID-19. METHODS This descriptive-analytical study was conducted on 46,747 patients who underwent PCR testing during a two-year period from February 22, 2020 to February 23, 2022, in South Khorasan province, Iran. Patient characteristics and symptoms were extracted based on self-report and the information system. The data were analyzed using logistic regression and artificial neural network approaches. The R software was used for analysis and a significance level of 0.05 was considered for the tests. RESULTS Among the 46,747 cases analyzed, 23,239 (49.7%) were male, and the mean age was 51.48 ± 21.41 years. There was a significant difference in symptoms among different variants of the disease (p < 0.001). The factors with a significant positive association were myalgia (OR: 2.04; 95% CI, 1.76 - 2.36), cough (OR: 1.93; 95% CI, 1.68-2.22), and taste or smell disorder (OR: 2.62; 95% CI, 2.1 - 3.28). Additionally, aging was found to increase the likelihood of testing positive across the six periods. CONCLUSION We found that older age, myalgia, cough and taste/smell disorder are better factors compared to dyspnea or high body temperature, for identifying a COVID-19 patient. As the disease evolved, chills and diarrhea, demonstrated prognostic strength as in Omicron.
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Affiliation(s)
- Seyed Hossein Torabi
- School of Medicine, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran
| | - Seyed Mohammad Riahi
- Epidemiology Department of Family and Community Medicine, School of Medicine Cardiovascular Diseases Research Center, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran
| | - Azadeh Ebrahimzadeh
- Department of Infectious Diseases, School of Medicine Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran
| | - Fatemeh Salmani
- Department of Epidemiology and Biostatistics, School of Health Social Determinants of Health Research Center, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran.
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13
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Sørensen AIV, Spiliopoulos L, Bager P, Nielsen NM, Hansen JV, Koch A, Meder IK, Hviid A, Ethelberg S. A Danish questionnaire study of acute symptoms of SARS-CoV-2 infection by variant, vaccination status, sex and age. Sci Rep 2023; 13:19863. [PMID: 37964010 PMCID: PMC10645837 DOI: 10.1038/s41598-023-47273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/11/2023] [Indexed: 11/16/2023] Open
Abstract
It is not well-described how the acute symptoms of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) differ by variant, vaccination, sex and age. A cross-sectional questionnaire study linked to national testing- and registry data was conducted among 148,874 SARS-CoV-2 first time reverse transcription polymerase chain reaction (RT-PCR) test-positive individuals and corresponding date-matched symptomatic test-negative controls. Major SARS-CoV-2 variants (Index/wild type, Alpha, Delta and Omicron) were defined using periods of predominance. Risk differences (RDs) were estimated for each of 21 predefined acute symptoms comparing: (1) test-positive and -negative individuals, by variant period, (2) vaccinated and unvaccinated test-positives, by variant period, (3) individuals tested positive during the Omicron and Delta periods, by vaccination status, and (4) vaccinated Omicron test-positive and -negative individuals, by age and sex. Compared to pre-Omicron, RDs between test-positive and test-negative individuals during the Omicron period were lower for most symptoms. RDs for altered sense of smell (dysosmia) and taste (dysgeusia) were highest for Delta (RD = 50.8 (49.4-52.0) and RD = 54.7 (53.4-56.0), respectively) and lowest for Omicron (RD = 12.8 (12.1-13.5) and RD = 11.8 (11.1-12.4), respectively). Across variants, vaccinated individuals reported fewer symptoms. During Omicron, females and 30-59 year-old participants reported more symptoms.
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Affiliation(s)
- Anna Irene Vedel Sørensen
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, 2300, Copenhagen S, Denmark.
| | - Lampros Spiliopoulos
- Department of Epidemiology Research, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | - Peter Bager
- Department of Epidemiology Research, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | - Nete Munk Nielsen
- Department of Epidemiology Research, Statens Serum Institut, 2300, Copenhagen S, Denmark
- Focused Research Unit in Neurology, Department of Neurology, Hospital of Southern Jutland, University of Southern Denmark, 6200, Aabenraa, Denmark
| | - Jørgen Vinsløv Hansen
- Department of Epidemiology Research, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | - Anders Koch
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, 2300, Copenhagen S, Denmark
- Department of Infectious Diseases, Rigshospitalet University Hospital, 2100, Copenhagen Ø, Denmark
- Department of Public Health, Global Health Section, University of Copenhagen, 1014, Copenhagen K, Denmark
| | - Inger Kristine Meder
- Department of Epidemiology Research, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | - Anders Hviid
- Department of Epidemiology Research, Statens Serum Institut, 2300, Copenhagen S, Denmark
- Pharmacovigilance Research Centre, Department of Drug Design and Pharmacology, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Steen Ethelberg
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, 2300, Copenhagen S, Denmark
- Department of Public Health, Global Health Section, University of Copenhagen, 1014, Copenhagen K, Denmark
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14
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Rao A, Lin J, Parsons R, Greenleaf M, Westbrook A, Lai E, Bowers HB, McClendon K, O’Sick W, Baugh T, Sifford M, Sullivan JA, Lam WA, Bassit L. Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.08.23297633. [PMID: 37986832 PMCID: PMC10659510 DOI: 10.1101/2023.11.08.23297633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Motivation The motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted 'low positives" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests. Summary SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator test's Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas® SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.
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Affiliation(s)
- Anuradha Rao
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jessica Lin
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Richard Parsons
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University School of Medicine, Atlanta, GA, USA
| | - Adrianna Westbrook
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eric Lai
- Personalized Science San Diego CA 05403 USA
| | - Heather B. Bowers
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
| | - Kaleb McClendon
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - William O’Sick
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Tyler Baugh
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Markayla Sifford
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Julie A. Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Leda Bassit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
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15
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Krenn F, Dächert C, Badell I, Lupoli G, Öztan GN, Feng T, Schneider N, Huber M, Both H, Späth PM, Muenchhoff M, Graf A, Krebs S, Blum H, Durner J, Czibere L, Kaderali L, Keppler OT, Baldauf HM, Osterman A. Ten rapid antigen tests for SARS-CoV-2 widely differ in their ability to detect Omicron-BA.4 and -BA.5. Med Microbiol Immunol 2023; 212:323-337. [PMID: 37561225 PMCID: PMC10501931 DOI: 10.1007/s00430-023-00775-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Since late 2021, the variant landscape of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been dominated by the variant of concern (VoC) Omicron and its sublineages. We and others have shown that the detection of Omicron-BA.1 and -BA.2-positive respiratory specimens by rapid antigen tests (RATs) is impaired compared to Delta VoC-containing samples. Here, in a single-center retrospective laboratory study, we evaluated the performance of ten most commonly used RATs for the detection of Omicron-BA.4 and -BA.5 infections. We used 171 respiratory swab specimens from SARS-CoV-2 RNA-positive patients, of which 71 were classified as BA.4 and 100 as BA.5. All swabs were collected between July and September 2022. 50 SARS-CoV-2 PCR-negative samples from healthy individuals, collected in October 2022, showed high specificity in 9 out of 10 RATs. When assessing analytical sensitivity using clinical specimens, the 50% limit of detection (LoD50) ranged from 7.6 × 104 to 3.3 × 106 RNA copies subjected to the RATs for BA.4 compared to 6.8 × 104 to 3.0 × 106 for BA.5. Overall, intra-assay differences for the detection of these two Omicron subvariants were not significant for both respiratory swabs and tissue culture-expanded virus isolates. In contrast, marked heterogeneity was observed among the ten RATs: to be positive in these point-of-care tests, up to 443-fold (BA.4) and up to 56-fold (BA.5) higher viral loads were required for the worst performing RAT compared to the best performing RAT. True-positive rates for Omicron-BA.4- or -BA.5-containing specimens in the highest viral load category (Ct values < 25) ranged from 94.3 to 34.3%, dropping to 25.6 to 0% for samples with intermediate Ct values (25-30). We conclude that the high heterogeneity in the performance of commonly used RATs remains a challenge for the general public to obtain reliable results in the evolving Omicron subvariant-driven pandemic.
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Affiliation(s)
- Franziska Krenn
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gaia Lupoli
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Tianle Feng
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M. Späth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | | | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
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16
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Zhang L, Kang X, Wang L, Yan R, Pan Y, Wang J, Chen Z. Clinical and virological features of asymptomatic and mild symptomatic patients with SARS-CoV-2 Omicron infection at Shanghai Fangcang shelter hospital. Immun Inflamm Dis 2023; 11:e1033. [PMID: 37773703 PMCID: PMC10524057 DOI: 10.1002/iid3.1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023] Open
Abstract
OBJECTIVE The objective of this study is to evaluate and compare clinical and virological characteristics of asymptomatic and mild symptomatic patients of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2.2 variant infection and identify risk factors associated with the prolonged viral negative conversion duration. METHODS We conducted a retrospective observational study in a Shanghai (China) Fangcang shelter hospital from April 9 to May 17, 2022. The patient-related demographic or clinical data were retrospectively recorded. Comparisons of demographic and clinical characteristics between asymptomatic and mild-symptomatic patients were performed. Cox regression was performed to identify the risk factors of prolonged viral negative conversion duration. RESULTS A total of 551 patients confirmed with SARS-CoV-2 Omicron variant infection were enrolled in the study. Of these, 297 patients (53.9%) were asymptomatic and 254 patients (46.1%) had mild symptoms. When comparing the clinical and virological characteristics between the asymptomatic and mild symptomatic groups, several clinical parameters, including age, gender, time to viral clearance from the first positive swab, chronic comorbidities, and vaccination dose did not show statistically significant differences. In mild symptomatic patients, the median viral negative conversion duration (NCD) was 7 days (interquartile range [IQR]: 5-9), which was comparable to the median of 7 days (IQR: 5-10) in asymptomatic patients (p = .943). Multivariate Cox analysis revealed that patients age ≥ 60 years had a significantly higher hazard ratio (HR) for prolonged viral NCD (HR: 1.313; 95% confidence interval: 1.014-1.701, p = .039). CONCLUSION Asymptomatic and symptomatic patients with non-severe SARS-CoV-2 Omicron BA.2.2 variant infection have similar clinical features and virological courses. Old age was an independent risk factor for prolonged SARS-CoV-2 conversion time.
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Affiliation(s)
- Lin Zhang
- Department of Internal MedicineCentral Medical Branch of Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Xiaoyu Kang
- The Fourth Unit of Third BranchFangcang Shelter Hospital of National Exhibition and Convention CenterShanghaiPeople's Republic of China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi'anPeople's Republic of China
| | - Liangliang Wang
- The Fourth Unit of Third BranchFangcang Shelter Hospital of National Exhibition and Convention CenterShanghaiPeople's Republic of China
- Department of Nutrition, Xijing HospitalFourth Military Medical UniversityXi'anPeople's Republic of China
| | - Rui Yan
- Department of Infectious Diseases, Xijing HospitalFourth Military Medical UniversityXi'anPeople's Republic of China
| | - Yanglin Pan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi'anPeople's Republic of China
| | - Jiuping Wang
- Department of Infectious Diseases, Xijing HospitalFourth Military Medical UniversityXi'anPeople's Republic of China
| | - Zhangqian Chen
- The Fourth Unit of Third BranchFangcang Shelter Hospital of National Exhibition and Convention CenterShanghaiPeople's Republic of China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi'anPeople's Republic of China
- Department of Infectious Diseases, Xijing HospitalFourth Military Medical UniversityXi'anPeople's Republic of China
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17
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Avigan ZM, Paredes R, Boussi LS, Lam BD, Shea ME, Weinstock MJ, Peters MLB. Updated COVID-19 clearance time among patients with cancer in the Delta and Omicron waves. Cancer Med 2023; 12:16869-16875. [PMID: 37392171 PMCID: PMC10501268 DOI: 10.1002/cam4.6311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND COVID-19 infection delays therapy and in-person evaluation for oncology patients, but clinic clearance criteria are not clearly defined. METHODS We conducted a retrospective review of oncology patients with COVID-19 at a tertiary care center during the Delta and Omicron waves and compared clearance strategies. RESULTS Median clearance by two consecutive negative tests was 32.0 days (Interquartile Range [IQR] 22.0-42.5, n = 153) and was prolonged in hematologic malignancy versus solid tumors (35.0 days for hematologic malignancy, 27.5 days for solid tumors, p = 0.01) and in patients receiving B-cell depletion versus other therapies. Median clearance by single negative test was reduced to 23.0 days (IQR 16.0-33.0), with recurrent positive rate 25.4% in hematologic malignancy versus 10.6% in solid tumors (p = 0.02). Clearance by a predefined waiting period required 41 days until an 80% negative rate. CONCLUSIONS COVID-19 clearance remains prolonged in oncology patients. Single-negative test clearance can balance delays in care with risk of infection in patients with solid tumors.
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Affiliation(s)
- Zachary M. Avigan
- Department of MedicineBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | - Rodrigo Paredes
- Division of Hematology/Oncology, Department of MedicineBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | - Leora S. Boussi
- Department of MedicineBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | - Barbara D. Lam
- Division of Hematology/Oncology, Department of MedicineBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | - Meghan E. Shea
- Division of Hematology/Oncology, Department of MedicineBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | - Matthew J. Weinstock
- Division of Hematology/Oncology, Department of MedicineBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | - Mary Linton B. Peters
- Division of Hematology/Oncology, Department of MedicineBeth Israel Deaconess Medical CenterBostonMassachusettsUSA
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18
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Al Hossain F, Tonmoy TH, Nuvvula S, Chapman BP, Gupta RK, Lover AA, Dinglasan RR, Carreiro S, Rahman T. Passive Monitoring of Crowd-Level Cough Counts in Waiting Areas produces Reliable Syndromic Indicator for Total COVID-19 Burden in a Hospital Emergency Clinic. RESEARCH SQUARE 2023:rs.3.rs-3084318. [PMID: 37461489 PMCID: PMC10350162 DOI: 10.21203/rs.3.rs-3084318/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Syndromic surveillance is an effective tool for enabling the timely detection of infectious disease outbreaks and facilitating the implementation of effective mitigation strategies by public health authorities. While various information sources are currently utilized to collect syndromic signal data for analysis, the aggregated measurement of cough, an important symptom for many illnesses, is not widely employed as a syndromic signal. With recent advancements in ubiquitous sensing technologies, it becomes feasible to continuously measure population-level cough incidence in a contactless, unobtrusive, and automated manner. In this work, we demonstrate the utility of monitoring aggregated cough count as a syndromic indicator to estimate COVID-19 cases. In our study, we deployed a sensor-based platform (Syndromic Logger) in the emergency room of a large hospital. The platform captured syndromic signals from audio, thermal imaging, and radar, while the ground truth data were collected from the hospital's electronic health record. Our analysis revealed a significant correlation between the aggregated cough count and positive COVID-19 cases in the hospital (Pearson correlation of 0.40, p-value < 0.001). Notably, this correlation was higher than that observed with the number of individuals presenting with fever (ρ = 0.22, p = 0.04), a widely used syndromic signal and screening tool for such diseases. Furthermore, we demonstrate how the data obtained from our Syndromic Logger platform could be leveraged to estimate various COVID-19-related statistics using multiple modeling approaches. Our findings highlight the efficacy of aggregated cough count as a valuable syndromic indicator associated with the occurrence of COVID-19 cases. Incorporating this signal into syndromic surveillance systems for such diseases can significantly enhance overall resilience against future public health challenges, such as emerging disease outbreaks or pandemics.
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Affiliation(s)
- Forsad Al Hossain
- College of Information and Computer Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Tanjid Hasan Tonmoy
- Halıcıoğlu Data Science Institute, University of California, San Diego, San Diego, CA, USA
| | - Sri Nuvvula
- Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Brittany P. Chapman
- Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Rajesh K. Gupta
- Halıcıoğlu Data Science Institute, University of California, San Diego, San Diego, CA, USA
| | - Andrew A. Lover
- School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Rhoel R. Dinglasan
- Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA
| | - Stephanie Carreiro
- Department of Emergency Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tauhidur Rahman
- Halıcıoğlu Data Science Institute, University of California, San Diego, San Diego, CA, USA
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19
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Tseng YJ, Olson KL, Bloch D, Mandl KD. Smart Thermometer-Based Participatory Surveillance to Discern the Role of Children in Household Viral Transmission During the COVID-19 Pandemic. JAMA Netw Open 2023; 6:e2316190. [PMID: 37261828 PMCID: PMC10236238 DOI: 10.1001/jamanetworkopen.2023.16190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/18/2023] [Indexed: 06/02/2023] Open
Abstract
Importance Children's role in spreading virus during the COVID-19 pandemic is yet to be elucidated, and measuring household transmission traditionally requires contact tracing. Objective To discern children's role in household viral transmission during the pandemic when enveloped viruses were at historic lows and the predominance of viral illnesses were attributed to COVID-19. Design, Setting, and Participants This cohort study of a voluntary US cohort tracked data from participatory surveillance using commercially available thermometers with a companion smartphone app from October 2019 to October 2022. Eligible participants were individuals with temperature measurements in households with multiple members between October 2019 and October 2022 who opted into data sharing. Main Outcomes and Measures Proportion of household transmissions with a pediatric index case and changes in transmissions during school breaks were assessed using app and thermometer data. Results A total of 862 577 individuals from 320 073 households with multiple participants (462 000 female [53.6%] and 463 368 adults [53.7%]) were included. The number of febrile episodes forecast new COVID-19 cases. Within-household transmission was inferred in 54 506 (15.4%) febrile episodes and increased from the fourth pandemic period, March to July 2021 (3263 of 32 294 [10.1%]) to the Omicron BA.1/BA.2 wave (16 516 of 94 316 [17.5%]; P < .001). Among 38 787 transmissions in 166 170 households with adults and children, a median (IQR) 70.4% (61.4%-77.6%) had a pediatric index case; proportions fluctuated weekly from 36.9% to 84.6%. A pediatric index case was 0.6 to 0.8 times less frequent during typical school breaks. The winter break decrease was from 68.4% (95% CI, 57.1%-77.8%) to 41.7% (95% CI, 34.3%-49.5%) at the end of 2020 (P < .001). At the beginning of 2022, it dropped from 80.3% (95% CI, 75.1%-84.6%) to 54.5% (95% CI, 51.3%-57.7%) (P < .001). During summer breaks, rates dropped from 81.4% (95% CI, 74.0%-87.1%) to 62.5% (95% CI, 56.3%-68.3%) by August 2021 (P = .02) and from 83.8% (95% CI, 79.2%-87.5) to 62.8% (95% CI, 57.1%-68.1%) by July 2022 (P < .001). These patterns persisted over 2 school years. Conclusions and Relevance In this cohort study using participatory surveillance to measure within-household transmission at a national scale, we discerned an important role for children in the spread of viral infection within households during the COVID-19 pandemic, heightened when schools were in session, supporting a role for school attendance in COVID-19 spread.
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Affiliation(s)
- Yi-Ju Tseng
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Computer Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Karen L. Olson
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | | | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
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20
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Sakai-Tagawa Y, Yamayoshi S, Halfmann PJ, Wilson N, Bobholz M, Vuyk WC, Wei W, Ries H, O'Connor DH, Friedrich TC, Sordillo EM, van Bakel H, Simon V, Kawaoka Y. Sensitivity of rapid antigen tests for Omicron subvariants of SARS-CoV-2. J Med Virol 2023; 95:e28788. [PMID: 37212288 DOI: 10.1002/jmv.28788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 05/23/2023]
Abstract
Diagnosis by rapid antigen tests (RATs) is useful for early initiation of antiviral treatment. Because RATs are easy to use, they can be adapted for self-testing. Several kinds of RATs approved for such use by the Japanese regulatory authority are available from drug stores and websites. Most RATs for COVID-19 are based on antibody detection of the SARS-CoV-2 N protein. Since Omicron and its subvariants have accumulated several amino acid substitutions in the N protein, such amino acid changes might affect the sensitivity of RATs. Here, we investigated the sensitivity of seven RATs available in Japan, six of which are approved for public use and one of which is approved for clinical use, for the detection of BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1, as well as the delta variant (B.1.627.2). All tested RATs detected the delta variant with a detection level between 7500 and 75 000 pfu per test, and all tested RATs showed similar sensitivity to the Omicron variant and its subvariants (BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1). Human saliva did not reduce the sensitivity of the RATs tested. Espline SARS-CoV-2 N showed the highest sensitivity followed by Inspecter KOWA SARS-CoV-2 and V Trust SARS-CoV-2 Ag. Since the RATs failed to detect low levels of infectious virus, individuals whose specimens contained less infectious virus than the detection limit would be considered negative. Therefore, it is important to note that RATs may miss individuals shedding low levels of infectious virus.
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Affiliation(s)
- Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Max Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - William C Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hunter Ries
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Infection and Advanced Research Center, The University of Tokyo Pandemic Preparedness, Tokyo, Japan
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21
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Normandin E, Valizadeh N, Rudmann EA, Uddin R, Dobbins ST, MacInnis BL, Padera RF, Siddle KJ, Lemieux JE, Sabeti PC, Mukerji SS, Solomon IH. Neuropathological features of SARS-CoV-2 delta and omicron variants. J Neuropathol Exp Neurol 2023; 82:283-295. [PMID: 36847705 PMCID: PMC10025880 DOI: 10.1093/jnen/nlad015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continually evolving resulting in variants with increased transmissibility, more severe disease, reduced effectiveness of treatments or vaccines, or diagnostic detection failure. The SARS-CoV-2 Delta variant (B.1.617.2 and AY lineages) was the dominant circulating strain in the United States from July to mid-December 2021, followed by the Omicron variant (B.1.1.529 and BA lineages). Coronavirus disease 2019 (COVID-19) has been associated with neurological sequelae including loss of taste/smell, headache, encephalopathy, and stroke, yet little is known about the impact of viral strain on neuropathogenesis. Detailed postmortem brain evaluations were performed for 22 patients from Massachusetts, including 12 who died following infection with Delta variant and 5 with Omicron variant, compared to 5 patients who died earlier in the pandemic. Diffuse hypoxic injury, occasional microinfarcts and hemorrhage, perivascular fibrinogen, and rare lymphocytes were observed across the 3 groups. SARS-CoV-2 protein and RNA were not detected in any brain samples by immunohistochemistry, in situ hybridization, or real-time quantitative PCR. These results, although preliminary, demonstrate that, among a subset of severely ill patients, similar neuropathological features are present in Delta, Omicron, and non-Delta/non-Omicron variant patients, suggesting that SARS-CoV-2 variants are likely to affect the brain by common neuropathogenic mechanisms.
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Affiliation(s)
- Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Navid Valizadeh
- Division of Neuroimmunology and Neuro-infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Emily A Rudmann
- Division of Neuroimmunology and Neuro-infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rockib Uddin
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Robert F Padera
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Jacob E Lemieux
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shibani S Mukerji
- Division of Neuroimmunology and Neuro-infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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22
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Omiya Y, Mizuguchi D, Tokuno S. Distinguish the Severity of Illness Associated with Novel Coronavirus (COVID-19) Infection via Sustained Vowel Speech Features. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3415. [PMID: 36834110 PMCID: PMC9960121 DOI: 10.3390/ijerph20043415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The authors are currently conducting research on methods to estimate psychiatric and neurological disorders from a voice by focusing on the features of speech. It is empirically known that numerous psychosomatic symptoms appear in voice biomarkers; in this study, we examined the effectiveness of distinguishing changes in the symptoms associated with novel coronavirus infection using speech features. Multiple speech features were extracted from the voice recordings, and, as a countermeasure against overfitting, we selected features using statistical analysis and feature selection methods utilizing pseudo data and built and verified machine learning algorithm models using LightGBM. Applying 5-fold cross-validation, and using three types of sustained vowel sounds of /Ah/, /Eh/, and /Uh/, we achieved a high performance (accuracy and AUC) of over 88% in distinguishing "asymptomatic or mild illness (symptoms)" and "moderate illness 1 (symptoms)". Accordingly, the results suggest that the proposed index using voice (speech features) can likely be used in distinguishing the symptoms associated with novel coronavirus infection.
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Affiliation(s)
- Yasuhiro Omiya
- PST Inc., Yokohama 231-0023, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | | | - Shinichi Tokuno
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Graduate School of Health Innovation, Kanagawa University of Human Services, Yokosuka 210-0821, Japan
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von Bartheld CS, Wang L. Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-Analysis. Cells 2023; 12:430. [PMID: 36766771 PMCID: PMC9913864 DOI: 10.3390/cells12030430] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The omicron variant is thought to cause less olfactory dysfunction than previous variants of SARS-CoV-2, but the reported prevalence differs greatly between populations and studies. Our systematic review and meta-analysis provide information regarding regional differences in prevalence as well as an estimate of the global prevalence of olfactory dysfunction based on 62 studies reporting information on 626,035 patients infected with the omicron variant. Our estimate of the omicron-induced prevalence of olfactory dysfunction in populations of European ancestry is 11.7%, while it is significantly lower in all other populations, ranging between 1.9% and 4.9%. When ethnic differences and population sizes are considered, the global prevalence of omicron-induced olfactory dysfunction in adults is estimated to be 3.7%. Omicron's effect on olfaction is twofold to tenfold lower than that of the alpha or delta variants according to previous meta-analyses and our analysis of studies that directly compared the prevalence of olfactory dysfunction between omicron and previous variants. The profile of the prevalence differences between ethnicities mirrors the results of a recent genome-wide association study that connected a gene locus encoding an odorant-metabolizing enzyme, UDP glycosyltransferase, to the extent of COVID-19-related loss of smell. Our analysis is consistent with the hypothesis that this enzyme contributes to the observed population differences.
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Affiliation(s)
- Christopher S. von Bartheld
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV 89557-0352, USA
| | - Lingchen Wang
- School of Public Health, University of Nevada, Reno, NV 89557-0275, USA
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von Bartheld CS, Wang L. Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2022.12.16.22283582. [PMID: 36561176 PMCID: PMC9774228 DOI: 10.1101/2022.12.16.22283582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The omicron variant is thought to cause less olfactory dysfunction than previous variants of SARS-CoV-2, but the reported prevalence differs greatly between populations and studies. Our systematic review and meta-analysis provide information about regional differences in prevalence as well as an estimate of the global prevalence of olfactory dysfunction based on 62 studies reporting on 626,035 patients infected with the omicron variant. Our estimate of the omicron-induced prevalence of olfactory dysfunction in populations of European ancestry is 11.7%, while it is significantly lower in all other populations, ranging between 1.9% and 4.9%. When ethnic differences and population sizes are taken into account, the global prevalence of omicron-induced olfactory dysfunction in adults is estimated at 3.7%. Omicron’s effect on olfaction is twofold to tenfold lower than that of the alpha or delta variant, according to previous meta-analyses and our analysis of studies that directly compared prevalence of olfactory dysfunction between omicron and previous variants. The profile of prevalence differences between ethnicities mirrors the results of a recent genome-wide association study that implicated a gene locus encoding an odorant-metabolizing enzyme, UDP glycosyltransferase, to be linked to the extent of COVID-related loss of smell. Our analysis is consistent with the hypothesis that this enzyme contributes to the observed population differences.
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Affiliation(s)
- Christopher S. von Bartheld
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557-0352, United States
| | - Lingchen Wang
- School of Public Health, University of Nevada, Reno, Reno, NV, 89557-0275, United States
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