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Christofferson RC, Giovanni JE, Koumans EH, Ategbole M, Clark SD, Godfred-Cato S, Menon MP, Sastalla I, Schweitzer BK, Uyeki TM. A Systematic Review of Prolonged SARS-CoV-2 Shedding in Immunocompromised Persons. Influenza Other Respir Viruses 2025; 19:e70121. [PMID: 40394759 DOI: 10.1111/irv.70121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 05/07/2025] [Accepted: 05/11/2025] [Indexed: 05/22/2025] Open
Abstract
BACKGROUND Although reports have documented prolonged SARS-CoV-2 RNA detection in immunocompromised patients, few studies have systematically analyzed data on duration of SARS-CoV-2 in respiratory specimens of immunocompromised patients. METHODS A systematic review was undertaken to describe SARS-CoV-2 RNA and infectious virus detection in immunocompromised patients from published data between January 1, 2020 and July 1, 2022. Patients were included if there was ≥ 1 positive SARS-CoV-2 RNA result in respiratory specimens collected > 20 days since symptom onset or first positive SARS-CoV-2 RT-PCR result. RESULTS Of the 183 patients, 175 were symptomatic with 83 (47.4%) that experienced intermittent relapsing symptoms, while pneumonia was reported in 122 (66.7%). Immunocompromising conditions represented were hematologic malignancy treatment (89, 48.6%), solid organ transplant (47, 25.7%), autoimmune disease treatment (14, 7.7%), solid tumor treatment (3, 1.6%), HIV infection (15, 8.2%), and primary immunodeficiency (15, 8.2%). Median duration from the first to the last positive SARS-CoV-2 RT-PCR result was 56 days in upper respiratory and 60 days in lower respiratory tract specimens. Significant differences in median duration of SARS-CoV-2 RNA detection were observed between patients with and without pneumonia and for patients with hematologic malignancies compared to solid organ transplant patients. Among patients with viral culture performed, median duration of replication-competent SARS-CoV-2 was 60.5 days from symptom onset (maximum 238 days) and 59 days from first RT-PCR positive result (maximum 268 days). CONCLUSIONS Immunocompromised persons can have replication-competent SARS-CoV-2 in respiratory tissues for months, including while asymptomatic. Serial SARS-CoV-2 testing can inform the duration of isolation for immunocompromised patients with SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Emily H Koumans
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Muyiwa Ategbole
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Samantha D Clark
- Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana, USA
| | | | - Manoj P Menon
- Fred Hutchinson Cancer Center Seattle, Seattle, Washington, USA
| | - Inka Sastalla
- Office of Genomics and Advanced Technologies, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Beth K Schweitzer
- Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana, USA
| | - Timothy M Uyeki
- Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana, USA
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2
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Bolis M, Uceda Renteria S, Alagna L, Liparoti A, Passerini BZ, Pastena A, Parisi A, Callegaro A, Bandera A, Muscatello A, Alteri C. SARS-CoV-2 genomic evolution during a severe and long-lasting omicron infection under antiviral therapy. BMC Infect Dis 2025; 25:359. [PMID: 40082784 PMCID: PMC11907959 DOI: 10.1186/s12879-025-10740-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Accepted: 03/03/2025] [Indexed: 03/16/2025] Open
Abstract
BACKGROUND Prolonged SARS-CoV-2 infection observed in immunocompromised individuals even in the presence of antiviral treatment provides opportunities for viruses to evolve in immune escape and drug-resistant variants. CASE PRESENTATION A 72-year-old male with IgG4-related disease was admitted to the Emergency Department of a city Hospital in Milan and then transferred to Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico in December 2023, due to respiratory distress due to SARS-CoV-2 infection diagnosed in November 2023. After 117 days since the onset of the infection, and two cycles of sotrovimab/remdesivir combined therapy, the clinical improvement allowed the hospital discharge, notwithstanding the persistent SARS-CoV-2 positivity. Fifteen days later, the patient was re-admitted to the hospital due to worsening clinical conditions. After a third cycle of sotrovimab/remdesivir combined therapy prolonged with nirmatrelvir/ritonavir, nasopharyngeal load dropped and clinical conditions improved, ending with a successful discharge. SARS-CoV-2 whole genome sequences, obtained at six time-points of infection, showed an FL.1.5.1 recombinant form infection and a genetic distance of median (IQR) 0.00052 (0.00041-0.00066) similar to the genetic distance observed among the 43 contemporaneous FL.1.5.1 recombinant forms (p = 0.098). De novo SNPs were observed at all time points, with a peak (n = 70) at day 133 of infection, corresponding to the time of the second hospitalization. Six non-synonymous mutations (three in the RdRp and three in the spike protein, four of them known to be associated with drug resistance) appeared transiently, after the third and fourth course of sotrovimab 500 mg/remdesivir combination. Five de novo SNPs, three of them in the spike protein, were fixed over the long-lasting infection. The spike N856K, associated with reduced fusogenicity and infectivity in Omicron BA.1, was completely replaced by constitutive N at day 136. CONCLUSIONS This clinical case confirms the intra-host evolution dynamics of SARS-CoV-2 in an immunocompromised, prolonged-infected individual, involving positions associated with drug resistance and fusogenic traits of SARS-CoV-2. These results underscore the importance of the early detection of SARS-CoV-2 infection in immunocompromised individuals, and its rapid containment using highly effective treatment, to limit serious complications and the risk of new and potentially concerning viral variants emergence.
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Affiliation(s)
- Matteo Bolis
- Infectious Diseases Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
| | - Sara Uceda Renteria
- Microbiology and Virology Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
| | - Laura Alagna
- Infectious Diseases Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
| | - Arianna Liparoti
- Infectious Diseases Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
| | | | - Andrea Pastena
- Infectious Diseases Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
| | - Alessandra Parisi
- Residency in Microbiology and Virology School, University of Milan, Milan, Italy
| | - Annapaola Callegaro
- Microbiology and Virology Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy
| | - Claudia Alteri
- Microbiology and Virology Unit, IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation, Milan, Italy.
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
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3
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Trauer JM, Hughes AE, Shipman DS, Meehan MT, Henderson AS, McBryde ES, Ragonnet R. A data science pipeline applied to Australia's 2022 COVID-19 Omicron waves. Infect Dis Model 2025; 10:99-109. [PMID: 39364337 PMCID: PMC11447346 DOI: 10.1016/j.idm.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 08/04/2024] [Accepted: 08/22/2024] [Indexed: 10/05/2024] Open
Abstract
The field of software engineering is advancing at astonishing speed, with packages now available to support many stages of data science pipelines. These packages can support infectious disease modelling to be more robust, efficient and transparent, which has been particularly important during the COVID-19 pandemic. We developed a package for the construction of infectious disease models, integrated it with several open-source libraries and applied this composite pipeline to multiple data sources that provided insights into Australia's 2022 COVID-19 epidemic. We aimed to identify the key processes relevant to COVID-19 transmission dynamics and thereby develop a model that could quantify relevant epidemiological parameters. The pipeline's advantages include markedly increased speed, an expressive application programming interface, the transparency of open-source development, easy access to a broad range of calibration and optimisation tools and consideration of the full workflow from input manipulation through to algorithmic generation of the publication materials. Extending the base model to include mobility effects slightly improved model fit to data, with this approach selected as the model configuration for further epidemiological inference. Under our assumption of widespread immunity against severe outcomes from recent vaccination, incorporating an additional effect of the main vaccination programs rolled out during 2022 on transmission did not further improve model fit. Our simulations suggested that one in every two to six COVID-19 episodes were detected, subsequently emerging Omicron subvariants escaped 30-60% of recently acquired natural immunity and that natural immunity lasted only one to eight months on average. We documented our analyses algorithmically and present our methods in conjunction with interactive online code notebooks and plots. We demonstrate the feasibility of integrating a flexible domain-specific syntax library with state-of-the-art packages in high performance computing, calibration, optimisation and visualisation to create an end-to-end pipeline for infectious disease modelling. We used the resulting platform to demonstrate key epidemiological characteristics of the transition from the emergency to the endemic phase of the COVID-19 pandemic.
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Affiliation(s)
- James M. Trauer
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Angus E. Hughes
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - David S. Shipman
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Michael T. Meehan
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Alec S. Henderson
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Emma S. McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Romain Ragonnet
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
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4
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Vijatov-Đurić G, Milanović B, Barišić N, Ivetić J, Đuretić A, Kesić J, Ležakov O, Vorgučin I, Vilotijević-Dautović G, Ristić M, Koprivšek K, Stojanović V. Characteristics of Multisystem Inflammatory Syndrome in Children Across COVID-19 Variants in Vojvodina. J Clin Med 2024; 13:6672. [PMID: 39597816 PMCID: PMC11594632 DOI: 10.3390/jcm13226672] [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: 10/05/2024] [Revised: 11/03/2024] [Accepted: 11/05/2024] [Indexed: 11/29/2024] Open
Abstract
Background/Objectives: To investigate if the severity and presentation of multisystem inflammatory syndrome in children (MIS-C) vary between different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Methods: This retrospective study included 59 patients aged 0-18 years, diagnosed with COVID-19 and MIS-C, treated and monitored over a one-year period after discharge from hospital. The patients were grouped according to the predominant SARS-CoV-2 variant. The predominant variant of SARS-CoV-2 was assumed by the date of hospitalization. The following patient data were collected: demographic data (age, sex), information on comorbidities, body mass index, clinical data (fever and duration of febrile periods, symptoms of Kawasaki-like phenotypes, and presence of respiratory, cardiovascular, gastrointestinal, neurological and other symptoms), and laboratory and imaging findings. Results: In total, 24 (41%), 19 (32%), and 15 (25%) patients were diagnosed with MIS-C during the Alpha, Delta, and Omicron periods, respectively (63.8% were males; 36.2% were females). Comorbidities were present in 49% of patients. Respiratory symptoms were the most common during the Delta period (73%, p = 0.028). There was no statistically significant difference in the occurrence of other symptoms, laboratory findings, treatment, complications, and long-term outcomes between groups. Conclusions: No significant correlation was found between hospitalization date (used to estimate COVID-19 variant) and presentation/severity of MIS-C.
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Affiliation(s)
- Gordana Vijatov-Đurić
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Borko Milanović
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Nenad Barišić
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Jelena Ivetić
- Faculty of Technical Sciences, Univerity of Novi Sad, 21000 Novi Sad, Serbia;
| | - Andrea Đuretić
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Jelena Kesić
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Ognjen Ležakov
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Ivana Vorgučin
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Gordana Vilotijević-Dautović
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Mioljub Ristić
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute of Public Health of Vojvodina, Department of Epidemiology, 21000 Novi Sad, Serbia
| | - Katarina Koprivšek
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
| | - Vesna Stojanović
- Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia; (G.V.-Đ.); (B.M.); (A.Đ.); (J.K.); (I.V.); (G.V.-D.); (M.R.); (K.K.); (V.S.)
- Institute for Child and Youth Healthcare of Vojvodina, 21000 Novi Sad, Serbia
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5
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Harris JE. A tight fit of the SIR dynamic epidemic model to daily cases of COVID-19 reported during the 2021-2022 Omicron surge in New York City: A novel approach. Stat Methods Med Res 2024; 33:1877-1898. [PMID: 39559983 DOI: 10.1177/09622802241277956] [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] [Indexed: 11/20/2024]
Abstract
We describe a novel approach for recovering the underlying parameters of the SIR dynamic epidemic model from observed data on case incidence. We formulate a discrete-time approximation of the original continuous-time model and search for the parameter vector that minimizes the standard least squares criterion function. We show that the gradient vector and matrix of second-order derivatives of the criterion function with respect to the parameters adhere to their own systems of difference equations and thus can be exactly calculated iteratively. Applying our new approach, we estimated a four-parameter SIR model from daily reported cases of COVID-19 during the SARS-CoV-2 Omicron/BA.1 surge of December 2021-March 2022 in New York City. The estimated SIR model showed a tight fit to the observed data, but less so when we excluded residual cases attributable to the Delta variant during the initial upswing of the wave in December. Our analyses of both the real-world COVID-19 data and simulated case incidence data revealed an important problem of weak parameter identification. While our methods permitted for the separate estimation of the infection transmission parameter and the infection persistence parameter, only a linear combination of these two key parameters could be estimated with precision. The SIR model appears to be an adequate reduced-form description of the Omicron surge, but it is not necessarily the correct structural model. Prior information above and beyond case incidence data may be required to sharply identify the parameters and thus distinguish between alternative epidemic models.
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Affiliation(s)
- Jeffrey E Harris
- Department of Economics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Adult Medicine Department, Eisner Health, Los Angeles, CA, USA
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6
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Kitano T, Kitagawa D, Murata M, Onishi M, Mori T, Hachisuka S, Okubo T, Yamamoto N, Nishikawa H, Onaka M, Suzuki R, Sekine M, Suzuki S, Nakamura F, Yoshida S. Duration of PCR positivity by type of respiratory virus among children using a multiplex PCR test. J Med Virol 2024; 96:e29890. [PMID: 39188069 DOI: 10.1002/jmv.29890] [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: 04/23/2024] [Revised: 07/31/2024] [Accepted: 08/18/2024] [Indexed: 08/28/2024]
Abstract
Prolonged positive polymerase chain reaction (PCR) results, irrespective of the transmission risk, can lead to prolonged restrictions on daily activities and infection precaution interventions. Studies evaluating the duration of PCR positivity for multiple pathogens in a single patient cohort are scarce. This study aimed to evaluate and compare the durations of PCR positivity for multiple respiratory viruses among children and adolescents. This retrospective study was conducted between April 2018 and March 2024 using a multiplex PCR respiratory panel for symptomatic children and adolescents who had at least two tests within 90 days of study period, with the first PCR test positive. The rate and likelihood of persistent PCR positivity were evaluated for multiple respiratory viruses. For 1325 positive results, repeat tests were conducted within 90 days. The persistent PCR positivity rate at repeat testing decreased over time (60.6%, Days 1-15 and 21.7%, Days 76-90, after the first test). In multivariate logistic regression analysis, an increased likelihood of persistent PCR positivity was observed for rhinovirus/enterovirus and adenovirus, whereas decreased likelihood of persistent positivity was seen in influenza and seasonal coronaviruses, compared with parainfluenza viruses. Persistent PCR positivity is common for multiple respiratory viruses in symptomatic children.
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Affiliation(s)
- Taito Kitano
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Daisuke Kitagawa
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Masayuki Murata
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Mai Onishi
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Takahiro Mori
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Soshi Hachisuka
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Tenshin Okubo
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Naohiro Yamamoto
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Hiroki Nishikawa
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Masayuki Onaka
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Rika Suzuki
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Madoka Sekine
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Soma Suzuki
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Fumihiko Nakamura
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Sayaka Yoshida
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
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7
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Baumgart SWL, McLachlan A, Kenny H, McKew G, Maddocks S, Chen SCA, Kok J. Deisolation in the Healthcare Setting Following Recent COVID-19 Infection. Viruses 2024; 16:1131. [PMID: 39066294 PMCID: PMC11281359 DOI: 10.3390/v16071131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Deisolation of persons infected with SARS-CoV-2, the virus that causes COVID-19, presented a substantial challenge for healthcare workers and policy makers, particularly during the early phases of the pandemic. Data to guide deisolation of SARS-CoV-2-infected patients remain limited, and the risk of transmitting and acquiring infection has changed with the evolution of SARS-CoV-2 variants and population immunity from previous vaccination or infection, or both. AIMS This review examines the evidence to guide the deisolation of SARS-CoV-2-infected inpatients within the hospital setting when clinically improving and also of healthcare workers with COVID-19 prior to returning to work. METHODS A review was performed using relevant search terms in Medline, EMBASE, Google Scholar, and PubMed. RESULTS AND DISCUSSION The evidence is reviewed with regards to the nature of SARS-CoV-2 transmission, the role of testing to guide deisolation, and the impact of SARS-CoV-2-specific immunity. A paradigm and recommendations are proposed to guide deisolation for inpatients and return to work for healthcare workers.
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Affiliation(s)
- Samuel W. L. Baumgart
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Aidan McLachlan
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Hayden Kenny
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Genevieve McKew
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Susan Maddocks
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
| | - Sharon C.-A. Chen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
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8
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Pourriyahi H, Hajizadeh N, Khosravi M, Pourriahi H, Soleimani S, Hosseini NS, Mohammad AP, Goodarzi A. New variants of COVID-19 (XBB.1.5 and XBB.1.16, the "Arcturus"): A review of highly questioned concerns, a brief comparison between different peaks in the COVID-19 pandemic, with a focused systematic review on expert recommendations for prevention, vaccination, and treatment measures in the general population and at-risk groups. Immun Inflamm Dis 2024; 12:e1323. [PMID: 38938013 PMCID: PMC11211615 DOI: 10.1002/iid3.1323] [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: 01/01/2024] [Revised: 04/11/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
INTRODUCTION The COVID-19 pandemic has taken many forms and continues to evolve, now around the Omicron wave, raising concerns over the globe. With COVID-19 being declared no longer a "public health emergency of international concern (PHEIC)," the COVID pandemic is still far from over, as new Omicron subvariants of interest and concern have risen since January of 2023. Mainly with the XBB.1.5 and XBB.1.16 subvariants, the pandemic is still very much "alive" and "breathing." METHODS This review consists of five highly concerning questions about the current state of the COVID Omicron peak. We searched four main online databases to answer the first four questions. For the last one, we performed a systematic review of the literature, with keywords "Omicron," "Guidelines," and "Recommendations." RESULTS A total of 31 articles were included. The main symptoms of the current Omicron wave include a characteristically high fever, coughing, conjunctivitis (with itching eyes), sore throat, runny nose, congestion, fatigue, body ache, and headache. The median incubation period of the symptoms is shorter than the previous peaks. Vaccination against COVID can still be considered effective for the new subvariants. CONCLUSION Guidelines recommend continuation of personal protective measures, third and fourth dose boosters, along with administration of bivalent messenger RNA vaccine boosters. The consensus antiviral treatment is combination therapy using Nirmatrelvir and Ritonavir, and the consensus for pre-exposure prophylaxis is Tixagevimab and Cilgavimab combination. We hope the present paper raises awareness for the continuing presence of COVID and ways to lower the risks, especially for at-risk groups.
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Affiliation(s)
- Homa Pourriyahi
- Student Research Committee, School of MedicineIran University of Medical SciencesTehranIran
| | - Nima Hajizadeh
- School of MedicineIran University of Medical SciencesTehranIran
| | - Mina Khosravi
- School of MedicineIran University of Medical SciencesTehranIran
| | - Homayoun Pourriahi
- Student Research Committee, School of MedicineIran University of Medical SciencesTehranIran
| | - Sanaz Soleimani
- Student Research Committee, School of MedicineIran University of Medical SciencesTehranIran
- Rasool Akram Medical Complex Clinical Research Development Center (RCRDC), School of MedicineIran University of Medical SciencesTehranIran
| | | | | | - Azadeh Goodarzi
- Department of Dermatology, Rasool Akram Medical Complex Clinical Research Development Center (RCRDC), School of MedicineIran University of Medical SciencesTehranIran
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9
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Corado KC, Chew KW, Giganti MJ, Mu Y, Fletcher CV, Currier JS, Daar ES, Wohl DA, Li JZ, Moser CB, Ritz J, Javan AC, Neytman G, Caskey M, Hughes MD, Smith DM, Eron JJ, ACTIV-2/A5401 Study Team. Safety, Efficacy, and Pharmacokinetics of Combination SARS-CoV-2 Neutralizing Monoclonal Antibodies BMS-986414 (C135-LS) and BMS-986413 (C144-LS) Administered Subcutaneously in Non-Hospitalized Persons with COVID-19 in a Phase 2 Trial. Pathog Immun 2024; 9:138-155. [PMID: 38746756 PMCID: PMC11093219 DOI: 10.20411/pai.v9i1.660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/06/2024] [Indexed: 08/18/2024] Open
Abstract
Background Outpatient COVID-19 monoclonal antibody (mAb) treatment via subcutaneous delivery, if effective, overcomes the logistical burdens of intravenous administration. Methods ACTIV-2/A5401 was a randomized, masked placebo-controlled platform trial where participants with COVID-19 at low risk for progression were randomized 1:1 to subcutaneously administered BMS-986414 (C135-LS) 200 mg, plus BMS-986413 (C144-LS) 200 mg, (BMS mAbs), or placebo. Coprimary outcomes were time to symptom improvement through 28 days; nasopharyngeal SARS-CoV-2 RNA below the lower limit of quantification (LLoQ) on days 3, 7, or 14; and treatment-emergent grade 3 or higher adverse events (TEAEs) through 28 days. Results A total of 211 participants (105 BMS mAbs and 106 placebo) initiated study product. Time to symptom improvement favored the active therapy but was not significant (median 8 vs 10 days, P=0.19). There was no significant difference in the proportion with SARS-CoV-2 RNA Conclusions While safe, the BMS mAbs delivered subcutaneously were not effective at treating COVID-19 at low risk for progression. The lack of clinically significant activity may relate to the pharmacokinetics of subcutaneous administration of mAbs.
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Affiliation(s)
- Katya C. Corado
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Kara W. Chew
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, California
| | - Mark J. Giganti
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ying Mu
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska
| | - Courtney V. Fletcher
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska
| | - Judith S. Currier
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, California
| | - Eric S. Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - David A. Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jonathan Z. Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Carlee B. Moser
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Justin Ritz
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | | | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York
| | | | | | - Joseph J. Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - ACTIV-2/A5401 Study Team
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, California
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
- National Institutes of Health, Rockville, Maryland
- Quantum Clinical Trials, Miami, Florida
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York
- University of California, San Diego, California
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10
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Owens K, Esmaeili S, Schiffer JT. Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses. JCI Insight 2024; 9:e176286. [PMID: 38573774 PMCID: PMC11141931 DOI: 10.1172/jci.insight.176286] [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: 09/29/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
The viral kinetics of documented SARS-CoV-2 infections exhibit a high degree of interindividual variability. We identified 6 distinct viral shedding patterns, which differed according to peak viral load, duration, expansion rate, and clearance rate, by clustering data from 768 infections in the National Basketball Association cohort. Omicron variant infections in previously vaccinated individuals generally led to lower cumulative shedding levels of SARS-CoV-2 than other scenarios. We then developed a mechanistic mathematical model that recapitulated 1,510 observed viral trajectories, including viral rebound and cases of reinfection. Lower peak viral loads were explained by a more rapid and sustained transition of susceptible cells to a refractory state during infection as well as by an earlier and more potent late, cytolytic immune response. Our results suggest that viral elimination occurs more rapidly during Omicron infection, following vaccination, and following reinfection due to enhanced innate and acquired immune responses. Because viral load has been linked with COVID-19 severity and transmission risk, our model provides a framework for understanding the wide range of observed SARS-CoV-2 infection outcomes.
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Affiliation(s)
- Katherine Owens
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shadisadat Esmaeili
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Joshua T. Schiffer
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
- University of Washington, Department of Medicine, Seattle, Washington, USA
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11
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Xia Q, Yang Y, Wang F, Huang Z, Qiu W, Mao A. Case fatality rates of COVID-19 during epidemic periods of variants of concern: A meta-analysis by continents. Int J Infect Dis 2024; 141:106950. [PMID: 38309460 DOI: 10.1016/j.ijid.2024.01.017] [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: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
OBJECTIVES To calculate the case fatality rates (CFR) of COVID-19 during epidemic periods of different variants of concern (VOC) by continents. METHODS We systematically searched five authoritative databases (Web of Science, PubMed, Embase, Cochrane Library, and MedRxiv) for epidemiological studies on the CFR of COVID-19 published between January 1, 2020, and March 31, 2023. After identifying the epidemic trends of variants, we used a random-effects model to calculate the pooled CFRs during periods of different VOCs. This meta-analysis was conducted following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and registered with PROSPERO (CRD42023431572). RESULTS There were variations in the CFRs among different variants of COVID-19 (Alpha: 2.62%, Beta: 4.19%, Gamma: 3.60%, Delta: 2.01%, Omicron: 0.70%), and disparities in CFRs also existed among continents. On the whole, the CFRs of COVID-19 in Europe and Oceania were slightly lower than in other continents. There was a statistically significant association between the variant, HDI value, age distribution, coverage of full vaccination of cases, and the CFR. CONCLUSIONS The CFRs of COVID-19 varied across the epidemic periods of different VOCs, and disparities existed among continents. The CFR value reflected combined effects of various factors within a certain context. Caution should be exercised when comparing CFRs due to disparities in testing capabilities and age distribution among countries, etc.
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Affiliation(s)
- Qianhang Xia
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Yujie Yang
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Fengling Wang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong China
| | - Zhongyue Huang
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Wuqi Qiu
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China
| | - Ayan Mao
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China; Peking Union Medical College, Beijing, China.
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12
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Dzieciolowska S, Charest H, Roy T, Fafard J, Carazo S, Levade I, Longtin J, Parkes L, Beaulac SN, Villeneuve J, Savard P, Corbeil J, De Serres G, Longtin Y. Timing and Predictors of Loss of Infectivity Among Healthcare Workers With Mild Primary and Recurrent COVID-19: A Prospective Observational Cohort Study. Clin Infect Dis 2024; 78:613-624. [PMID: 37675577 PMCID: PMC10954326 DOI: 10.1093/cid/ciad535] [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: 06/20/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND There is a need to understand the duration of infectivity of primary and recurrent coronavirus disease 2019 (COVID-19) and identify predictors of loss of infectivity. METHODS Prospective observational cohort study with serial viral culture, rapid antigen detection test (RADT) and reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal specimens of healthcare workers with COVID-19. The primary outcome was viral culture positivity as indicative of infectivity. Predictors of loss of infectivity were determined using multivariate regression model. The performance of the US Centers for Disease Control and Prevention (CDC) criteria (fever resolution, symptom improvement, and negative RADT) to predict loss of infectivity was also investigated. RESULTS In total, 121 participants (91 female [79.3%]; average age, 40 years) were enrolled. Most (n = 107, 88.4%) had received ≥3 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine doses, and 20 (16.5%) had COVID-19 previously. Viral culture positivity decreased from 71.9% (87/121) on day 5 of infection to 18.2% (22/121) on day 10. Participants with recurrent COVID-19 had a lower likelihood of infectivity than those with primary COVID-19 at each follow-up (day 5 odds ratio [OR], 0.14; P < .001]; day 7 OR, 0.04; P = .003]) and were all non-infective by day 10 (P = .02). Independent predictors of infectivity included prior COVID-19 (adjusted OR [aOR] on day 5, 0.005; P = .003), an RT-PCR cycle threshold [Ct] value <23 (aOR on day 5, 22.75; P < .001) but not symptom improvement or RADT result.The CDC criteria would identify 36% (24/67) of all non-infectious individuals on day 7. However, 17% (5/29) of those meeting all the criteria had a positive viral culture. CONCLUSIONS Infectivity of recurrent COVID-19 is shorter than primary infections. Loss of infectivity algorithms could be optimized.
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Affiliation(s)
| | - Hugues Charest
- Faculté de médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Tonya Roy
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Sara Carazo
- Institut National de Santé Publique du Québec, Québec City, Canada
- Université Laval, Québec City, Canada
| | - Ines Levade
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | - Jean Longtin
- CHU de Québec—Université Laval, Québec City, Canada
| | - Leighanne Parkes
- McGill University Faculty of Medicine, Montréal, Canada
- Jewish General Hospital Sir Mortimer B. Davis, Montréal, Canada
| | - Sylvie Nancy Beaulac
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Institut National de Santé Publique du Québec, Québec City, Canada
| | | | - Patrice Savard
- Faculté de médecine, Université de Montréal, Montréal, Canada
- Centre Hospitalier de l’Université de Montréal (CHUM) and CHUM Research Center, Montréal, Canada
| | | | - Gaston De Serres
- Institut National de Santé Publique du Québec, Québec City, Canada
- Université Laval, Québec City, Canada
| | - Yves Longtin
- McGill University Faculty of Medicine, Montréal, Canada
- Jewish General Hospital Sir Mortimer B. Davis, Montréal, Canada
- Lady Davis Research Institute, Montréal, Canada
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13
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Owens K, Esmaeili-Wellman S, Schiffer JT. Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.20.23294350. [PMID: 37662228 PMCID: PMC10473815 DOI: 10.1101/2023.08.20.23294350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The viral kinetics of documented SARS-CoV-2 infections exhibit a high degree of inter-individual variability. We identified six distinct viral shedding patterns, which differed according to peak viral load, duration, expansion rate and clearance rate, by clustering data from 768 infections in the National Basketball Association cohort. Omicron variant infections in previously vaccinated individuals generally led to lower cumulative shedding levels of SARS-CoV-2 than other scenarios. We then developed a mechanistic mathematical model that recapitulated 1510 observed viral trajectories, including viral rebound and cases of reinfection. Lower peak viral loads were explained by a more rapid and sustained transition of susceptible cells to a refractory state during infection, as well as an earlier and more potent late, cytolytic immune response. Our results suggest that viral elimination occurs more rapidly during omicron infection, following vaccination, and following re-infection due to enhanced innate and acquired immune responses. Because viral load has been linked with COVID-19 severity and transmission risk, our model provides a framework for understanding the wide range of observed SARS-CoV-2 infection outcomes.
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Affiliation(s)
- Katherine Owens
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division
| | | | - Joshua T Schiffer
- Fred Hutchinson Cancer Center, Vaccine and Infectious Diseases Division
- University of Washington, Department of Medicine
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14
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Specht IOA, Petros BA, Moreno GK, Brock-Fisher T, Krasilnikova LA, Schifferli M, Yang K, Cronan P, Glennon O, Schaffner SF, Park DJ, MacInnis BL, Ozonoff A, Fry B, Mitzenmacher MD, Varilly P, Sabeti PC. Inferring Viral Transmission Pathways from Within-Host Variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.14.23297039. [PMID: 37873325 PMCID: PMC10593003 DOI: 10.1101/2023.10.14.23297039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop a robust evolutionary model for transmission reconstruction that tracks the genetic composition of within-host viral populations over time and the lineages transmitted between hosts. We confirm that our model reliably describes within-host variant frequencies in a dataset of 134,682 SARS-CoV-2 deep-sequenced genomes from Massachusetts, USA. We then demonstrate that our reconstruction approach infers transmissions more accurately than two leading methods on synthetic data, as well as in a controlled outbreak of bovine respiratory syncytial virus and an epidemiologically-investigated SARS-CoV-2 outbreak in South Africa. Finally, we apply our transmission reconstruction tool to 5,692 outbreaks among the 134,682 Massachusetts genomes. Our methods and results demonstrate the utility of within-host variation for transmission inference of SARS-CoV-2 and other pathogens, and provide an adaptable mathematical framework for tracking within-host evolution.
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Affiliation(s)
- Ivan O. A. Specht
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard College, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Brittany A. Petros
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
- Harvard/MIT MD-PhD Program, Boston, MA 02115, USA
- Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gage K. Moreno
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Taylor Brock-Fisher
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Lydia A. Krasilnikova
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | | | - Paul Cronan
- Fathom Information Design, Boston, MA 02114, USA
| | | | | | - Daniel J. Park
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bronwyn L. MacInnis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Al Ozonoff
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ben Fry
- Fathom Information Design, Boston, MA 02114, USA
| | - Michael D. Mitzenmacher
- Department of Computer Science, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Patrick Varilly
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pardis C. Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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15
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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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16
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Laird-Gion J, Dionne A, Gauvreau K, Baker A, Day-Lewis M, de Ferranti S, Friedman K, Khan N, Mahanta S, Son MB, Sperotto F, Newburger JW. MIS-C across three SARS-CoV-2 variants: Changes in COVID-19 testing and clinical characteristics in a cohort of U.S. children. Eur J Pediatr 2023; 182:2865-2872. [PMID: 37055630 PMCID: PMC10101535 DOI: 10.1007/s00431-023-04968-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/15/2023]
Abstract
As new variants of SARS-Co-V 2 have emerged over time and Omicron sub-variants have become dominant, the severity of illness from COVID-19 has declined despite greater transmissibility. There are fewer data on how the history, diagnosis, and clinical characteristics of multisystem inflammatory syndrome in children (MIS-C) have changed with evolution in SARS-CoV-2 variants. We conducted a retrospective cohort study of patients hospitalized with MIS-C between April 2020 and July 2022 in a tertiary referral center. Patients were sorted into Alpha, Delta, and Omicron variant cohorts by date of admission and using national and regional data on variant prevalence. Among 108 patients with MIS-C, significantly more patients had a documented history of COVID-19 in the two months before MIS-C during Omicron (74%) than during Alpha (42%) (p = 0.03). Platelet count and absolute lymphocyte count were lowest during Omicron, without significant differences in other laboratory tests. However, markers of clinical severity, including percentage with ICU admission, length of ICU stay, use of inotropes, or left ventricular dysfunction, did not differ across variants. This study is limited by its small, single-center case series design and by classification of patients into era of variant by admission date rather than genomic testing of SARS- CoV-2 samples. Conclusion: Antecedent COVID-19 was more often documented in the Omicron than Alpha or Delta eras, but clinical severity of MIS-C was similar across variant eras. What is Known: • There has been a decrease in incidence of MIS-C in children despite widespread infection with new variants of COVID-19. • Data has varied on if the severity of MIS-C has changed over time across different variant infections. What is New: • MIS-C patients were significantly more likely to report a known prior infection with SARS-CoV-2 during Omicron than during Alpha. • There was no difference in severity of MIS-C between the Alpha, Delta, and Omicron cohorts in our patient population.
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Affiliation(s)
- Jessica Laird-Gion
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Audrey Dionne
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Kimberlee Gauvreau
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Annette Baker
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Megan Day-Lewis
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Sarah de Ferranti
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Kevin Friedman
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Numaira Khan
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Simran Mahanta
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Mary Beth Son
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Francesca Sperotto
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jane W Newburger
- Division of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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17
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Morrison H, Jackson S, McShane H. Controlled human infection models in COVID-19 and tuberculosis: current progress and future challenges. Front Immunol 2023; 14:1211388. [PMID: 37304270 PMCID: PMC10248465 DOI: 10.3389/fimmu.2023.1211388] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Controlled Human Infection Models (CHIMs) involve deliberately exposing healthy human volunteers to a known pathogen, to allow the detailed study of disease processes and evaluate methods of treatment and prevention, including next generation vaccines. CHIMs are in development for both tuberculosis (TB) and Covid-19, but challenges remain in their ongoing optimisation and refinement. It would be unethical to deliberately infect humans with virulent Mycobacteria tuberculosis (M.tb), however surrogate models involving other mycobacteria, M.tb Purified Protein Derivative or genetically modified forms of M.tb either exist or are under development. These utilise varying routes of administration, including via aerosol, per bronchoscope or intradermal injection, each with their own advantages and disadvantages. Intranasal CHIMs with SARS-CoV-2 were developed against the backdrop of the evolving Covid-19 pandemic and are currently being utilised to both assess viral kinetics, interrogate the local and systemic immunological responses post exposure, and identify immune correlates of protection. In future it is hoped they can be used to assess new treatments and vaccines. The changing face of the pandemic, including the emergence of new virus variants and increasing levels of vaccination and natural immunity within populations, has provided a unique and complex environment within which to develop a SARS-CoV-2 CHIM. This article will discuss current progress and potential future developments in CHIMs for these two globally significant pathogens.
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