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Lupi L, Vitiello A, Parolin C, Calistri A, Garzino-Demo A. The Potential Role of Viral Persistence in the Post-Acute Sequelae of SARS-CoV-2 Infection (PASC). Pathogens 2024; 13:388. [PMID: 38787240 PMCID: PMC11123686 DOI: 10.3390/pathogens13050388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
The infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated not only with the development of acute disease but also with long-term symptoms or post-acute sequelae of SARS-CoV-2 (PASC). Multiple lines of evidence support that some viral antigens and RNA can persist for up to 15 months in multiple organs in the body, often after apparent clearance from the upper respiratory system, possibly leading to the persistence of symptoms. Activation of the immune system to viral antigens is observed for a prolonged time, providing indirect evidence of the persistence of viral elements after acute infection. In the gastrointestinal tract, the persistence of some antigens could stimulate the immune system, shaping the local microbiota with potential systemic effects. All of these interactions need to be investigated, taking into account predisposing factors, multiplicity of pathogenic mechanisms, and stratifying populations of vulnerable individuals, particularly women, children, and immunocompromised individuals, where SARS-CoV-2 may present additional challenges.
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Affiliation(s)
- Lorenzo Lupi
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (L.L.); (A.V.); (C.P.); (A.C.)
| | - Adriana Vitiello
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (L.L.); (A.V.); (C.P.); (A.C.)
| | - Cristina Parolin
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (L.L.); (A.V.); (C.P.); (A.C.)
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (L.L.); (A.V.); (C.P.); (A.C.)
| | - Alfredo Garzino-Demo
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (L.L.); (A.V.); (C.P.); (A.C.)
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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Jacobson MA, Blanc PD, Tulsky J, Tilly M, Meister R, Huen W, McNicholas JE. Risk of subsequent SARS-CoV-2 infection among vaccinated employees with or without hybrid immunity acquired early in the Omicron-predominant era of the COVID-19 pandemic. Am J Ind Med 2024; 67:334-340. [PMID: 38316635 DOI: 10.1002/ajim.23570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Hybrid immunity, from COVID-19 vaccination followed by SARS-CoV-2 infection acquired after its Omicron variant began predominating, has provided greater protection than vaccination alone against subsequent infection over 1-3 months of observation. Its longer-term protection is unknown. METHODS We conducted a retrospective cohort study of COVID-19 case incidence among healthcare personnel (HCP) mandated to be vaccinated and report on COVID-19-associated symptoms, high-risk exposures, or known-positive test results to an employee health hotline. We compared cases with hybrid immunity, defined as incident COVID-19 during the first 6 weeks of Omicron-variant predominance (run-in period), to those with immunity from vaccination alone during the run-in period. Time until COVID-19 infection over 13 subsequent months (observation period) was analyzed by standard survival analysis. RESULTS Of 5867 employees, 641 (10.9%, 95% confidence interval [CI]: 10.1%-11.8%) acquired hybrid immunity during the run-in period. Of these, 104 (16.2%, 95% CI: 13.5%-19.3%) experienced new SARS-CoV-2 infection during the 13-month observation period, compared to 2177 (41.7%, 95% CI: 40.3%-43.0%) of the 5226 HCP without hybrid immunity. Time until incident infection was shorter among the latter (hazard ratio: 3.09, 95% CI: 2.54-3.78). CONCLUSIONS In a cohort of vaccinated employees, Omicron-era acquired SARS-CoV-2 hybrid immunity was associated with significantly lower risk of subsequent infection over more than a year of observation-a time period far longer than previously reported and during which three, progressively more resistant, Omicron subvariants became predominant. These findings can inform institutional policy and planning for future COVID-19 additional vaccine dosing requirements for employees, for surveillance programs, and for risk modification efforts.
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Affiliation(s)
- Mark A Jacobson
- Department of Medicine, Division of Occupational, Environmental, and Climate Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, Division of HIV, Infectious Diseases, and Global Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Paul D Blanc
- Department of Medicine, Division of Occupational, Environmental, and Climate Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Jacqueline Tulsky
- Department of Medicine, Division of Occupational, Environmental, and Climate Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, Division of HIV, Infectious Diseases, and Global Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Monica Tilly
- Department of Medicine, Division of Occupational, Environmental, and Climate Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Raymond Meister
- Department of Medicine, Division of Occupational, Environmental, and Climate Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Will Huen
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - James E McNicholas
- Department of Medicine, Division of Occupational, Environmental, and Climate Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
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Murad D, Zafar Paracha R, Saeed MT, Ahmad J, Mushtaq A, Humayun M. Modelling and analysis of the complement system signalling pathways: roles of C3, C5a and pro-inflammatory cytokines in SARS-CoV-2 infection. PeerJ 2023; 11:e15794. [PMID: 37744234 PMCID: PMC10517668 DOI: 10.7717/peerj.15794] [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: 02/08/2023] [Accepted: 07/04/2023] [Indexed: 09/26/2023] Open
Abstract
The complement system is an essential part of innate immunity. It is activated by invading pathogens causing inflammation, opsonization, and lysis via complement anaphylatoxins, complement opsonin's and membrane attack complex (MAC), respectively. However, in SARS-CoV-2 infection overactivation of complement system is causing cytokine storm leading to multiple organs damage. In this study, the René Thomas kinetic logic approach was used for the development of biological regulatory network (BRN) to model SARS-CoV-2 mediated complement system signalling pathways. Betweenness centrality analysis in cytoscape was adopted for the selection of the most biologically plausible states in state graph. Among the model results, in strongly connected components (SCCs) pro-inflammatory cytokines (PICyts) oscillatory behaviour between recurrent generation and downregulation was found as the main feature of SARS-CoV-2 infection. Diversion of trajectories from the SCCs leading toward hyper-inflammatory response was found in agreement with in vivo studies that overactive innate immunity response caused PICyts storm during SARS-CoV-2 infection. The complex of negative regulators FI, CR1 and DAF in the inhibition of complement peptide (C5a) and PICyts was found desirable to increase immune responses. In modelling role of MAC and PICyts in lowering of SARS-CoV-2 titre was found coherent with experimental studies. Intervention in upregulation of C5a and PICyts by C3 was found helpful in back-and-forth variation of signalling pattern linked with the levels of PICyts. Moreover, intervention in upregulation of PICyts by C5a was found productive in downregulation of all activating factors in the normal SCCs. However, the computational model predictions require experimental studies to be validated by exploring the activation role of C3 and C5a which could change levels of PICyts at various phases of SARS-CoV-2 infection.
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Affiliation(s)
- Didar Murad
- School of Interdisciplinary Engineering and Sciences/Department of Sciences, National University of Science and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering and Sciences/Department of Sciences, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Tariq Saeed
- School of Interdisciplinary Engineering and Sciences/Department of Sciences, National University of Science and Technology, Islamabad, Pakistan
| | - Jamil Ahmad
- Department of Computer Science and Information Technology, University of Malakand, Chakdara, Malakand, Pakistan
| | - Ammar Mushtaq
- School of Interdisciplinary Engineering and Sciences/Department of Sciences, National University of Science and Technology, Islamabad, Pakistan
| | - Maleeha Humayun
- School of Interdisciplinary Engineering and Sciences/Department of Sciences, National University of Science and Technology, Islamabad, Pakistan
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4
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A simulation of undiagnosed population and excess mortality during the COVID-19 pandemic. RESULTS IN CONTROL AND OPTIMIZATION 2023; 12:100262. [PMCID: PMC10290741 DOI: 10.1016/j.rico.2023.100262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2024]
Abstract
Whereas the extent of outbreak of COVID-19 is usually accessed via the number of reported cases and the number of patients succumbed to the disease, the officially recorded overall excess mortality numbers during the pandemic waves, which are significant and often followed the rise and fall of the pandemic waves, put a question mark on the above methodology. Gradually it has been recognized that estimating the size of the undiagnosed population (which includes asymptomatic cases and symptomatic cases but not reported) is also crucial. Here we used the classical mathematical SEIR model having an additional compartment, that is the undiagnosed group in addition to the susceptible, exposed, diagnosed, recovered and deceased groups, to link the undiagnosed COVID-19 cases to the reported excess mortality numbers and thereby try to know the actual size of the disease outbreak. The developed model wase successfully applied to relevant COVID-19 waves in USA (initial months of 2020), South Africa (mid of 2021) and Russia (2020–21) when a large discrepancy between the reported COVID-19 mortality and the overall excess mortality had been noticed.
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Shaum A, Harlow T, Gulati RK, Berro A, House J. COVID-19 cases reported in Colorado following screening at selected US airports, January - July 2020. BMC Res Notes 2023; 16:67. [PMID: 37106467 PMCID: PMC10139659 DOI: 10.1186/s13104-023-06339-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/19/2022] [Indexed: 04/29/2023] Open
Abstract
OBJECTIVE We sought to estimate the proportion of air travelers who may have been infected with SARS-CoV-2 upon arrival to Colorado by comparing data on Colorado residents screened upon entering the US to COVID-19 cases reported in the state. Data on Colorado's screened passengers arriving into the US between January 17 and July 30, 2020 were compared to Colorado's Electronic Disease Reporting System. We conducted a descriptive analysis of true matches, including age, gender, case status, symptom status, time from arrival to symptom onset (days), and time from arrival to specimen collection date (days). RESULTS Fourteen confirmed COVID-19 cases in travelers who were diagnosed within 14 days after arriving in Colorado were matched to the 8,272 travelers who underwent screening at 15 designated airports with a recorded destination of Colorado, or 0.2%. Most (N = 13/14 or 93%) of these infected travelers arrived in Colorado in March 2020; 12 (86%) of them were symptomatic. Entry screening for COVID-19 and the sharing of traveler information with the Colorado Department of Public Health and Environment appeared to identify few cases early in the pandemic. Symptom-based entry screening and sharing of traveler information was minimally effective at decreasing travel-associated COVID-19 transmission.
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Affiliation(s)
- Anna Shaum
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, USA.
| | - Tye Harlow
- Colorado Department of Public Health and Environment, Colorado, USA
| | - Reena K Gulati
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, USA
- Bill & Melinda Gates Foundation, Seattle, USA
| | - Andre Berro
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, USA
| | - Jennifer House
- Colorado Department of Public Health and Environment, Colorado, USA
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Klussmann JP, Grosheva M, Meiser P, Lehmann C, Nagy E, Szijártó V, Nagy G, Konrat R, Flegel M, Holzer F, Groß D, Steinmetz C, Scherer B, Gruell H, Schlotz M, Klein F, de Aragão PA, Morr H, Al Saleh H, Bilstein A, Russo B, Müller-Scholtz S, Acikel C, Sahin H, Werkhäuser N, Allekotte S, Mösges R. Early intervention with azelastine nasal spray may reduce viral load in SARS-CoV-2 infected patients. Sci Rep 2023; 13:6839. [PMID: 37100830 PMCID: PMC10132439 DOI: 10.1038/s41598-023-32546-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/29/2023] [Indexed: 04/28/2023] Open
Abstract
With the changing epidemiology of COVID-19 and its impact on our daily lives, there is still an unmet need of COVID-19 therapies treating early infections to prevent progression. The current study was a randomized, parallel, double-blind, placebo-controlled trial. Ninety SARS-CoV-2 positive patients were randomized into 3 groups receiving placebo, 0.02% or 0.1% azelastine nasal spray for 11 days, during which viral loads were assessed by quantitative PCR. Investigators assessed patients' status throughout the trial including safety follow-ups (days 16 and 60). Symptoms were documented in patient diaries. Initial viral loads were log10 6.85 ± 1.31 (mean ± SD) copies/mL (ORF 1a/b gene). After treatment, virus load was reduced in all groups (p < 0.0001) but was greater in the 0.1% group compared to placebo (p = 0.007). In a subset of patients (initial Ct < 25) viral load was strongly reduced on day 4 in the 0.1% group compared to placebo (p = 0.005). Negative PCR results appeared earlier and more frequently in the azelastine treated groups: being 18.52% and 21.43% in the 0.1% and 0.02% groups, respectively, compared to 0% for placebo on day 8. Comparable numbers of adverse events occurred in all treatment groups with no safety concerns. The shown effects of azelastine nasal spray may thus be suggestive of azelastine's potential as an antiviral treatment.Trial registration: The study was registered in the German Clinical Trial Register (DRKS-ID: DRKS00024520; Date of Registration in DRKS: 12/02/2021). EudraCT number: 2020-005544-34.
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Affiliation(s)
- Jens Peter Klussmann
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Medical Faculty, Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Maria Grosheva
- Medical Faculty, Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Peter Meiser
- URSAPHARM Arzneimittel GmbH, Industriestraße 35, 66129, Saarbruecken, Germany
| | - Clara Lehmann
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Department I of Internal Medicine, Division of Infectious Diseases, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- German Center for Infection Research (DZIF) Location Bonn-Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Eszter Nagy
- CEBINA GmbH, Karl-Farkas-Gasse 22, 1030, Vienna, Austria
| | | | - Gábor Nagy
- CEBINA GmbH, Karl-Farkas-Gasse 22, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Michael Flegel
- URSAPHARM Arzneimittel GmbH, Industriestraße 35, 66129, Saarbruecken, Germany
| | - Frank Holzer
- URSAPHARM Arzneimittel GmbH, Industriestraße 35, 66129, Saarbruecken, Germany
| | - Dorothea Groß
- URSAPHARM Arzneimittel GmbH, Industriestraße 35, 66129, Saarbruecken, Germany
| | - Charlotte Steinmetz
- URSAPHARM Arzneimittel GmbH, Industriestraße 35, 66129, Saarbruecken, Germany
| | - Barbara Scherer
- URSAPHARM Arzneimittel GmbH, Industriestraße 35, 66129, Saarbruecken, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Florian Klein
- German Center for Infection Research (DZIF) Location Bonn-Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Paula Aguiar de Aragão
- Medical Faculty, Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Henning Morr
- Medical Faculty, Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Helal Al Saleh
- Medical Faculty, Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | | | - Belisa Russo
- ClinCompetence Cologne GmbH, Theodor-Heuss-Ring 14, 50668, Cologne, Germany
| | | | - Cengizhan Acikel
- ClinCompetence Cologne GmbH, Theodor-Heuss-Ring 14, 50668, Cologne, Germany
| | - Hacer Sahin
- ClinCompetence Cologne GmbH, Theodor-Heuss-Ring 14, 50668, Cologne, Germany
| | - Nina Werkhäuser
- ClinCompetence Cologne GmbH, Theodor-Heuss-Ring 14, 50668, Cologne, Germany
| | - Silke Allekotte
- ClinCompetence Cologne GmbH, Theodor-Heuss-Ring 14, 50668, Cologne, Germany
| | - Ralph Mösges
- ClinCompetence Cologne GmbH, Theodor-Heuss-Ring 14, 50668, Cologne, Germany.
- Institute of Medical Statistics and Computational Biology (IMSB), Faculty of Medicine, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
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Costa dos Santos J, Ximenes Rabelo M, Mattana Sebben L, de Souza Carneiro MV, Bosco Lopes Botelho J, Cardoso Neto J, Nogueira Barbosa A, Monteiro de Carvalho D, Pontes GS. Persistence of SARS-CoV-2 Antigens in the Nasal Mucosa of Eight Patients with Inflammatory Rhinopathy for over 80 Days following Mild COVID-19 Diagnosis. Viruses 2023; 15:v15040899. [PMID: 37112879 PMCID: PMC10143909 DOI: 10.3390/v15040899] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The nasal mucosa is the main gateway for entry, replication and elimination of the SARS-CoV-2 virus, the pathogen that causes severe acute respiratory syndrome (COVID-19). The presence of the virus in the epithelium causes damage to the nasal mucosa and compromises mucociliary clearance. The aim of this study was to investigate the presence of SARS-CoV-2 viral antigens in the nasal mucociliary mucosa of patients with a history of mild COVID-19 and persistent inflammatory rhinopathy. We evaluated eight adults without previous nasal diseases and with a history of COVID-19 and persistent olfactory dysfunction for more than 80 days after diagnosis of SARS-CoV-2 infection. Samples of the nasal mucosa were collected via brushing of the middle nasal concha. The detection of viral antigens was performed using immunofluorescence through confocal microscopy. Viral antigens were detected in the nasal mucosa of all patients. Persistent anosmia was observed in four patients. Our findings suggest that persistent SARS-CoV-2 antigens in the nasal mucosa of mild COVID-19 patients may lead to inflammatory rhinopathy and prolonged or relapsing anosmia. This study sheds light on the potential mechanisms underlying persistent symptoms of COVID-19 and highlights the importance of monitoring patients with persistent anosmia and nasal-related symptoms.
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Yang M, Yang Q, Bi X, Shi H, Yang J, Cheng X, Yan T, Zhang H, Cheng Z. The Synergy of Chicken Anemia Virus and Gyrovirus Homsa 1 in Chickens. Viruses 2023; 15:v15020515. [PMID: 36851729 PMCID: PMC9964263 DOI: 10.3390/v15020515] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/28/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Chicken anemia virus (CAV) and Gyrovirus homsa 1 (GyH1) are members of the Gyrovirus genus. The two viruses cause similar clinical manifestations in chickens, aplastic anemia and immunosuppression. Our previous investigation displays that CAV and GyH1 often co-infect chickens. However, whether they have synergistic pathogenicity in chickens remains elusive. Here, we established a co-infection model of CAV and GyH1 in specific pathogen-free (SPF) chickens to explore the synergy between CAV and GyH1. We discovered that CAV and GyH1 significantly inhibited weight gain, increased mortality, and hindered erythropoiesis in co-infected chickens. Co-infected chickens exhibited severe immune organ atrophy and lymphocyte exhaustion. The proventriculus and gizzard had severe hemorrhagic necrosis and inflammation. We also discovered that the viral loads and shedding levels were higher and lasted longer in CAV and GyH1 co-infected chickens than in mono-infected chickens. Our results demonstrate that CAV and GyH1 synergistically promote immunosuppression, pathogenicity, and viral replication in co-infected chicken, highlighting the interaction between CAV and GyH1 in the disease process and increasing potential health risk in the poultry breeding industry, and needs further attention.
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Amanati A, Shahriari M, Bordbar MR, Hedayati SB, Ziyaeyan M, Jamalidoust M, Kalani M, Heydari Marandi N. Severe acute respiratory syndrome coronavirus-2 Alpha variant (B.1.1.7), original wild-type severe acute respiratory syndrome coronavirus 2, and cytomegalovirus co-infection in a young adult with acute lymphoblastic leukemia, case report, and review of the possible cytomegalovirus reactivation mechanisms. J Med Case Rep 2023; 17:66. [PMID: 36765433 PMCID: PMC9913040 DOI: 10.1186/s13256-022-03750-8] [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: 01/19/2022] [Accepted: 12/29/2022] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Like other viral infections, severe acute respiratory syndrome coronavirus-2 infection could affect different human body systems, including host immune responses. Three years after its pandemic, we learn more about this novel coronavirus. As we expected, different co-infections with various organisms, such as viruses, bacteria, and even fungi, have been reported. However, concurrent infection with two severe acute respiratory syndrome coronavirus-2 strains and cytomegalovirus is extremely unusual. We have only a rudimentary understanding of such co-infections and their long-term consequences for patients with cancer. CASE PRESENTATION An 18-year-old young Iranian adult with acute lymphoblastic leukemia presented with abdominal pain, diarrhea, nausea, and vomiting following a recent history of severe acute respiratory syndrome coronavirus-2 infection. The patient never experienced respiratory symptoms, and the chest imaging study was normal on admission. His primary laboratory investigation revealed prerenal azotemia and severe abnormal liver function tests (blood urea nitrogen 32 mg/dL, creatinine 1.75 mg/dL, prothrombin time 66 s, partial thromboplastin time 44.5 s, international normalized ratio 5.14, total bilirubin 2.9 mg/dL, and direct bilirubin 2.59 mg/dL). Cytomegalovirus disease was diagnosed by polymerase chain reaction in his blood and stool samples. The patient's gastrointestinal signs and symptoms improved shortly after receiving intravenous ganciclovir treatment. His gastrointestinal symptoms continued intermittently for weeks despite maintenance valganciclovir prescription, necessitating frequent hospitalizations. The patient was complicated by the recurrence of gastrointestinal symptoms during the sixth hospitalization, even though he had no respiratory symptoms, and the nasopharyngeal test revealed severe acute respiratory syndrome coronavirus-2 Wuhan strain for the first time. Remdesivir and valganciclovir were administrated due to persistent enteritis and evidence of intestinal tissue invasion by severe acute respiratory syndrome coronavirus 2 and cytomegalovirus on multiple intestinal biopsies, which led to partial clinical responses. Cytomegalovirus and severe acute respiratory syndrome coronavirus-2 fecal shedding continued for more than 6 months despite repeated antiviral therapy, and the Wuhan and Alpha strains were also detected in his nasopharyngeal samples through repeated sampling (confirmed by four nasopharyngeal sampling and multiple stool specimens and several intestinal biopsies). Finally, during the Delta-variant (B.1.617.2) outbreak in Iran, the patient was admitted again with febrile neutropenia and decreased level of consciousness, necessitating respiratory support and mechanical ventilation. During the Delta-variant peak, the patient's nasopharyngeal sample once more tested positive for severe acute respiratory syndrome coronavirus 2. The patient died a few days later from cardiopulmonary arrest. CONCLUSION The coronavirus disease 2019 pandemic has encountered patients with cancer with critical diagnostic and treatment challenges. Patients who are immunocompromised may co-infect with multiple severe acute respiratory syndrome coronavirus-2 strains and cytomegalovirus, and even with timely diagnosis and treatment, the prognosis may be poor.
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Affiliation(s)
- Ali Amanati
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. .,Departments of Pediatrics, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Mahdi Shahriari
- The Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | | | - Mazyar Ziyaeyan
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marzieh Jamalidoust
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Kalani
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Heydari Marandi
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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11
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Ong RYL, Seah VXF, Chong CY, Thoon KC, Tan NWH, Li J, Nadua KD, Soh SY, Seng MSF, Pham TNA, Yung CF, Kam KQ. A cohort study of COVID-19 infection in pediatric oncology patients plus the utility and safety of remdesivir treatment. Acta Oncol 2023; 62:53-57. [PMID: 36661030 DOI: 10.1080/0284186x.2023.2169079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Rina Yue Ling Ong
- Department of Pharmacy, KK Women's and Children's Hospital, Singapore, Singapore
| | - Valerie Xue Fen Seah
- Department of Pharmacy, KK Women's and Children's Hospital, Singapore, Singapore
| | - Chia Yin Chong
- Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Koh Cheng Thoon
- Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Natalie Woon Hui Tan
- Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jiahui Li
- Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Karen Donceras Nadua
- Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Shui Yen Soh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Haematology/Oncology Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Michaela Su-Fern Seng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Haematology/Oncology Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Thi Ngoc Anh Pham
- Nursing Clinical Services, Division of Nursing, KK Women's and Children's Hospital, Singapore, Singapore
| | - Chee Fu Yung
- Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Kai-Qian Kam
- Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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12
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Muacevic A, Adler JR, Lakra MS, Wanjari MB. A Rare Case of Persistent COVID-19 Infection With Aspergillosis in a 12-Year-Old Child. Cureus 2023; 15:e33973. [PMID: 36820111 PMCID: PMC9938724 DOI: 10.7759/cureus.33973] [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: 12/30/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
At the end of 2019, coronavirus disease 2019 (COVID-19) was first detected in Wuhan. In March 2020, COVID-19 became a global pandemic. Saudi Arabia registered the first case of COVID-19 on March 2, 2020. COVID-19 can affect any organ in the body. It affects the respiratory system predominantly. Reverse transcriptase-polymerase chain reaction (RT-PCR) is used to diagnose COVID-19, and the preferred swab is the nasopharyngeal swab. The shedding of the virus continues for about 20 days after the onset of the symptoms. There may be prolonged shedding in a few cases without any symptoms. Viral cultures are used for the confirmation of the shedding. Although the preferred mode of diagnosis is RT-PCR, enzyme-linked immunosorbent assay helps in the diagnosis of antibodies. Here, we report a rare case of prolonged viral shedding for more than 14 weeks. The patient had a prolonged COVID-19 infection, which caused immunosuppression, following which the patient presented with an infection.
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13
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Gedda MR, Danaher P, Shao L, Ongkeko M, Chen L, Dinh A, Thioye Sall M, Reddy OL, Bailey C, Wahba A, Dzekunova I, Somerville R, De Giorgi V, Jin P, West K, Panch SR, Stroncek DF. Longitudinal transcriptional analysis of peripheral blood leukocytes in COVID-19 convalescent donors. J Transl Med 2022; 20:587. [PMID: 36510222 PMCID: PMC9742656 DOI: 10.1186/s12967-022-03751-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SARS-CoV2 can induce a strong host immune response. Many studies have evaluated antibody response following SARS-CoV2 infections. This study investigated the immune response and T cell receptor diversity in people who had recovered from SARS-CoV2 infection (COVID-19). METHODS Using the nCounter platform, we compared transcriptomic profiles of 162 COVID-19 convalescent donors (CCD) and 40 healthy donors (HD). 69 of the 162 CCDs had two or more time points sampled. RESULTS After eliminating the effects of demographic factors, we found extensive differential gene expression up to 241 days into the convalescent period. The differentially expressed genes were involved in several pathways, including virus-host interaction, interleukin and JAK-STAT signaling, T-cell co-stimulation, and immune exhaustion. A subset of 21 CCD samples was found to be highly "perturbed," characterized by overexpression of PLAU, IL1B, NFKB1, PLEK, LCP2, IRF3, MTOR, IL18BP, RACK1, TGFB1, and others. In addition, one of the clusters, P1 (n = 8) CCD samples, showed enhanced TCR diversity in 7 VJ pairs (TRAV9.1_TCRVA_014.1, TRBV6.8_TCRVB_016.1, TRAV7_TCRVA_008.1, TRGV9_ENST00000444775.1, TRAV18_TCRVA_026.1, TRGV4_ENST00000390345.1, TRAV11_TCRVA_017.1). Multiplexed cytokine analysis revealed anomalies in SCF, SCGF-b, and MCP-1 expression in this subset. CONCLUSIONS Persistent alterations in inflammatory pathways and T-cell activation/exhaustion markers for months after active infection may help shed light on the pathophysiology of a prolonged post-viral syndrome observed following recovery from COVID-19 infection. Future studies may inform the ability to identify druggable targets involving these pathways to mitigate the long-term effects of COVID-19 infection. TRIAL REGISTRATION https://clinicaltrials.gov/ct2/show/NCT04360278 Registered April 24, 2020.
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Affiliation(s)
- Mallikarjuna R. Gedda
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.280030.90000 0001 2150 6316Section of Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Patrick Danaher
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Lipei Shao
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Martin Ongkeko
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Leonard Chen
- grid.94365.3d0000 0001 2297 5165Blood Services Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Anh Dinh
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mame Thioye Sall
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Opal L. Reddy
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Christina Bailey
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Amy Wahba
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Inna Dzekunova
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Robert Somerville
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Valeria De Giorgi
- grid.94365.3d0000 0001 2297 5165Infectious Disease Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ping Jin
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Kamille West
- grid.94365.3d0000 0001 2297 5165Blood Services Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sandhya R. Panch
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.34477.330000000122986657Department of Medicine (Hematology Division), University of Washington/Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - David F. Stroncek
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
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14
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Dudouet P, Colson P, Aherfi S, Levasseur A, Beye M, Delerce J, Burel E, Lavrard P, Bader W, Lagier JC, Fournier PE, La Scola B, Raoult D. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding. Sci Rep 2022; 12:18721. [PMID: 36333340 PMCID: PMC9636146 DOI: 10.1038/s41598-022-22060-z] [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: 07/12/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
At the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p < 0.001). In the detailed analysis, we found a greater difference between persistent and non-persistent patients with non-severe COVID 19, and between the two groups infected with clade 20A. Furthermore, we found minority N501Y and P681H mutation clouds in all patients, with no significant differences found both groups. The question of the SARS-CoV-2 viral variants' genesis remains to be further investigated, with the need to prevent new viral propagations and their consequences, and quasi-species analysis could be an important key to watch out.
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Affiliation(s)
- Pierre Dudouet
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sarah Aherfi
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Anthony Levasseur
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Mamadou Beye
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jeremy Delerce
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Emilie Burel
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Lavrard
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Wahiba Bader
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Christophe Lagier
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Bernard La Scola
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
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15
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Strati A, Zavridou M, Paraskevis D, Magiorkinis G, Sapounas S, Lagiou P, Thomaidis NS, Lianidou ES. Development and Analytical Validation of a One-Step Five-Plex RT-ddPCR Assay for the Quantification of SARS-CoV-2 Transcripts in Clinical Samples. Anal Chem 2022; 94:12314-12322. [PMID: 35960711 PMCID: PMC9397566 DOI: 10.1021/acs.analchem.2c00868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022]
Abstract
Highly sensitive methodologies for SARS-CoV-2 detection are essential for the control of COVID-19 pandemic. We developed and analytically validated a highly sensitive and specific five-plex one-step RT-ddPCR assay for SARS-CoV-2. We first designed in-silico novel primers and probes for the simultaneous absolute quantification of three different regions of the nucleoprotein (N) gene of SARS-CoV-2 (N1, N2, N3), a synthetic RNA as an external control (RNA-EC), and Beta-2-Microglobulin (B2M) as an endogenous RNA internal control (RNA-IC). The developed assay was analytically validated using synthetic DNA and RNA calibrator standards and then was applied to 100 clinical specimens previously analyzed with a commercially available CE-IVD RT-qPCR assay. The analytical validation of the developed assay resulted in very good performance characteristics in terms of analytical sensitivity, linearity, analytical specificity, and reproducibility and recovery rates even at very low viral concentrations. The simultaneous absolute quantification of the RNA-EC and RNA-IC provides the necessary metrics for quality control assessment. Direct comparison of the developed one-step five-plex RT-ddPCR assay with a CE-IVD RT-qPCR kit revealed a very high concordance and a higher sensitivity [concordance: 99/100 (99.0%, Spearman's correlation coefficient: -0.850, p < 0.001)]. The developed assay is highly sensitive, specific, and reproducible and has a broad linear dynamic range, providing absolute quantification of SARS-COV-2 transcripts. The inclusion of two RNA quality controls, an external and an internal, is highly important for standardization of SARS-COV-2 molecular testing in clinical and wastewater samples.
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Affiliation(s)
- Areti Strati
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Martha Zavridou
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | | | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | - Nikolaos S. Thomaidis
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Evi S. Lianidou
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
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16
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Dowran R, Damavandi AR, Azad TM. Reinfection and reactivation of SARS-CoV-2. Future Virol 2022. [PMID: 36176508 PMCID: PMC9514089 DOI: 10.2217/fvl-2021-0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/31/2022] [Indexed: 11/21/2022]
Abstract
As the cases of SARS-CoV-2 infection escalates, the essence of in-depth knowledge around acquired immunity and emergence of reinfection and reactivation have to be captured. While being a rare phenomenon, reinfection occurs as the result of diminishing protection conferred by antibodies, especially IgG. Reactivation is more concerned with the role of various elements including shedding lingering viral RNA for a prolonged time and incomplete resolution of infection along with the insight of dormant viral exosomes’ role. The concept of testing positive after two consecutive negative results requires proper discrimination of reinfection from reactivation. In this review, we summarized the current evidence for possible mechanisms leading to viral reactivation or test re-positivity. We also pointed out risk factors associated with both reinfection and reactivation.
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Affiliation(s)
- Razieh Dowran
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Association of Virology, Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirmasoud Rayati Damavandi
- Student Scientific Association of Virology, Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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17
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Caccuri F, Messali S, Bortolotti D, Di Silvestre D, De Palma A, Cattaneo C, Bertelli A, Zani A, Milanesi M, Giovanetti M, Campisi G, Gentili V, Bugatti A, Filippini F, Scaltriti E, Pongolini S, Tucci A, Fiorentini S, d’Ursi P, Ciccozzi M, Mauri P, Rizzo R, Caruso A. Competition for Dominance Within Replicating Quasispecies During Prolonged SARS-CoV-2 Infection in an Immunocompromised Host. Virus Evol 2022; 8:veac042. [PMID: 35706980 PMCID: PMC9129230 DOI: 10.1093/ve/veac042] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/10/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge for their capability to better adapt to the human host aimed and enhance human-to-human transmission. Mutations in spike largely contributed to adaptation. Viral persistence is a prerequisite for intra-host virus evolution, and this likely occurred in immunocompromised patients who allow intra-host long-term viral replication. The underlying mechanism leading to the emergence of variants during viral persistence in the immunocompromised host is still unknown. Here, we show the existence of an ensemble of minor mutants in the early biological samples obtained from an immunocompromised patient and their dynamic interplay with the master mutant during a persistent and productive long-term infection. In particular, after 222 days of active viral replication, the original master mutant, named MB610, was replaced by a minor quasispecies (MB61222) expressing two critical mutations in spike, namely Q493K and N501T. Isolation of the two viruses allowed us to show that MB61222 entry into target cells occurred mainly by the fusion at the plasma membrane (PM), whereas endocytosis characterized the entry mechanism used by MB610. Interestingly, coinfection of two human cell lines of different origin with the SARS-CoV-2 isolates highlighted the early and dramatic predominance of MB61222 over MB610 replication. This finding may be explained by a faster replicative activity of MB61222 as compared to MB610 as well as by the capability of MB61222 to induce peculiar viral RNA-sensing mechanisms leading to an increased production of interferons (IFNs) and, in particular, of IFN-induced transmembrane protein 1 (IFITM1) and IFITM2. Indeed, it has been recently shown that IFITM2 is able to restrict SARS-CoV-2 entry occurring by endocytosis. In this regard, MB61222 may escape the antiviral activity of IFITMs by using the PM fusion pathway for entry into the target cell, whereas MB610 cannot escape this host antiviral response during MB61222 coinfection, since it has endocytosis as the main pathway of entry. Altogether, our data support the evidence of quasispecies fighting for host dominance by taking benefit from the cell machinery to restrict the productive infection of competitors in the viral ensemble. This finding may explain, at least in part, the extraordinary rapid worldwide turnover of VOCs that use the PM fusion pathway to enter into target cells over the original pandemic strain.
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Affiliation(s)
- Francesca Caccuri
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Serena Messali
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Daria Bortolotti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Dario Di Silvestre
- Proteomic and Metabolomic Laboratory, Institute of Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Antonella De Palma
- Proteomic and Metabolomic Laboratory, Institute of Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Chiara Cattaneo
- Department of Hematology, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Anna Bertelli
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alberto Zani
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Maria Milanesi
- Section of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Giovanni Campisi
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Antonella Bugatti
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Federica Filippini
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 43126 Parma, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 43126 Parma, Italy
| | - Alessandra Tucci
- Department of Hematology, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Simona Fiorentini
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Pasqualina d’Ursi
- Institute of Technologies in Biomedicine, National Research Council, 20090 Segrate, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Pierluigi Mauri
- Proteomic and Metabolomic Laboratory, Institute of Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Arnaldo Caruso
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
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18
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Pivoting Novel Exosome-Based Technologies for the Detection of SARS-CoV-2. Viruses 2022; 14:v14051083. [PMID: 35632824 PMCID: PMC9148162 DOI: 10.3390/v14051083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
The National Institutes of Health (NIH) launched the Rapid Acceleration of Diagnostics (RADx) initiative to meet the needs for COVID-19 diagnostic and surveillance testing, and to speed its innovation in the development, commercialization, and implementation of new technologies and approaches. The RADx Radical (RADx-Rad) initiative is one component of the NIH RADx program which focuses on the development of new or non-traditional applications of existing approaches, to enhance their usability, accessibility, and/or accuracy for the detection of SARS-CoV-2. Exosomes are a subpopulation of extracellular vesicles (EVs) 30–140 nm in size, that are critical in cell-to-cell communication. The SARS-CoV-2 virus has similar physical and molecular properties as exosomes. Therefore, the novel tools and technologies that are currently in development for the isolation and detection of exosomes, may prove to be invaluable in screening for SARS-CoV-2 viral infection. Here, we describe how novel exosome-based technologies are being pivoted for the detection of SARS-CoV-2 and/or the diagnosis of COVID-19. Considerations for these technologies as they move toward clinical validation and commercially viable diagnostics is discussed along with their future potential. Ultimately, the technologies in development under the NIH RADx-Rad exosome-based non-traditional technologies toward multi-parametric and integrated approaches for SARS-CoV-2 program represent a significant advancement in diagnostic technology, and, due to a broad focus on the biophysical and biochemical properties of nanoparticles, the technologies have the potential to be further pivoted as tools for future infectious agents.
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19
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Liang G, Gao H, Bushman FD. The pediatric virome in health and disease. Cell Host Microbe 2022; 30:639-649. [PMID: 35550667 DOI: 10.1016/j.chom.2022.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
Associations between the global microbiome and diseases of children have been studied extensively; however, research on the viral component of the microbiome, the "virome," is less advanced. The analysis of disease associations with the virome is often technically challenging, requiring a close examination of the "virome dark matter." The gut is a particularly rich source of viral particles, and now multiple studies have reported intriguing associations of the virome with childhood diseases. For example, virome studies have elucidated new lineages of gut viruses that appear to be tightly associated with childhood diarrhea, and consistent patterns are starting to emerge from virome studies in pediatric IBD. In this review, we summarize the methods for studying the virome and recent research on the nature of the virome during childhood, focusing on specific studies of the intestinal virome in pediatric diseases.
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Affiliation(s)
- Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Hongyan Gao
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA.
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20
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Bianco A, Capozzi L, Del Sambro L, Simone D, Pace L, Rondinone V, Difato LM, Miccolupo A, Manzari C, Fedele A, Parisi A. Persistent SARS-CoV-2 Infection in a Patient With Non-hodgkin Lymphoma: Intra-Host Genomic Diversity Analysis. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.758191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, threatening global public health. Several cases of persistent infection have been described, but there are few reports that compared the genetic variability among samples collected from the patient during infection. In the current study, we reported a viral genetic analysis of a diabetic male patient with Non-Hodgkin Lymphoma affected by persistent SARS-CoV-2 infection. We sequenced the patient-derived viral isolated both from oro/nasopharyngeal swab and VeroE6 cell line, collected from the same patient at different points of the infection. Due to the insufficient material of the second swab received, in order to obtain a complete coverage of the viral genome, it was convenient to perform a virus isolation after cell culture. Both genomes belonged to Pangolin Lineage B.1, Nextstrain clade 20A and GISAID clade G. The mutation spectrum predicted for the two viral genomes reveal three additionally mutations in the sequence of second sample when compared with mutations set identified in the first sample. Our findings show the evolution of the intra-host variability during the course of a long-lasting infection.
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21
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Kukull B, Shakir SM, Hanson KE. Performance of Non-Nasopharyngeal Sample Types for Molecular Detection of SARS-CoV-2. Clin Lab Med 2022; 42:249-259. [PMID: 35636825 PMCID: PMC8860668 DOI: 10.1016/j.cll.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Smith DR, Singh C, Green J, Lueder MR, Arnold CE, Voegtly LJ, Long KA, Rice GK, Luquette AE, Miner HL, Glang L, Bennett AJ, Miller RH, Malagon F, Cer RZ, Bishop-Lilly KA. Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel. Front Med (Lausanne) 2022; 8:836658. [PMID: 35155489 PMCID: PMC8829001 DOI: 10.3389/fmed.2021.836658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to trace the movement of variants, and to monitor effectiveness of countermeasures. Additionally, determining the amount of viable virus present in clinical samples is helpful to better understand the impact these variants have on viral shedding. In this study, we analyzed nasal swab samples collected between March 2020 and early November 2021 from a cohort of United States (U.S.) military personnel and healthcare system beneficiaries stationed worldwide as a part of the Defense Health Agency's (DHA) Global Emerging Infections Surveillance (GEIS) program. SARS-CoV-2 quantitative real time reverse-transcription PCR (qRT-PCR) positive samples were characterized by next-generation sequencing and a subset was analyzed for isolation and quantification of viable virus. Not surprisingly, we found that the Delta variant is the predominant strain circulating among U.S. military personnel beginning in July 2021 and primarily represents cases of vaccine breakthrough infections (VBIs). Among VBIs, we found a 50-fold increase in viable virus in nasal swab samples from Delta variant cases when compared to cases involving other variants. Notably, we found a 40-fold increase in viable virus in nasal swab samples from VBIs involving Delta as compared to unvaccinated personnel infected with other variants prior to the availability of approved vaccines. This study provides important insight about the genomic and virological characterization of SARS-CoV-2 isolates from a unique study population with a global presence.
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Affiliation(s)
- Darci R. Smith
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Christopher Singh
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
- Parsons, Centreville, VA, United States
| | - Jennetta Green
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Matthew R. Lueder
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Catherine E. Arnold
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Logan J. Voegtly
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Kyle A. Long
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Gregory K. Rice
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Andrea E. Luquette
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Haven L. Miner
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Lindsay Glang
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Andrew J. Bennett
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Robin H. Miller
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Regina Z. Cer
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
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23
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Sobsey MD. Absence of virological and epidemiological evidence that SARS-CoV-2 poses COVID-19 risks from environmental fecal waste, wastewater and water exposures. JOURNAL OF WATER AND HEALTH 2022; 20:126-138. [PMID: 35100160 DOI: 10.2166/wh.2021.182] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This review considers evidence for infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presence and COVID-19 infection and illness resulting from exposure to environmental fecal wastes and waters. There is no documented evidence that (1) infectious, replication-capable SARS-CoV-2 is present in environmental fecal wastes, wastewater or water, and (2) well-documented epidemiological evidence of COVID-19 infection, illness or death has never been reported for these exposure media. COVID-19 is transmitted mainly by direct personal contact and respiratory secretions as airborne droplets and aerosols, and less so by respiratory-secreted fomites via contact (touch) exposures. While SARS-CoV-2 often infects the gastrointestinal tract of infected people, its presence as infectious, replication-capable virus in environmental fecal wastes and waters has never been documented. There is only rare and unquantified evidence of infectious, replication-capable SARS-CoV-2 in recently shed feces of COVID-19 hospital patients. The human infectivity dose-response relationship of SARS-CoV-2 is unknown, thereby making it impossible to estimate evidence-based quantitative health effects assessments by quantitative microbial risk assessment methods requiring both known exposure assessment and health effects assessment data. The World Health Organization, Water Environment Federation, US Centers for Disease Control and Prevention and others do not consider environmental fecal wastes and waters as sources of exposure to infectious SARS-CoV-2 causing COVID-19 infection and illness.
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Affiliation(s)
- Mark D Sobsey
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA E-mail:
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24
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Hicks JT, Das S, Matanock A, Griego-Fisher A, Sosin D. Characteristics of Persons With Secondary Detection of Severe Acute Respiratory Syndrome Coronavirus 2 ≥90 days After First Detection, New Mexico 2020. J Infect Dis 2021; 224:1684-1689. [PMID: 34491360 PMCID: PMC8522360 DOI: 10.1093/infdis/jiab448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/06/2021] [Indexed: 12/22/2022] Open
Abstract
The New Mexico Department of Health (NMDOH) conducted a matched case-control study to compare 315 persons (cases) with and 945 persons (controls) without severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) secondary detection (ie, positive SARS-CoV-2 test ≥90 days after first detection as of December 10, 2020). Compared with controls, cases had greater odds of higher SARS-CoV-2 testing frequency (adjusted odds ratio [aOR] = 1.2), being female (aOR = 1.6), being non-Hispanic American Indian/Alaska Native (aOR = 2.3), having diabetes mellitus (aOR = 1.8), and residing and/or working in detention and/or correctional facilities (aOR = 4.7). Diagnostic tools evaluating infectiousness at secondary detection are urgently needed to inform infection control practices.
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Affiliation(s)
- Joseph T Hicks
- Epidemic Intellgence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Smita Das
- Epidemiology and Response Division, New Mexico Department of Health, Santa Fe, New Mexico, USA
| | - Almea Matanock
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anastacia Griego-Fisher
- Scientific Laboratory Division, New Mexico Department of Health, Albuquerque, New Mexico, USA
| | - Daniel Sosin
- Epidemiology and Response Division, New Mexico Department of Health, Santa Fe, New Mexico, USA
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25
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Alsagaby SA, Aljouie A, Alshammari TH, Mir SA, Alhumaydhi FA, Al Abdulmonem W, Alshaalan H, Alomaish H, Daghistani R, Alsehawi A, Alharbi NK. Haematological and radiological-based prognostic markers of COVID-19. J Infect Public Health 2021; 14:1650-1657. [PMID: 34627060 PMCID: PMC8482558 DOI: 10.1016/j.jiph.2021.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/16/2021] [Accepted: 09/26/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has emerged in 2019 and caused a global pandemic in 2020, manifesting in the coronavirus disease 2019 (COVID-19). The majority of patients exhibit a mild form of the disease with no major complications; however, moderate to severe and fatal cases are of public health concerns. Predicting the potential prognosis of COVID-19 could assist healthcare workers in managing cases and controlling the pandemic in an effective way. Therefore, the objectives of the study were to search for biomarkers associated with COVID-19 mortality and predictors of the overall survival (OS). METHODS Here, clinical data of 6026 adult COVID-19 patients admitted to two large centers in Saudi Arabia (Riyadh and Hafar Al-Batin cities) between April and June 2020 were retrospectively analysed. RESULTS More than 23% of the study subjects with available data have died, enabling the prediction of mortality in our cohort. Markers that were significantly associated with mortality in this study were older age, increased d-dimer in the blood, higher counts of WBCs, higher percentage of neutrophil, and a higher chest X-ray (CXR) score. The CXR scores were also positively associated with age, d-dimer, WBC count, and percentage of neutrophil. This supports the utility of CXR scores in the absence of blood testing. Predicting mortality based on Ct values of RT-PCR was not successful, necessitating a more quantitative RT-PCR to determine virus quantity in samples. Our work has also identified age, d-dimer concentration, leukocyte parameters and CXR score to be prognostic markers of the OS of COVID-19 patients. CONCLUSION Overall, this retrospective study on hospitalised cohort of COVID-19 patients presents that age, haematological, and radiological data at the time of diagnosis are of value and could be used to guide better clinical management of COVID-19 patients.
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Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah 11932, Saudi Arabia.
| | - Abdulrhman Aljouie
- Bioinformatics Section, King Abdullah Medical Research Center, Riyadh, Saudi Arabia; Health Informatics, King Saud bin Abdulaziz University for Health Sciences, National Guard Health Affairs, Riyadh, Saudi Arabia.
| | - Talal H Alshammari
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah 11932, Saudi Arabia; King Khaled General Hospital in Hafar Albaten, Saudi Arabia.
| | - Shabir Ahmad Mir
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah 11932, Saudi Arabia.
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia.
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia.
| | - Hesham Alshaalan
- Department of Medical Imaging, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia.
| | - Hassan Alomaish
- Department of Medical Imaging, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia.
| | - Rayyan Daghistani
- Department of Medical Imaging, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia.
| | - Ali Alsehawi
- Department of Medical Imaging, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia.
| | - Naif Khalaf Alharbi
- Department of Infectious Disease Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
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26
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Laubscher F, Cordey S, Friedlaender A, Schweblin C, Noetzlin S, Simand PF, Bordry N, De Sousa F, Pigny F, Baggio S, Getaz L, Dietrich PY, Kaiser L, Vu DL. SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. Microorganisms 2021; 9:2145. [PMID: 34683466 PMCID: PMC8540785 DOI: 10.3390/microorganisms9102145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Oncological patients have a higher risk of prolonged SARS-CoV-2 shedding, which, in turn, can lead to evolutionary mutations and emergence of novel viral variants. The aim of this study was to analyze biological samples of a cohort of oncological patients by deep sequencing to detect any significant viral mutations. METHODS High-throughput sequencing was performed on selected samples from a SARS-CoV-2-positive oncological patient cohort. Analysis of variants and minority variants was performed using a validated bioinformatics pipeline. RESULTS Among 54 oncological patients, we analyzed 12 samples of 6 patients, either serial nasopharyngeal swab samples or samples from the upper and lower respiratory tracts, by high-throughput sequencing. We identified amino acid changes D614G and P4715L as well as mutations at nucleotide positions 241 and 3037 in all samples. There were no other significant mutations, but we observed intra-host evolution in some minority variants, mainly in the ORF1ab gene. There was no significant mutation identified in the spike region and no minority variants common to several hosts. CONCLUSIONS There was no major and rapid evolution of viral strains in this oncological patient cohort, but there was minority variant evolution, reflecting a dynamic pattern of quasi-species replication.
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Affiliation(s)
- Florian Laubscher
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Samuel Cordey
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
| | - Alex Friedlaender
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Cecilia Schweblin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Sarah Noetzlin
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Pierre-François Simand
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Natacha Bordry
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Filipe De Sousa
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Fiona Pigny
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Stephanie Baggio
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Prison Health, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Laurent Getaz
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Prison Health, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Pierre-Yves Dietrich
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Laurent Kaiser
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Center for Emerging Viruses, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Diem-Lan Vu
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
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27
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Diwakar K, Gupta BK, Uddin MW, Sharma A, Jhajra S. Multisystem inflammatory syndrome with persistent neutropenia in neonate exposed to SARS-CoV-2 virus: A case report and review of literature. J Neonatal Perinatal Med 2021; 15:373-377. [PMID: 34459420 DOI: 10.3233/npm-210839] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Multisystem inflammatory syndrome in Children (MIS-C) is a postinfectious immune mediated hyperinflammatory state seen in children and adolescent below 21 year of age and develop after 4-6 weeks of severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2) infection, however, it is rare in neonates. We report an extremely rare and first of its kind case of MIS-C in a neonate with persistent neutropenia. CASE DESCRIPTION A 19-day old boy presented with complaints of fever and loose stools for 1 day and developed rash after admission. Baby was investigated for sepsis and commenced on IV antibiotics empirically. In view of persistent fever, diarrhoea, rash and absence of obvious microbial etiology of inflammation, with elevated inflammatory marker and an epidemiologic link to SARS-CoV-2 infection, the diagnosis of MIS-C-was made. Intravenous immunoglobulin (IVIg) was administered and defervescence occurred within 24 hours. He also developed neutropenia during course of illness which persisted on follow up. CONCLUSION MIS-C in neonates is uncommon and fever with elevated inflammatory markers during COVID-19 pandemic should alert the pediatrician to the possibility of MIS-C. Neutropenia may be associated with MIS-C in neonates and warrants prolonged follow up.
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Affiliation(s)
- K Diwakar
- Department of Paediatrics, Tata Main Hospital, Jamshedpur, Jharkhand, India
| | - B K Gupta
- Department of Paediatrics, Tata Main Hospital, Jamshedpur, Jharkhand, India
| | - M W Uddin
- Department of Paediatrics, Tata Main Hospital, Jamshedpur, Jharkhand, India
| | - A Sharma
- Department of Paediatrics, Post Graduate Institute of Medical Education and Research, Rohtak, Haryana, India
| | - S Jhajra
- Department of Paediatrics, Tata Main Hospital, Jamshedpur, Jharkhand, India
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28
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Martínez-Urbistondo M, Gutiérrez-Rojas Á, Andrés A, Gutiérrez I, Escudero G, García S, Gutiérrez A, Sánchez E, Herráiz J, De La Fuente S, Callejas A, De Mendoza C, Moreno-Torres V. Severe Lymphopenia as a Predictor of COVID-19 Mortality in Immunosuppressed Patients. J Clin Med 2021; 10:jcm10163595. [PMID: 34441891 PMCID: PMC8396991 DOI: 10.3390/jcm10163595] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/08/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
Background. Coronavirus disease 2019 (COVID-19) has a high mortality in certain group of patients. We analysed the impact of baseline immunosuppression in COVID-19 mortality and the role of severe lymphopenia in immunocompromised subjects. Methods. We analysed all patients admitted with COVID-19 in a tertiary hospital in Madrid between March 1st and April 30th 2020. Epidemiological and clinical data, including severe lymphopenia (<500 lymphocytes/mm3) during admission, were analysed and compared based on their baseline immunosuppression condition. Results. A total of 1594 patients with COVID-19 pneumonia were hospitalised during the study period. 166 (10.4%) were immunosuppressed. Immunocompromised patients were younger (64 vs. 67 years, p = 0.02) but presented higher rates of hypertension, diabetes, heart, neurological, lung, kidney and liver disease (p < 0.05). They showed more severe lymphopenia (53% vs 24.1%, p < 0.001), lower SapO2/FiO2 ratios (251 vs 276, p = 0.02) during admission and higher mortality rates (27.1% vs 13.5%, p < 0.001). After adjustment, immunosuppression remained as an independent factor related to mortality (Odds Ratio (OR): 2.24, p < 0.001). In the immunosuppressed group, age (OR = 1.06, p = 0.01), acute respiratory distress syndrome (ARDS) (OR = 12.27, p = 0.017) and severe lymphopenia (OR = 3.48, p = 0.04) were the factors related to high mortality rate. Conclusion. Immunosuppression is an independent mortality risk factor in COVID-19. Severe lymphopenia should be promptly identified in these patients.
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Sahbudak Bal Z, Ozkul A, Bilen M, Kurugol Z, Ozkinay F. The Longest Infectious Virus Shedding in a Child Infected With the G614 Strain of SARS-CoV-2. Pediatr Infect Dis J 2021; 40:e263-e265. [PMID: 33990523 DOI: 10.1097/inf.0000000000003158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
COVID-19 spread globally and caused over 97 million cases with more than 2 million deaths. There is still ongoing discussion on the duration of infectious interval SARS-CoV-2 infection. Symptomatic children had longer virus shedding and there are some reports of prolonged infectious virus shedding in adults particularly patients having an immunocompromised status. A missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe and is spreading worldwide that can result in higher viral loads in patients. Herein, we described the longest infectious virus shedding in a previously healthy child infected with SARS-CoV-2 expressing spike D614G substitution.
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Affiliation(s)
- Zumrut Sahbudak Bal
- From the Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir, Turkey
| | - Aykut Ozkul
- Department of Virology, Faculty of Veterinary Medicine, Ankara, Turkey
| | - Melis Bilen
- From the Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir, Turkey
| | - Zafer Kurugol
- From the Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir, Turkey
| | - Ferda Ozkinay
- From the Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir, Turkey
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30
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Marcolungo L, Beltrami C, Degli Esposti C, Lopatriello G, Piubelli C, Mori A, Pomari E, Deiana M, Scarso S, Bisoffi Z, Grosso V, Cosentino E, Maestri S, Lavezzari D, Iadarola B, Paterno M, Segala E, Giovannone B, Gallinaro M, Rossato M, Delledonne M. ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections. Genomics 2021; 113:1628-1638. [PMID: 33839270 PMCID: PMC8028595 DOI: 10.1016/j.ygeno.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 01/04/2023]
Abstract
Sequencing the SARS-CoV-2 genome from clinical samples can be challenging, especially in specimens with low viral titer. Here we report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. The protocol was optimized to improve flexibility and the combination of technical replicates was established as the central strategy to achieve accurate analysis of low-titer/suboptimal samples. We demonstrated the utility of the approach by achieving complete genome reconstruction and the identification of false-positive variants in >170 clinical samples, thus avoiding the generation of inaccurate and/or incomplete sequences. Most importantly, ACoRE was crucial to identify the correct viral strain responsible of a relapse case, that would be otherwise mis-classified as a re-infection due to missing or incorrect variant identification by a standard workflow.
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Affiliation(s)
- Luca Marcolungo
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Cristina Beltrami
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Chiara Degli Esposti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Giulia Lopatriello
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Chiara Piubelli
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Antonio Mori
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Elena Pomari
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Michela Deiana
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Salvatore Scarso
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy,Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Valentina Grosso
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Emanuela Cosentino
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Simone Maestri
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Denise Lavezzari
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Barbara Iadarola
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Marta Paterno
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Elena Segala
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Barbara Giovannone
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Martina Gallinaro
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy,Genartis srl, via IV Novembre 24, 37126 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy,Genartis srl, via IV Novembre 24, 37126 Verona, Italy,Corresponding author at: Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
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Kaila V, Sirkeoja S, Blomqvist S, Rannikko J, Viskari H, Lyly-Yrjänäinen T, Syrjänen J. SARS-CoV-2 late shedding may be infectious between immunocompromised hosts. Infect Dis (Lond) 2021; 53:880-882. [PMID: 34137349 PMCID: PMC8220436 DOI: 10.1080/23744235.2021.1939891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background Immunocompromised patients shed SARS-CoV-2 for extended periods, but to our knowledge person-to-person transmission from late shedding has not been reported. The case We present a case in which a COVID-19 patient infected another over 28 days after the patient’s initial symptoms, past current guideline recommendations of 20 days for length of isolation in immunocompromised patients. Whole genome sequencing of their viruses was performed to ascertain the transmission. Discussion Severely immunocompromised patients, whose clearance of the virus is impaired, may remain infectious for extended periods. Caution should be taken particularly in hospital settings where lapses in isolation procedures might pose increased risk, especially to other immunocompromised patients.
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Affiliation(s)
- Ville Kaila
- Department of Infectious Disease, Tampere University Hospital, Tampere, Finland
| | - Simo Sirkeoja
- Department of Infectious Disease, Tampere University Hospital, Tampere, Finland
| | - Soile Blomqvist
- Expert Microbiology, National Institute for Health and Welfare, Helsinki, Finland
| | - Juha Rannikko
- Department of Infectious Disease, Tampere University Hospital, Tampere, Finland
| | - Hanna Viskari
- Department of Infectious Disease, Tampere University Hospital, Tampere, Finland
| | | | - Jaana Syrjänen
- Department of Infectious Disease, Tampere University Hospital, Tampere, Finland
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Sisó-Almirall A, Brito-Zerón P, Conangla Ferrín L, Kostov B, Moragas Moreno A, Mestres J, Sellarès J, Galindo G, Morera R, Basora J, Trilla A, Ramos-Casals M. Long Covid-19: Proposed Primary Care Clinical Guidelines for Diagnosis and Disease Management. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:4350. [PMID: 33923972 PMCID: PMC8073248 DOI: 10.3390/ijerph18084350] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/02/2021] [Accepted: 04/16/2021] [Indexed: 01/08/2023]
Abstract
Long COVID-19 may be defined as patients who, four weeks after the diagnosis of SARS-Cov-2 infection, continue to have signs and symptoms not explainable by other causes. The estimated frequency is around 10% and signs and symptoms may last for months. The main long-term manifestations observed in other coronaviruses (Severe Acute Respiratory Syndrome (SARS), Middle East respiratory syndrome (MERS)) are very similar to and have clear clinical parallels with SARS-CoV-2: mainly respiratory, musculoskeletal, and neuropsychiatric. The growing number of patients worldwide will have an impact on health systems. Therefore, the main objective of these clinical practice guidelines is to identify patients with signs and symptoms of long COVID-19 in primary care through a protocolized diagnostic process that studies possible etiologies and establishes an accurate differential diagnosis. The guidelines have been developed pragmatically by compiling the few studies published so far on long COVID-19, editorials and expert opinions, press releases, and the authors' clinical experience. Patients with long COVID-19 should be managed using structured primary care visits based on the time from diagnosis of SARS-CoV-2 infection. Based on the current limited evidence, disease management of long COVID-19 signs and symptoms will require a holistic, longitudinal follow up in primary care, multidisciplinary rehabilitation services, and the empowerment of affected patient groups.
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Affiliation(s)
- Antoni Sisó-Almirall
- Permanent Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain; (L.C.F.); (J.M.)
- Primary Care Centre Les Corts, Consorci d’Atenció Primària de Salut Barcelona Esquerra (CAPSBE), 08028 Barcelona, Spain;
- Primary Healthcare Transversal Research Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Pilar Brito-Zerón
- Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, 08036 Barcelona, Spain; (P.B.-Z.); (M.R.-C.)
- Autoimmune Diseases Unit, Department of Medicine, Hospital CIMA-Sanitas, 08034 Barcelona, Spain
- Department of Autoimmune Diseases, ICMiD, Hospital Clínic, 08036 Barcelona, Spain
| | - Laura Conangla Ferrín
- Permanent Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain; (L.C.F.); (J.M.)
| | - Belchin Kostov
- Primary Care Centre Les Corts, Consorci d’Atenció Primària de Salut Barcelona Esquerra (CAPSBE), 08028 Barcelona, Spain;
- Primary Healthcare Transversal Research Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya (UPC), 08034 Barcelona, Spain
| | - Anna Moragas Moreno
- Jaume I Health Centre, Institut Català de la Salut, Universitat Rovira i Virgili, 43005 Tarragona, Spain;
| | - Jordi Mestres
- Permanent Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain; (L.C.F.); (J.M.)
| | | | - Gisela Galindo
- Permanent Board of the Spanish Society of Family and Community Medicine (semFYC), 08009 Barcelona, Spain;
| | - Ramon Morera
- Board of Spanish Society of Managers of Primary Care (SEDAP), 28026 Madrid, Spain;
| | | | - Antoni Trilla
- Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
| | - Manuel Ramos-Casals
- Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, 08036 Barcelona, Spain; (P.B.-Z.); (M.R.-C.)
- Department of Autoimmune Diseases, ICMiD, Hospital Clínic, 08036 Barcelona, Spain
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33
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How long can SARS-CoV-2 persist in human corpses? Int J Infect Dis 2021; 106:1-2. [PMID: 33746091 PMCID: PMC7970835 DOI: 10.1016/j.ijid.2021.03.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/11/2021] [Accepted: 03/14/2021] [Indexed: 12/23/2022] Open
Abstract
We report the finding of the SARS-CoV-2 genome in the corpse of an exhumed infected person, one month after her death. The viral gene targets were still present in her lungs and heart, however, the virus was no longer alive. Infectious risks from human corpses should be considered.
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34
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Alsaud AE, Nair AP, Matarneh AS, Sasi S, El Hassan R, Khan F, Coyle P, Abu Khattab M, Mohamed MFH. Case Report: Prolonged Viral Shedding in Six COVID-19 Patients. Am J Trop Med Hyg 2021; 104:1472-1475. [PMID: 33626020 PMCID: PMC8045623 DOI: 10.4269/ajtmh.20-0933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
COVID-19 has surfaced as a multi-organ disease predominantly affecting the respiratory system. Detection of the viral RNA through reverse transcriptase–PCR (RT-PCR) from a nasopharyngeal or throat sample is the preferred method of diagnosis. Recent evidence has suggested that COVID-19 patients can shed the SARS-CoV-2 for several weeks. Herein, we report six cases of COVID-19 who had persistently positive SARS-CoV-2 on repeat RT-PCR testing reaching up to 9 weeks. The spectrum of cases described ranges from asymptomatic infection to severe COVID-19 pneumonia. A full understanding of the virus’s transmission dynamics needs further research. Prolonged viral shedding currently has unclear implications on the management and isolation decisions—the role of the cycle threshold (Ct) value in guiding therapeutic decisions is yet to be clarified. More data on the relationship between Ct values and viral cultivation are needed, especially in patients with prolonged viral shedding, to understand the virus’s viability and infectivity.
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Affiliation(s)
- Arwa E Alsaud
- 1Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Arun Prabhakaran Nair
- 2Department of Infectious Diseases, Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Ahmad S Matarneh
- 1Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Sreethish Sasi
- 1Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Rania El Hassan
- 1Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Fahmi Khan
- 1Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Peter Coyle
- 3Department of Virology, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Mohamed Abu Khattab
- 2Department of Infectious Diseases, Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Mouhand F H Mohamed
- 1Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
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35
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Abstract
The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.
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