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Chen X, Balliew J, Bauer CX, Deegan J, Gitter A, Hanson BM, Maresso AW, Tisza MJ, Troisi CL, Rios J, Mena KD, Boerwinkle E, Wu F. RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.12.24310301. [PMID: 39040200 PMCID: PMC11261926 DOI: 10.1101/2024.07.12.24310301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.
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Affiliation(s)
- Xingwen Chen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Blake M Hanson
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anthony W Maresso
- TAILOR Labs, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Michael J Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Catherine L Troisi
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
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Nakayama T, Todaka R, Sawada A, Ito T, Fujino M, Haga K, Katayama K. Different immunological responses following immunization with two mRNA vaccines. J Infect Chemother 2024; 30:439-449. [PMID: 38000497 DOI: 10.1016/j.jiac.2023.11.020] [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: 08/07/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
INTRODUCTION Immunological responses were investigated following immunization with two mRNA vaccines: BNT162b2 and mRNA-1273. METHODS Neutralizing antibody (NAb) was assayed before, 2-4 weeks after, and 3 and 6 months after the primary immunization, and the same time-points after booster dose with 6- or 8-months interval. Whole-blood culture was stimulated with spike antigen, and cytokine production was assayed. RESULTS NAb was detected after primary immunization, NAb titers began to decrease three months after primary immunization with BNT162b2, lower than those after mRNA-1273, and elevated after booster immunization. The NAb level was 1/2 lower against δ variant, and 1/16 lower against omicron variant in comparison with that against α variant. Cytokine production following immunization with mRNA-1273 was maintained within three months at higher levels of Th1 (TNF-α), Th2 (IL-4 and IL-5), and inflammatory cytokines (IL-6 and IL-17) than that following immunization with BNT162b2, reflecting prominent levels of NAb following immunization with mRNA-1273. Cytokine production decreased six months after primary immunization in both vaccine recipients and was enhanced following booster doses. During the omicron outbreak, medical staff members in the outpatient office experienced asymptomatic infection, with a greater than 4-fold increase in NAb titers against omicron variant even after booster immunization. Asymptomatic infection enhanced the production of Th2 and inflammatory cytokines. CONCLUSION mRNA-1273 induced stronger NAb responses with wide-range cross-reactive antibodies against δ and omicron variants. mRNA-1273 induced higher levels of Th1, Th2, and inflammatory cytokines than BNT162b2 did, reflecting higher levels of NAb against variant strains.
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Affiliation(s)
- Tetsuo Nakayama
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Reiko Todaka
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Akihito Sawada
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Takashi Ito
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan; Department of Pediatrics, Kitasato University Hospital, Sagamihara, Kanagawa, 252-0329, Japan.
| | - Motoko Fujino
- Department of Pediatrics, Saiseikai Central Hospital Tokyo, Tokyo, 108-0073, Japan.
| | - Kei Haga
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Ömura Satoshi Memorial Institute, Tokyo, 108-8641, Japan.
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Ciaccio L, Donnan PT, Parcell BJ, Marwick CA. Community antibiotic prescribing in patients with COVID-19 across three pandemic waves: a population-based study in Scotland, UK. BMJ Open 2024; 14:e081930. [PMID: 38643000 PMCID: PMC11033633 DOI: 10.1136/bmjopen-2023-081930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 04/22/2024] Open
Abstract
OBJECTIVES This study aims to examine community antibiotic prescribing across a complete geographical area for people with a positive COVID-19 test across three pandemic waves, and to examine health and demographic factors associated with antibiotic prescribing. DESIGN A population-based study using administrative data. SETTING A complete geographical region within Scotland, UK. PARTICIPANTS Residents of two National Health Service Scotland health boards with SARS-CoV-2 virus test results from 1 February 2020 to 31 March 2022 (n=184 954). Individuals with a positive test result (n=16 025) had data linked to prescription and hospital admission data ±28 days of the test, general practice data for high-risk comorbidities and demographic data. OUTCOME MEASURES The associations between patient factors and the odds of antibiotic prescription in COVID-19 episodes across three pandemic waves from multivariate binary logistic regression. RESULTS Data included 768 206 tests for 184 954 individuals, identifying 16 240 COVID-19 episodes involving 16 025 individuals. There were 3263 antibiotic prescriptions ±28 days for 2395 episodes. 35.6% of episodes had a prescription only before the test date, 52.3% of episodes after and 12.1% before and after. Antibiotic prescribing reduced over time: 20.4% of episodes in wave 1, 17.7% in wave 2 and 12.0% in wave 3. In multivariate logistic regression, being female (OR 1.31, 95% CI 1.19 to 1.45), older (OR 3.02, 95% CI 2.50 to 3.68 75+ vs <25 years), having a high-risk comorbidity (OR 1.45, 95% CI 1.31 to 1.61), a hospital admission ±28 days of an episode (OR 1.58, 95% CI 1.42 to 1.77) and health board region (OR 1.14, 95% CI 1.03 to 1.25, board B vs A) increased the odds of receiving an antibiotic. CONCLUSION Community antibiotic prescriptions in COVID-19 episodes were uncommon in this population and likelihood was associated with patient factors. The reduction over pandemic waves may represent increased knowledge regarding COVID-19 treatment and/or evolving symptomatology.
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Affiliation(s)
- Laura Ciaccio
- Division of Population Health and Genomics, University of Dundee School of Medicine, Dundee, UK
| | - Peter T Donnan
- Division of Population Health and Genomics, University of Dundee School of Medicine, Dundee, UK
| | - Benjamin J Parcell
- Department of Medical Microbiology, Ninewells Hospital and Medical School, Dundee, UK
| | - Charis A Marwick
- Division of Population Health and Genomics, University of Dundee School of Medicine, Dundee, UK
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Evans S, Naylor NR, Fowler T, Hopkins S, Robotham J. The effectiveness and efficiency of asymptomatic SARS-CoV-2 testing strategies for patient and healthcare workers within acute NHS hospitals during an omicron-like period. BMC Infect Dis 2024; 24:64. [PMID: 38191324 PMCID: PMC10775431 DOI: 10.1186/s12879-023-08948-9] [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: 09/08/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Asymptomatic SARS-CoV-2 testing of hospitalised patients began in April-2020, with twice weekly healthcare worker (HCW) testing introduced in November-2020. Guidance recommending asymptomatic testing was withdrawn in August-2022. Assessing the impact of this decision from data alone is challenging due to concurrent changes in infection prevention and control practices, community transmission rates, and a reduction in ascertainment rate from reduced testing. Computational modelling is an effective tool for estimating the impact of this change. METHODS Using a computational model of SARS-CoV-2 transmission in an English hospital we estimate the effectiveness of several asymptomatic testing strategies, namely; (1) Symptomatic testing of patients and HCWs, (2) testing of all patients on admission with/without repeat testing on days 3 and 5-7, and (3) symptomatic testing plus twice weekly asymptomatic HCW testing with 70% compliance. We estimate the number of patient and HCW infections, HCW absences, number of tests, and tests per case averted or absence avoided, with differing community prevalence rates over a 12-week period. RESULTS Testing asymptomatic patients on admission reduces the rate of nosocomial SARS-CoV-2 infection by 8.1-21.5%. Additional testing at days 3 and 5-7 post admission does not significantly reduce infection rates. Twice weekly asymptomatic HCW testing can reduce the proportion of HCWs infected by 1.0-4.4% and monthly absences by 0.4-0.8%. Testing asymptomatic patients repeatedly requires up to 5.5 million patient tests over the period, and twice weekly asymptomatic HCW testing increases the total tests to almost 30 million. The most efficient patient testing strategy (in terms of tests required to prevent a single patient infection) was testing asymptomatic patients on admission across all prevalence levels. The least efficient was repeated testing of patients with twice weekly asymptomatic HCW testing in a low prevalence scenario, and in all other prevalence levels symptomatic patient testing with regular HCW testing was least efficient. CONCLUSIONS Testing patients on admission can reduce the rate of nosocomial SARS-CoV-2 infection but there is little benefit of additional post-admission testing. Asymptomatic HCW testing has little incremental benefit for reducing patient cases at low prevalence but has a potential role at higher prevalence or with low community transmission. A full health-economic evaluation is required to determine the cost-effectiveness of these strategies.
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Affiliation(s)
- Stephanie Evans
- Clinical and Public Health Group, UK Health Security Agency, London, UK.
- Data, Analytics and Surveillance Group, UK Health Security Agency, London, UK.
| | - Nichola R Naylor
- Clinical and Public Health Group, UK Health Security Agency, London, UK.
- Data, Analytics and Surveillance Group, UK Health Security Agency, London, UK.
| | - Tom Fowler
- Clinical and Public Health Group, UK Health Security Agency, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Susan Hopkins
- Clinical and Public Health Group, UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with the UK Health Security Agency, Oxford, UK
| | - Julie Robotham
- Clinical and Public Health Group, UK Health Security Agency, London, UK
- Data, Analytics and Surveillance Group, UK Health Security Agency, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
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Al Shibli A, Al Jufaili M, Al Alawi A, Balkhair A, Al Zakwani I, Al Azri F, Al Maamari K, Ba Alawi F, Al Qayoudhi A, Al Ghafri H. Identification of Asymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 Infections Among Healthcare Workers at Sultan Qaboos University Hospital, Oman. Sultan Qaboos Univ Med J 2023; 23:336-343. [PMID: 37655090 PMCID: PMC10467539 DOI: 10.18295/squmj.1.2023.008] [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: 09/14/2022] [Revised: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 02/25/2023] Open
Abstract
Objectives This study aimed to describe the incidence and features of asymptomatic COVID-19 infections among healthcare workers (HCWs) at a tertiary hospital in Oman. Methods This cross-sectional study was conducted between August 2020 and February 2021 among HCWs with no history of COVID-19 infection. An online questionnaire collected sociodemographic and clinical data. COVID-19 infection was diagnosed using nasopharyngeal/throat swabs, which were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Analyses were performed using the Chi-squared test, Fisher's exact test or univariate ordinary least squares regression, as appropriate. Results A total of 583 HCWs participated in the study, most of whom were female (56.6%), and the mean age was 35 ± 8 years. Only 9.6% (95% confidence interval [CI]: 7.3-12.3%) of the HCWs were at high exposure risk as they were directly involved in the care of COVID-19-infected patients. Overall, 4.1% (95% CI: 2.7-6.1%) of the HCWs screened positive for SARS-CoV-2, of which 20.8% developed symptoms within two weeks. The frequency of SARS-CoV-2 positivity among HCWs working in high-, intermediate-, low- and miscellaneous-risk areas was 1.8% (95% CI: <0.1-9.6%), 2.6% (95% CI: <0.1-6.5%), 5.3% (95% CI: 0.3-9.3%) and 4.8% (95% CI: <0.1-69.3%), respectively. Working in high-risk areas was associated with increased compliance with various infection control strategies (P <0.001). Conclusion There was a greater frequency of SARS-CoV-2 positivity among HCWs working in low-risk areas, whereas HCWs who worked in high-risk areas were significantly more likely to report increased compliance with infection control strategies.
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Affiliation(s)
- Amal Al Shibli
- Department of Emergency Medicine, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Mahmood Al Jufaili
- Department of Emergency Medicine, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Awatif Al Alawi
- Department of Emergency Medicine, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Abdullah Balkhair
- Department of Internal Medicine, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Ibrahim Al Zakwani
- Department of Pharmacology & Clinical Pharmacy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Faisal Al Azri
- Department of Radiology & Molecular Imaging, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Khuloud Al Maamari
- Department of Microbiology & Immunology, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Fatma Ba Alawi
- Department of Microbiology & Immunology, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Azza Al Qayoudhi
- Department of Microbiology & Immunology, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Hajar Al Ghafri
- Department of Microbiology & Immunology, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
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Kaboré NF, Ouédraogo S, Mamguem AK, Traoré IT, Kania D, Badolo H, Sanou G, Koné A, Yara M, Kagoné T, Ouédraogo E, Konaté B, Médah R, de Rekeneire N, Poda A, Diendéré AE, Ouédraogo B, Billa O, Paradis G, Dabakuyo-Yonli TS, Tinto H. Incidence rate and predictors of COVID-19 in the two largest cities of Burkina Faso - prospective cohort study in 2021 (ANRS-COV13). BMC Infect Dis 2023; 23:394. [PMID: 37308819 DOI: 10.1186/s12879-023-08361-2] [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: 03/08/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Early data on COVID-19 (based primarily on PCR testing) indicated a low burden in Sub-Saharan Africa. To better understand this, this study aimed to estimate the incidence rate and identify predictors of SARS-CoV-2 seroconversion in the two largest cities of Burkina Faso. This study is part of the EmulCOVID-19 project (ANRS-COV13). METHODS Our study utilized the WHO Unity protocol for cohort sero-epidemiological studies of COVID-19 in general population. We conducted random sampling stratified by age group and sex. Individuals aged 10 years and older in the cities of Ouagadougou and Bobo-Dioulasso, Burkina Faso were included and surveyed at 4 time points, each 21 days apart, from March 3 to May 15, 2021. WANTAI SARS-CoV-2 Ab ELISA serological tests were used to detect total antibodies (IgM, IgG) in serum. Predictors were investigated using Cox proportional hazards regression. RESULTS We analyzed the data from 1399 participants (1051 in Ouagadougou, 348 in Bobo-Dioulasso) who were SARS-CoV-2 seronegative at baseline and had at least one follow-up visit. The incidence rate of SARS-CoV-2 seroconversion was 14.3 cases [95%CI 13.3-15.4] per 100 person-weeks. The incidence rate was almost three times higher in Ouagadougou than in Bobo-Dioulasso (Incidence rate ratio: IRR = 2.7 [2.2-3.2], p < 0.001). The highest incidence rate was reported among women aged 19-59 years in Ouagadougou (22.8 cases [19.6-26.4] per 100 person-weeks) and the lowest among participants aged 60 years and over in Bobo-Dioulasso, 6.3 cases [4.6-8.6] per 100 person-weeks. Multivariable analysis showed that participants aged 19 years and older were almost twice as likely to seroconvert during the study period compared with those aged 10 to 18 years (Hazard ratio: HR = 1.7 [1.3-2.3], p < 0.001). Those aged 10-18 years exhibited more asymptomatic forms than those aged 19 years and older, among those who achieved seroconversion (72.9% vs. 40.4%, p < 0.001). CONCLUSION The spread of COVID-19 is more rapid in adults and in large cities. Strategies to control this pandemic in Burkina Faso, must take this into account. Adults living in large cities should be the priority targets for vaccination efforts against COVID-19.
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Affiliation(s)
- Nongodo Firmin Kaboré
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso.
| | - Samiratou Ouédraogo
- Observatoire national de la santé de la population (ONSP), Institut National de Santé Publique, Ouagadougou, Burkina Faso
- Institut National de Santé Publique du Québec (INSPQ), Montréal, Québec, Canada
- The Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Ariane Kamga Mamguem
- Epidemiology and Quality of Life Research Unit, INSERM U1231, Georges Francois Leclerc Centre - UNICANCER, Dijon, France
| | - Isidore Tiandiogo Traoré
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
- Institut Supérieur des Sciences de la Santé (INSSA), Université Nazi Boni (UNB), Bobo Dioulasso, Burkina Faso
| | - Dramane Kania
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | - Hermann Badolo
- Observatoire national de la santé de la population (ONSP), Institut National de Santé Publique, Ouagadougou, Burkina Faso
| | - Guillaume Sanou
- Centre National de Recherche et de Formation sur le Paludisme, Institut National de Santé Publique, Ouagadougou, Burkina Faso
| | - Amariane Koné
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | - Mimbouré Yara
- Observatoire national de la santé de la population (ONSP), Institut National de Santé Publique, Ouagadougou, Burkina Faso
| | - Thérèse Kagoné
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | - Esperance Ouédraogo
- Département de médicine, pharmacopée traditionnelle et pharmacie, Institut de Recherche en Sciences de la Santé (IRSS) - Centre National de la Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
| | - Blahima Konaté
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
- Département de Socio-Économie et d'Anthropologie du Développement (DSEAD), Institut des Sciences des Sociétés (INSS) - Centre National de la Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
| | - Rachel Médah
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
| | | | - Armel Poda
- Institut Supérieur des Sciences de la Santé (INSSA), Université Nazi Boni (UNB), Bobo Dioulasso, Burkina Faso
- Service des maladies infectieuses, Centre Hospitalier Universitaire Sourô Sanou, Bobo Dioulasso, Burkina Faso
| | | | - Boukary Ouédraogo
- Direction des systèmes d'information en santé (DSIS), ministère de la Santé et de l'Hygiène Publique, Ouagadougou, Burkina Faso
| | - Oumar Billa
- Epidemiology and Quality of Life Research Unit, INSERM U1231, Georges Francois Leclerc Centre - UNICANCER, Dijon, France
| | - Gilles Paradis
- Institut National de Santé Publique du Québec (INSPQ), Montréal, Québec, Canada
- The Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | | | - Halidou Tinto
- Centre MURAZ, Institut National de Santé Publique (INSP), BP 390, Bobo-Dioulasso, Burkina Faso
- Institut de Recherche en Sciences de la Santé (IRSS) - Unité de Recherche Clinique de Nanoro, Centre National de la Recherche Scientifique et Technologique (CNRST), Ouagadougou, Burkina Faso
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Rogawski McQuade ET, Blake IM, Brennhofer SA, Islam MO, Sony SSS, Rahman T, Bhuiyan MH, Resha SK, Wettstone EG, Hughlett L, Reagan C, Elwood SE, Mira Y, Mahmud AS, Hosan K, Hoque MR, Alam MM, Rahman M, Shirin T, Haque R, Taniuchi M. Real-time sewage surveillance for SARS-CoV-2 in Dhaka, Bangladesh versus clinical COVID-19 surveillance: a longitudinal environmental surveillance study (December, 2019-December, 2021). THE LANCET. MICROBE 2023; 4:e442-e451. [PMID: 37023782 PMCID: PMC10069819 DOI: 10.1016/s2666-5247(23)00010-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND Clinical surveillance for COVID-19 has typically been challenging in low-income and middle-income settings. From December, 2019, to December, 2021, we implemented environmental surveillance in a converging informal sewage network in Dhaka, Bangladesh, to investigate SARS-CoV-2 transmission across different income levels of the city compared with clinical surveillance. METHODS All sewage lines were mapped, and sites were selected with estimated catchment populations of more than 1000 individuals. We analysed 2073 sewage samples, collected weekly from 37 sites, and 648 days of case data from eight wards with varying socioeconomic statuses. We assessed the correlations between the viral load in sewage samples and clinical cases. FINDINGS SARS-CoV-2 was consistently detected across all wards (low, middle, and high income) despite large differences in reported clinical cases and periods of no cases. The majority of COVID-19 cases (26 256 [55·1%] of 47 683) were reported from Ward 19, a high-income area with high levels of clinical testing (123 times the number of tests per 100 000 individuals compared with Ward 9 [middle-income] in November, 2020, and 70 times the number of tests per 100 000 individuals compared with Ward 5 [low-income] in November, 2021), despite containing only 19·4% of the study population (142 413 of 734 755 individuals). Conversely, a similar quantity of SARS-CoV-2 was detected in sewage across different income levels (median difference in high-income vs low-income areas: 0·23 log10 viral copies + 1). The correlation between the mean sewage viral load (log10 viral copies + 1) and the log10 clinical cases increased with time (r = 0·90 in July-December, 2021 and r=0·59 in July-December, 2020). Before major waves of infection, viral load quantity in sewage samples increased 1-2 weeks before the clinical cases. INTERPRETATION This study demonstrates the utility and importance of environmental surveillance for SARS-CoV-2 in a lower-middle-income country. We show that environmental surveillance provides an early warning of increases in transmission and reveals evidence of persistent circulation in poorer areas where access to clinical testing is limited. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Elizabeth T Rogawski McQuade
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Epidemiology, Emory University, Atlanta, GA, USA
| | - Isobel M Blake
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK
| | - Stephanie A Brennhofer
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | - Erin G Wettstone
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Lauren Hughlett
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Claire Reagan
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Sarah E Elwood
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Ayesha S Mahmud
- Department of Demography, University of California at Berkeley, Berkeley, CA, USA
| | - Kawsar Hosan
- a2i, Dhaka, Bangladesh; Department of Economics, Jahangirnagar University, Dhaka, Bangladesh
| | | | | | - Mahbubur Rahman
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | | | - Mami Taniuchi
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Civil and Environmental Engineering Systems and Environment, University of Virginia, Charlottesville, VA, USA.
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Shimada R, Tsukagoshi H, Kubota R, Shinoda D, Shinohara Y, Saito A, Inoue F, Endo T, Saruki N. A nosocomial outbreak caused by human rhinovirus species A type 61 in a welfare facility in Gunma Prefecture, Japan. Jpn J Infect Dis 2023. [PMID: 37121671 DOI: 10.7883/yoken.jjid.2023.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The human rhinovirus (HRV) is generally considered as the common cold and its mild symptoms' main cause. However, HRV are also implicated in severe respiratory infections. This study reports on a nosocomial outbreak of bronchitis and pneumonia caused by HRV in a hospital during the COVID-19 epidemic in September 2022 in Gunma Prefecture, Japan. Patients continued to become infected for 9 days. During this outbreak, all 15 residents had respiratory symptoms, and HRV-A was detected in 12 of the 12 samples and phylogenetic analysis showed that it was classified into HRV-A type 61. HRV and COVID-19 or other respiratory infections cannot be differentiated from clinical symptoms; therefore, a surveillance system to monitor them may be needed.
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Affiliation(s)
- Ryo Shimada
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Japan
| | - Hiroyuki Tsukagoshi
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Japan
| | - Rina Kubota
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Japan
| | - Daisuke Shinoda
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Japan
| | - Yuri Shinohara
- Department of Nursing, National Hospital Organization Shibukawa Medical Center, Japan
| | - Akio Saito
- Department of Hematology, National Hospital Organization Shibukawa Medical Center, Japan
| | - Fumitaka Inoue
- Department of Neonatology, National Hospital Organization Shibukawa Medical Center, Japan
| | - Tadaaki Endo
- Health Section, Shibukawa Health and Welfare Office, Japan
| | - Nobuhiro Saruki
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Japan
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9
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Zhang Z, Chen Y, Li Q, Yang Y, Chen J, Lin Y, Xiao Z, Ma M, Wu C, Liu B, Xu R, Xiang J. Epidemiological characteristics of overseas imported COVID-19 cases into China: A scoping literature review. Front Public Health 2023; 11:1143468. [PMID: 37064698 PMCID: PMC10090422 DOI: 10.3389/fpubh.2023.1143468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Previous studies investigating the characteristics of imported cases were mostly limited to a certain province/city or a specific sub-group during a certain period with a small sample size, which may not provide an overall picture of the characteristics of imported cases. In this scoping literature review, we comprehensively synthesized the epidemiological characteristics of overseas imported COVID-19 cases into China by retrieving six literature databases, with aims to provide implications for more targeted control, prevention, and medical treatment of this disease. After dropping duplicates and reviewing titles, abstracts, and full-texts, 50 articles were included in the review finally, including 26 (52%) articles in English and 24 (48%) articles in Chinese. According to the type of data sources, the 50 studies were divided into three categories: 13 (26%) articles using data sourced from the Chinese Infectious Diseases Online Reporting System, 15 (30%) articles using data from the websites of national/local health departments, and 22 (44%) articles using hospital admission data. Most of the overseas imported COVID-19 cases were young and middle-aged Chinese students and businessmen returning from the United States, Europe, and some neighboring countries. Airport routine health screening measures could not identify COVID-cases effectively, although scheduled multiple nucleic acid tests were required before boarding. Almost all imported cases were identified during the hotel quarantine period. Although a large proportion of imported cases were asymptomatic or with mild symptoms in the published literature, they may be due to participant selection bias. The exact proportion of asymptomatic cases may need to be further investigated especially through population-based large-scale studies.
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Affiliation(s)
- Zitong Zhang
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yifeng Chen
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Qingyu Li
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yan Yang
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jiake Chen
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yan Lin
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Zhihong Xiao
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Marie Ma
- Magill Medical Center, Adelaide, SA, Australia
| | - Chuancheng Wu
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Baoying Liu
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Rongxian Xu
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jianjun Xiang
- School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
- *Correspondence: Jianjun Xiang,
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Sarría-Santamera A, Mukhtarova K, Baizhaxynova A, Kanatova K, Zhumambayeva S, Akilzhanova A, Azizan A. Association of CYP24A1 Gene rs6127099 (A > T) Polymorphism with Lower Risk to COVID-19 Infection in Kazakhstan. Genes (Basel) 2023; 14:genes14020307. [PMID: 36833234 PMCID: PMC9957291 DOI: 10.3390/genes14020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
In December 2019, SARS-CoV-2 was identified in Wuhan, China. Infection by SARS-CoV-2 causes coronavirus disease 2019 (COVID-19), which is characterized by fever, cough, dyspnea, anosmia, and myalgia in many cases. There are discussions about the association of vitamin D levels with COVID-19 severity. However, views are conflicting. The aim of the study was to examine associations of vitamin D metabolism pathway gene polymorphisms with symptomless COVID-19 susceptibility in Kazakhstan. The case-control study examined the association between asymptomatic COVID-19 and vitamin D metabolism pathway gene polymorphisms in 185 participants, who previously reported not having COVID-19, were PCR negative at the moment of data collection, and were not vaccinated. A dominant mutation in rs6127099 (CYP24A1) was found to be protective of asymptomatic COVID-19. Additionally, the G allele of rs731236 TaqI (VDR), dominant mutation in rs10877012 (CYP27B1), recessive rs1544410 BsmI (VDR), and rs7041 (GC) are worth consideration since they were statistically significant in bivariate analysis, although their independent effect was not found in the adjusted multivariate logistic regression model.
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Affiliation(s)
| | - Kymbat Mukhtarova
- School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan
| | | | - Kaznagul Kanatova
- School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan
| | - Saule Zhumambayeva
- Department of Propedeutics of Children Disease, Astana Medical University, Astana 010000, Kazakhstan
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Azliyati Azizan
- College of Osteopathic Medicine, Touro University Nevada, Henderson, NV 89014, USA
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11
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Predicting the aggravation of coronavirus disease-19 pneumonia using chest computed tomography scans. PLoS One 2022; 17:e0276738. [PMID: 36327268 PMCID: PMC9632883 DOI: 10.1371/journal.pone.0276738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Presently, coronavirus disease-19 (COVID-19) is spreading worldwide without an effective treatment method. For COVID-19, which is often asymptomatic, it is essential to adopt a method that does not cause aggravation, as well as a method to prevent infection. Whether aggravation can be predicted by analyzing the extent of lung damage on chest computed tomography (CT) scans was examined. The extent of lung damage on pre-intubation chest CT scans of 277 patients with COVID-19 was assessed. It was observed that aggravation occurred when the CT scan showed extensive damage associated with ground-glass opacification and/or consolidation (p < 0.0001). The extent of lung damage was similar across the upper, middle, and lower fields. Furthermore, upon comparing the extent of lung damage based on the number of days after onset, a significant difference was found between the severe pneumonia group (SPG) with intubation or those who died and non-severe pneumonia group (NSPG) ≥3 days after onset, with aggravation observed when ≥14.5% of the lungs exhibited damage at 3–5 days (sensitivity: 88.2%, specificity: 72.4%) and when ≥20.1% of the lungs exhibited damage at 6–8 days (sensitivity: 88.2%, specificity: 69.4%). Patients with aggravation suddenly developed hypoxemia after 7 days from the onset; however, chest CT scans obtained in the paucisymptomatic phase without hypoxemia indicated that subsequent aggravation could be predicted based on the degree of lung damage. Furthermore, in subjects aged ≥65 years, a significant difference between the SPG and NSPG was observed in the extent of lung damage early beginning from 3 days after onset, and it was found that the degree of lung damage could serve as a predictor of aggravation. Therefore, to predict and improve prognosis through rapid and appropriate management, evaluating patients with factors indicating poor prognosis using chest CT is essential.
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12
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Zhang W, Zhou S, Wang G, Cao M, Sun D, Lu W, Shi L, Guo Y, Xu X, Pu Y, Chen C, Yang H, Sun Y, Hu H, Fang B. Clinical predictors and RT-PCR profile of prolonged viral shedding in patients with SARS-CoV-2 Omicron variant in Shanghai: A retrospective observational study. Front Public Health 2022; 10:1015811. [PMID: 36353283 PMCID: PMC9638094 DOI: 10.3389/fpubh.2022.1015811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 01/27/2023] Open
Abstract
Objective To evaluate determinants of prolonged viral RNA shedding in hospitalized patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant infection. Materials and methods Hospitalized patients tested SARS-CoV-2 positive by nasopharyngeal real-time reverse transcriptase-polymerase chain reaction (RT-PCR) were included in the single-center, retrospective study. Patients were divided into 2 groups according to the timing of viral clearance (≤ 8 days, "early clearance" and ≥15 days, "late clearance"). Results 4,084 patients were included in the study (1,023 late clearance, 3,061 early clearance), with median age of 50 years and a higher proportion (61.4%) of male. Univariate analyses showed that comorbidities (including hypertension, diabetes, and coronary heart disease), receiving vaccine, the number of vaccinations, cycle threshold (Ct) open reading frame 1ab (ORF 1ab), and nucleocapsid protein (N) gene values on admission were associated with late viral clearance. In the multivariable analysis, the number of vaccinations (P = 0.010) and Ct ORF 1ab gene (P < 0.001) values on admission were significantly associated with late viral clearance. Generalized Estimating Equations (GEE) analysis showed that the Ct value of ORF 1ab gene and N gene remained unchanged within 3 days, and showed progressively higher values with increasing days during late viral RNA clearance. Conclusion The number of vaccinations and Ct values of ORF 1ab gene were independently associated with a prolonged SARS-CoV-2 RNA shedding.
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Affiliation(s)
- Wen Zhang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuang Zhou
- School of Acupuncture-Moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gang Wang
- Department of Critical Care Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Min Cao
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ding Sun
- Department of Rheumatology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Lu
- Department of Nursing, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li Shi
- Department of Pediatrics, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong Guo
- Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiangru Xu
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuting Pu
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Caiyu Chen
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongqiang Yang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuting Sun
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongyi Hu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Hongyi Hu
| | - Bangjiang Fang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Institute of Emergency and Critical Care Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China,*Correspondence: Bangjiang Fang
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13
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Dufour P, Paridaens H, Senterre JM, Minon JM. Relevance of cycle threshold values in mass screening by reverse-transcription-PCR during COVID-19 pandemic in Belgium: a decision-making support? Future Virol 2022. [PMID: 36172257 PMCID: PMC9491372 DOI: 10.2217/fvl-2022-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022]
Abstract
Aim: The Belgium’s strategy against COVID-19 was partly based on mass screening. Here, we reported the results observed in a Belgian mass screening center. Materials & methods: Between October 2020 and February 2021, 32,089 samples were collected analyzed with reverse-transcription PCR (Thermo Fisher Scientific kits and apparatus). Patients were categorized according to their contagiousness (extrapolated from the cycle threshold [Ct] values and the recommendation of Sciensano). Results: We observed association between Ct values and age, with higher Ct observed in extreme age groups (<6 years and >75 years). Conclusion: The analysis of the evolution of the contagiousness of these patients tested twice within a 7-day period showed the relevancy of the recommendation edited by Sciensano. The Belgium’s strategy against COVID-19 was partly based on mass screening performed with reverse-transcription PCR analysis performed on nasopharyngeal samples. Reverse-transcription PCR allows the detection of individuals infected by the virus. In addition, it provides semi quantitative results correlated to the quantity of virus present in the patient, these results are difficult to interpret for the patients and numerous practitioners. In our study, we showed that the interpretation of these results should take into account the age of the patients. We also showed that the semi quantitative result observed in a positive patient is not predictive of the evolution of the viral load (quantity of virus present in the organism) in the 7 following days.
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Affiliation(s)
- Patrice Dufour
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
| | - Henry Paridaens
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
| | - Jean-Marc Senterre
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
| | - Jean-Marc Minon
- Department of Laboratory Medicine, Centre Hospitalier Régional de la Citadelle, Liège, 4000, Belgium
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14
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Hattori T, Saito T, Okuya K, Takahashi Y, Miyamoto H, Kajihara M, Igarashi M, Takada A. Human ACE2 Genetic Polymorphism Affecting SARS-CoV and SARS-CoV-2 Entry into Cells. Microbiol Spectr 2022; 10:e0087022. [PMID: 35862965 PMCID: PMC9430119 DOI: 10.1128/spectrum.00870-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have a single envelope glycoprotein (S protein) that binds to human angiotensin-converting enzyme 2 (ACE2) on the host cell membrane. Previous mutational scanning studies have suggested that some substitutions corresponding to single nucleotide variants (SNVs) in human ACE2 affect the binding affinity to the receptor binding domain (RBD) of the SARS-CoV-2 S protein. However, the importance of these substitutions in actual virus infection is still unclear. In this study, we investigated the effects of the reported ACE2 SNV substitutions on the entry of SARS-CoV and SARS-CoV-2 into cells, using vesicular stomatitis Indiana virus (VSIV) pseudotyped with S proteins of these coronaviruses (CoVs). HEK293T cells transfected with plasmids expressing ACE2 having each SNV substitution were infected with the pseudotyped VSIVs and relative infectivities were determined compared to the cells expressing wild-type ACE2. We found that some of the SNV substitutions positively or negatively affected the infectivities of the pseudotyped viruses. Particularly, the H505R substitution significantly enhanced the infection with the pseudotyped VSIVs, including those having the substitutions found in the S protein RBD of SARS-CoV-2 variants of concern. Our findings suggest that human ACE2 SNVs may potentially affect cell susceptibilities to SARS-CoV and SARS-CoV-2. IMPORTANCE SARS-CoV and SARS-CoV-2 are known to cause severe pneumonia in humans. The S protein of these CoVs binds to the ACE2 molecule on the plasma membrane and mediates virus entry into cells. The interaction between the S protein and ACE2 is thought to be important for host susceptibility to these CoVs. Although previous studies suggested that some SNV substitutions in ACE2 might affect the binding to the S protein, it remains elusive whether these SNV substitutions actually alter the efficiency of the entry of SARS CoVs into cells. We analyzed the impact of the ACE2 SNVs on the cellular entry of SARS CoVs using pseudotyped VSIVs having the S protein on the viral surface. We found that some of the SNV substitutions positively or negatively affected the infectivities of the viruses. Our data support the notion that genetic polymorphisms of ACE2 may potentially influence cell susceptibilities to SARS CoVs.
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Affiliation(s)
- Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kosuke Okuya
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuji Takahashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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Beltrán-Camacho L, Eslava-Alcón S, Rojas-Torres M, Sánchez-Morillo D, Martinez-Nicolás MP, Martín-Bermejo V, de la Torre IG, Berrocoso E, Moreno JA, Moreno-Luna R, Durán-Ruiz MC. The serum of COVID-19 asymptomatic patients up-regulates proteins related to endothelial dysfunction and viral response in circulating angiogenic cells ex-vivo. Mol Med 2022; 28:40. [PMID: 35397534 PMCID: PMC8994070 DOI: 10.1186/s10020-022-00465-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has already caused 6 million deaths worldwide. While asymptomatic individuals are responsible of many potential transmissions, the difficulty to identify and isolate them at the high peak of infection constitutes still a real challenge. Moreover, SARS-CoV-2 provokes severe vascular damage and thromboembolic events in critical COVID-19 patients, deriving in many related deaths and long-hauler symptoms. Understanding how these processes are triggered as well as the potential long-term sequelae, even in asymptomatic individuals, becomes essential.
Methods We have evaluated, by application of a proteomics-based quantitative approach, the effect of serum from COVID-19 asymptomatic individuals over circulating angiogenic cells (CACs). Healthy CACs were incubated ex-vivo with the serum of either COVID-19 negative (PCR −/IgG −, n:8) or COVID-19 positive asymptomatic donors, at different infective stages: PCR +/IgG − (n:8) and PCR −/IgG + (n:8). Also, a label free quantitative approach was applied to identify and quantify protein differences between these serums. Finally, machine learning algorithms were applied to validate the differential protein patterns in CACs.
Results Our results confirmed that SARS-CoV-2 promotes changes at the protein level in the serum of infected asymptomatic individuals, mainly correlated with altered coagulation and inflammatory processes (Fibrinogen, Von Willebrand Factor, Thrombospondin-1). At the cellular level, proteins like ICAM-1, TLR2 or Ezrin/Radixin were only up-regulated in CACs treated with the serum of asymptomatic patients at the highest peak of infection (PCR + /IgG −), but not with the serum of PCR −/IgG + individuals. Several proteins stood out as significantly discriminating markers in CACs in response to PCR or IgG + serums. Many of these proteins particiArticle title: Kindly check and confirm the edit made in the article
title.pate in the initial endothelial response against the virus. Conclusions The ex vivo incubation of CACs with the serum of asymptomatic COVID-19 donors at different stages of infection promoted protein changes representative of the endothelial dysfunction and inflammatory response after viral infection, together with activation of the coagulation process. The current approach constitutes an optimal model to study the response of vascular cells to SARS-CoV-2 infection, and an alternative platform to test potential inhibitors targeting either the virus entry pathway or the immune responses following SARS-CoV-2 infection. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00465-w.
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Comparison of the Characteristics of Asymptomatic and Presymptomatic Patients with Coronavirus Disease 2019 in the Republic of Korea. J Epidemiol Glob Health 2021; 11:354-363. [PMID: 34757529 PMCID: PMC8579178 DOI: 10.1007/s44197-021-00011-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/15/2021] [Indexed: 01/08/2023] Open
Abstract
PURPOSE This retrospective study aimed to evaluate the baseline characteristics of asymptomatic patients with coronavirus disease 2019 at admission and to follow-up their clinical manifestations and radiological findings during hospitalization. METHODS Patients with coronavirus disease 2019 who were asymptomatic at admission were divided into two groups-those with no symptoms until discharge (group A) and those who developed symptoms after admission (group B). Patients who could not express their own symptoms were excluded. RESULTS Overall, 127 patients were enrolled in the study, of whom 19 and 108 were assigned to groups A and B, respectively. The mean age and median C-reactive protein level were higher in group B than in group A. All patients in group A and one-third of patients in group B had normal initial chest radiographs; 15.8% and 48.1% of patients in groups A and B, respectively, had pneumonia during hospitalization. One patient in group B, whose condition was not severe at the time of admission, deteriorated due to aggravated pneumonia and was transferred to a tertiary hospital. CONCLUSION We summarize the clinical characteristics during hospitalization of patients with coronavirus disease 2019 who were purely asymptomatic at the time of admission. The majority of asymptomatic patients with coronavirus disease 2019 were discharged without significant events during hospitalization. However, it may be difficult to predict subsequent events from initial chest radiographs or oxygen saturation at admission.
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