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Lottes M, Grodd M, Grabenhenrich L, Wolkewitz M. Assessing the impact of Delta and Omicron in German intensive care units: a retrospective, nationwide multistate analysis. BMC Health Serv Res 2024; 24:1107. [PMID: 39313793 PMCID: PMC11421169 DOI: 10.1186/s12913-024-11493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 08/26/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND The spread of several severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants of concern (VOCs) has repeatedly led to increasing numbers of coronavirus disease 2019 (COVID-19) patients in German intensive care units (ICUs), resulting in capacity shortages and even transfers of COVID-19 intensive care patients between federal states in late 2021. In this respect, there is scarce evidence on the impact of predominant VOCs in German ICUs at the population level. METHODS A retrospective cohort study was conducted from July 01, 2021, to May 31, 2022, using daily nationwide inpatient billing data from German hospitals on COVID-19 intensive care patients and SARS-CoV-2 sequence data from Germany. A multivariable Poisson regression analysis was performed to estimate the incidence rate ratios (IRRs) of transfer (to another hospital during inpatient care), discharge (alive) and death of COVID-19 intensive care patients associated with Delta or Omicron, adjusted for age group and sex. In addition, a multistate approach was used for the clinical trajectories of COVID-19 intensive care patients to estimate their competing risk of transfer, discharge or death associated with Delta or Omicron, specifically concerning patient age. RESULTS A total of 6046 transfers, 33256 discharges, and 12114 deaths were included. Poisson regression analysis comparing Omicron versus Delta yielded an estimated adjusted IRR of 1.23 (95% CI 1.16-1.30) for transfers, 2.27 (95% CI 2.20-2.34) for discharges and 0.98 (95% CI 0.94-1.02) for deaths. For ICU deaths in particular, the estimated adjusted IRR increased from 0.14 (95% CI 0.08-0.22) for the 0-9 age group to 4.09 (95% CI 3.74-4.47) for those aged 90 and older compared to the reference group of 60-69-year-olds. Multistate analysis revealed that Omicron was associated with a higher estimated risk of discharge for COVID-19 intensive care patients across all ages, while Delta infection was associated with a higher estimated risk of transfer and death. CONCLUSIONS Retrospective, nationwide comparisons of transfers, discharges and deaths of COVID-19 intensive care patients during Delta- and Omicron-dominated periods in Germany suggested overall less severe clinical trajectories associated with Omicron. Age was confirmed to be an important determinant of fatal clinical outcomes in COVID-19 intensive care patients, necessitating close therapeutic care for elderly people and appropriate public health control measures.
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Affiliation(s)
- Matthäus Lottes
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Marlon Grodd
- Institute of Medical Biometry and Statistics, Medical Center-University of Freiburg, Stefan-Meier-Straße 26, 79104, Freiburg, Germany
| | - Linus Grabenhenrich
- Department of Method Development, Research Infrastructure and Information Technology, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | - Martin Wolkewitz
- Institute of Medical Biometry and Statistics, Medical Center-University of Freiburg, Stefan-Meier-Straße 26, 79104, Freiburg, Germany
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Liu Y, Guo Y, Zhan H, Liu X, Li X, Cui J, Li H, Feng S, Cheng L, Li X, Guo S, Li Y. Immune and inflammation features of severe and critical Omicron infected patients during Omicron wave in China. BMC Infect Dis 2024; 24:809. [PMID: 39123106 PMCID: PMC11316362 DOI: 10.1186/s12879-024-09652-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
OBJECTIVE The current study aimed to investigate the baseline immune and inflammatory features and in-hospital outcomes of patients infected with the Omicron variant (PIWO) who presented with different disease severities during the first wave of mass Omicron infections in the Chinese population has occurred. METHOD A cross-sectional study was conducted on 140 hospitalized PIWO between December 11, 2022, and February 16, 2023. The clinical features, antibodies against SARS-CoV-2, immune cells, and inflammatory cytokines among mildly, severely, and critically ill PIWO at baseline and during follow-up period were compared. RESULT Patients with severe (n = 49) and critical (n = 35) disease were primarily male, needed invasive mechanical ventilation treatment, and exhibited higher mortality than those with mild disease (n = 56). During acute infection, SARS-CoV-2-specific antibody levels fluctuated with disease severity, serum antibodies increased and the incidence of severe cases decreased in critically ill PIWO over time. Antibody titers in severe or critical PIWO with no antibody responses at baseline did not increase significantly over time. Meanwhile, CD4+T cell, CD8+T cell, and natural killer cell counts were negatively correlated with disease severity, whereas interleukin (IL)-6 and IL-10 levels were positively correlated. In addition, combined diabetes, immunosuppressive therapy before infection, serum amyloid A, IL-10 and neutrophil counts were independently associated with severe and critical illness in PIWO. Among the 11 nonsurvivors, 8, 2, 1 died of respiratory failure, sudden cardiac death, and renal failure, respectively. Compared with survivors, nonsurvivors exhibited lower seropositivity of SARS-CoV-2-specific antibody, reduced CD3+T and CD4+T cell counts, and higher IL-2R, IL-6, IL-8, and IL-10 levels. Of note, lactate dehydrogenase was a significant risk factor of death in severe or critically ill PIWO. CONCLUSION This present study assessed the dynamic changes of SARS-CoV-2-specific antibodies, immune cells and inflammatory indexes between severely and critically ill PIWO. Critical and dead PIWO featured compromised humoral immune response and excessive inflammation, which broadened the understanding of the pathophysiology of Omicron infection and provides warning markers for severe disease and poor prognosis.
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Affiliation(s)
- Yongmei Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Yaping Guo
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Haoting Zhan
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Xin Liu
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Xiaomeng Li
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
- Department of Clinical Laboratory, Peking University People's Hospital, NO.11, Xizhimen South Street, Beijing, 100035, China
| | - Jingjing Cui
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Haolong Li
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Sha Feng
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Linlin Cheng
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Xiaoyan Li
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Shuqin Guo
- Department of Endocrinology, Baoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China.
| | - Yongzhe Li
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China.
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de Prost N, Audureau E, Guillon A, Handala L, Préau S, Guigon A, Uhel F, Le Hingrat Q, Delamaire F, Grolhier C, Tamion F, Moisan A, Darreau C, Thomin J, Contou D, Henry A, Daix T, Hantz S, Saccheri C, Giordanengo V, Pham T, Chaghouri A, Bay P, Pawlotsky JM, Fourati S. Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron sublineage JN.1 in critically ill COVID-19 patients: a prospective, multicenter cohort study in France, November 2022 to January 2024. Ann Intensive Care 2024; 14:101. [PMID: 38940865 PMCID: PMC11213836 DOI: 10.1186/s13613-024-01319-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/25/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND A notable increase in severe cases of COVID-19, with significant hospitalizations due to the emergence and spread of JN.1 was observed worldwide in late 2023 and early 2024. However, no clinical data are available regarding critically-ill JN.1 COVID-19 infected patients. METHODS The current study is a substudy of the SEVARVIR prospective multicenter observational cohort study. Patients admitted to any of the 40 participating ICUs between November 17, 2022, and January 22, 2024, were eligible for inclusion in the SEVARVIR cohort study (NCT05162508) if they met the following inclusion criteria: age ≥ 18 years, SARS-CoV-2 infection confirmed by a positive reverse transcriptase-polymerase chain reaction (RT-PCR) in nasopharyngeal swab samples, ICU admission for acute respiratory failure. The primary clinical endpoint of the study was day-28 mortality. Evaluation of the association between day-28 mortality and sublineage group was conducted by performing an exploratory multivariable logistic regression model, after systematically adjusting for predefined prognostic factors previously shown to be important confounders (i.e. obesity, immunosuppression, age and SOFA score) computing odds ratios (OR) along with their corresponding 95% confidence intervals (95% CI). RESULTS During the study period (November 2022-January 2024) 56 JN.1- and 126 XBB-infected patients were prospectively enrolled in 40 French intensive care units. JN.1-infected patients were more likely to be obese (35.7% vs 20.8%; p = 0.033) and less frequently immunosuppressed than others (20.4% vs 41.4%; p = 0.010). JN.1-infected patients required invasive mechanical ventilation support in 29.1%, 87.5% of them received dexamethasone, 14.5% tocilizumab and none received monoclonal antibodies. Only one JN-1 infected patient (1.8%) required extracorporeal membrane oxygenation support during ICU stay (vs 0/126 in the XBB group; p = 0.30). Day-28 mortality of JN.1-infected patients was 14.6%, not significantly different from that of XBB-infected patients (22.0%; p = 0.28). In univariable logistic regression analysis and in multivariable analysis adjusting for confounders defined a priori, we found no statistically significant association between JN.1 infection and day-28 mortality (adjusted OR 1.06 95% CI (0.17;1.42); p = 0.19). There was no significant between group difference regarding duration of stay in the ICU (6.0 [3.5;11.0] vs 7.0 [4.0;14.0] days; p = 0.21). CONCLUSIONS Critically-ill patients with Omicron JN.1 infection showed a different clinical phenotype than patients infected with the earlier XBB sublineage, including more frequent obesity and less immunosuppression. Compared with XBB, JN.1 infection was not associated with higher day-28 mortality.
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Affiliation(s)
- Nicolas de Prost
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique - Hôpitaux de Paris (AP-HP), Créteil, France.
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France.
- Université Paris-Est-Créteil (UPEC), Créteil, France.
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France.
- Service de Médecine Intensive Réanimation, Hôpital Henri Mondor, Créteil, France.
| | - Etienne Audureau
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Public Health, Hôpitaux Universitaires Henri Mondor, Assistance Publique - Hôpitaux de Paris (AP-HP), Créteil, France
- IMRB INSERM U955, Team CEpiA, Créteil, France
| | - Antoine Guillon
- Intensive Care Unit, Research Center for Respiratory Diseases (CEPR), INSERM U1100, Tours University Hospital, University of Tours, Tours, France
| | - Lynda Handala
- INSERM U1259, Université de Tours, Tours, France
- National Reference Center for HIV-Associated Laboratory, , CHRU de Tours, Tours, France
| | - Sébastien Préau
- U1167 - RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, 59000, Lille, France
| | - Aurélie Guigon
- Service de Virologie, CHU de Lille, 59000, Lille, France
| | - Fabrice Uhel
- DMU ESPRIT, Service de Médecine Intensive Réanimation, Université Paris Cité, APHP, Hôpital Louis Mourier, Colombes, France
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades (INEM), Université Paris Cité, Paris, France
| | - Quentin Le Hingrat
- IAME INSERM UMR 1137, Service de Virologie, Université Paris Cité, Hôpital Bichat-Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Flora Delamaire
- CHU Rennes, Maladies Infectieuses et Réanimation Médicale, Rennes, France
| | | | - Fabienne Tamion
- Service de Médecine Intensive-Réanimation, CHU De Rouen, 76000, Rouen, France
| | - Alice Moisan
- INSERM DYNAMICURE UMR 1311 Department of Virology, Univ Rouen Normandie, Université de Caen Normandie, Normandie Univ, CHU Rouen, National Reference Center of HIV, 76000, Rouen, France
| | - Cédric Darreau
- Service de Réanimation Médico-Chirurgicale, Centre Hospitalier du Mans, Le Mans, France
| | - Jean Thomin
- Laboratoire de Microbiologie, Centre Hospitalier du Mans, Le Mans, France
| | - Damien Contou
- Service de Réanimation, Hôpital Victor Dupouy, Argenteuil, France
| | - Amandine Henry
- Service de Virologie, Hôpital Victor Dupouy, Argenteuil, France
| | - Thomas Daix
- INSERM CIC 1435 and UMR 1092, Réanimation Polyvalente, CHU Limoges, Limoges, France
| | - Sébastien Hantz
- Bacteriology, Virology, Hygiene Department, French National Reference Center for Herpesviruses, CHU Limoges, 87000, Limoges, France
- INSERM, RESINFIT, U1092, 87000, Limoges, France
| | | | | | - Tài Pham
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
- Service de Médecine Intensive-Réanimation, DMU 4 CORREVE Maladies du Cœur Et Des Vaisseaux, Assistance Publique - Hôpitaux de Paris, Hôpital de Bicêtre, FHU Sepsis, Le Kremlin-Bicêtre, France
- Inserm U1018, Equipe d'Epidémiologie Respiratoire Intégrative, CESP, 94807, Villejuif, France
| | - Amal Chaghouri
- Laboratoire de Virologie, Hôpital Paul Brousse, Assistance Publique - Hôpitaux de Paris, Villejuif, France
| | - Pierre Bay
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique - Hôpitaux de Paris (AP-HP), Créteil, France
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
- Université Paris-Est-Créteil (UPEC), Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
| | - Slim Fourati
- Université Paris-Est-Créteil (UPEC), Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
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Sakuramoto K, Wada D, Maruyama S, Muroya T, Saito F, Nakamori Y, Kuwagata Y. Evaluation of characteristics and prognosis of COVID-19 patients requiring invasive mechanical ventilation during dominance of nonvariant, alpha, delta, and omicron variants in tertiary hospitals of Japan. BMC Infect Dis 2024; 24:223. [PMID: 38374034 PMCID: PMC10877910 DOI: 10.1186/s12879-024-09131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND In November 2021, the B.1.1.529 (omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in South Africa and subsequently rapidly spread around the world. Despite the reduced severity of the omicron variants, many patients become severely ill after infection and undergo invasive mechanical ventilation, but there are few reports on their background and prognosis throughout all variant periods. This study aimed to evaluate risk factors affecting patients requiring invasive mechanical ventilation with each variant of COVID-19 pandemic in Japan from nonvariants to omicron variants. METHOD This retrospective observational study was conducted at the Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital and Kansai Medical University Medical Center, Osaka, Japan, from March 2020 to March 2023. Eligible patients were those who underwent invasive ventilation for COVID-19 pneumonia. We set the primary endpoint as in-hospital mortality. Multivariable logistic regression analysis adjusted for clinically important variables was performed to evaluate the clinical outcomes. RESULTS We included 377 patients: 118 in the Nonvariant group, 154 in the Alpha group, 42 in the Delta group, and 63 patients in the Omicron group. Mortality rates for each group were 23.7% for the Nonvariant group, 12.3% for the Alpha group, 7.1% for the Delta group, and 30.5% for the Omicron group. Patient age was significantly associated with increased mortality (adjusted odds ratio [AOR]: 1.097; 95% confidence interval [CI]: 1.057-0.138, P < 0.001). Immunodeficiency (AOR: 3.388, 95% CI: 1.377-8.333, P = 0.008), initial SOFA score (AOR: 1.190, 95% CI: 1.056-1.341, P = 0.004), dialysis prior to COVID-19 (AOR: 3.695, 95% CI: 1.117-11.663, P = 0.026), and smoking history (AOR: 2.548, 95% CI: 1.153-5.628, P = 0.021) were significantly associated with increased mortality. Differences in variants were not significant factors associated with high mortality. CONCLUSION We compared the background and prognosis of patients with COVID-19 pneumonia requiring invasive mechanical ventilation between SARS-CoV-2 variants. In these patients, differences in variants did not affect prognosis. Hospital mortality in critically ill COVID-19 patients was significantly higher in the older patients with bacterial coinfection, or patients with immunodeficiency, COPD, and chronic renal failure on dialysis.
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Affiliation(s)
- Kazuhito Sakuramoto
- Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital, 2-3-1 Shinmachi, Hirakata, Osaka, 573-1191, Japan
| | - Daiki Wada
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan.
| | - Shuhei Maruyama
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Takashi Muroya
- Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital, 2-3-1 Shinmachi, Hirakata, Osaka, 573-1191, Japan
| | - Fukuki Saito
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasushi Nakamori
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasuyuki Kuwagata
- Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital, 2-3-1 Shinmachi, Hirakata, Osaka, 573-1191, Japan
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Kodsi IA, Rayes DE, Koweyes J, Khoury CA, Rahy K, Thoumi S, Chamoun M, Haddad H, Mokhbat J, Tokajian S. Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon. Virus Res 2024; 339:199289. [PMID: 38036064 PMCID: PMC10704499 DOI: 10.1016/j.virusres.2023.199289] [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: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. METHODS A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. RESULTS Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). CONCLUSIONS The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
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Affiliation(s)
- Ibrahim Al Kodsi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Douaa El Rayes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Kelven Rahy
- School of Medicine, Lebanese American University, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Lebanon
| | | | - Hoda Haddad
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Jacques Mokhbat
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon.
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Bay P, Rodriguez C, Caruso S, Demontant V, Boizeau L, Soulier A, Woerther PL, Mekontso-Dessap A, Pawlotsky JM, de Prost N, Fourati S. Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in critically ill COVID-19 patients. J Med Virol 2023; 95:e29268. [PMID: 38050838 DOI: 10.1002/jmv.29268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
Severe coronavirus disease 2019 (COVID-19) is related to dysregulated immune responses. We aimed to explore the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on the immune response by nasopharyngeal transcriptomic in critically-ill patients. This prospective monocentric study included COVID-19 patients requiring intensive care unit (ICU) admission between March 2020 and 2022. Patients were classified according to VOC (ancestral, Alpha, Delta, and Omicron). Eighty-eight patients with severe COVID-19 were included after matching (on prespecified clinical criteria). Profiling of gene expression markers of innate and adaptive immune responses were investigated by respiratory transcriptomics at ICU admission. Eighty-eight patients were included in the study after matching (ancestral [n = 24], Alpha [n = 24], Delta [n = 22], and Omicron [n = 18] variants). Respiratory transcriptomic analysis revealed distinct innate and adaptive immune profiling between variants. In comparison with the ancestral variant, there was a reduced expression of neutrophil degranulation, T cell activation, cytokines signalling pathways in patients infected with Alpha and Delta variants. In contrast, there was a higher expression of neutrophil degranulation, T and B cells activation, and inflammatory interleukins pathways in patients infected with Omicron. To conclude, Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in patients with severe COVID-19, pointing to an evolving pathophysiology of severe COVID-19 in the Omicron era.
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Affiliation(s)
- Pierre Bay
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Christophe Rodriguez
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Stefano Caruso
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Pathologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Vanessa Demontant
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Laure Boizeau
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Alexandre Soulier
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Paul L Woerther
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- EA 7380 Dynamic, Université Paris-Est-Créteil (UPEC), École Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Armand Mekontso-Dessap
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Jean-Michel Pawlotsky
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Nicolas de Prost
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Slim Fourati
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
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Hedberg P, Baltzer N, Granath F, Fored M, Mårtensson J, Nauclér P. Clinical outcomes during and beyond different COVID-19 critical illness variant periods compared with other lower respiratory tract infections. Crit Care 2023; 27:427. [PMID: 37932793 PMCID: PMC10629059 DOI: 10.1186/s13054-023-04722-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND It is yet to be better understood how outcomes during and after the critical illness potentially differ between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from other lower respiratory tract infections (LRTIs). We aimed to compare outcomes in adults admitted to an intensive care unit (ICU) with coronavirus disease 2019 (COVID-19) during the Wild-type, Alpha, Delta, and Omicron periods with individuals admitted with other LRTI. METHODS Population-based cohort study in Stockholm, Sweden, using health registries with high coverage, including ICU-admitted adults from 1 January 2016 to 15 September 2022. Outcomes were in-hospital mortality, 180-day post-discharge mortality, 180-day hospital readmission, 180-day days alive and at home (DAAH), and incident diagnoses registered during follow-up. RESULTS The number of ICU admitted individuals were 1421 Wild-type, 551 Alpha, 190 Delta, 223 Omicron, and 2380 LRTI. In-hospital mortality ranged from 28% (n = 665) in the LRTI cohort to 35% (n = 77) in the Delta cohort. The adjusted cause-specific hazard ratio (CSHR) compared with the LRTI cohort was 1.33 (95% confidence interval [CI] 1.16-1.53) in the Wild-type cohort, 1.53 (1.28-1.82) in the Alpha cohort, 1.70 (1.30-2.24) in the Delta cohort, and 1.59 (1.24-2.02) in the Omicron cohort. Among patients discharged alive from their COVID-19 hospitalization, the post-discharge mortality rates were lower (1-3%) compared with the LRTI cohort (9%), and the risk of hospital readmission was lower (CSHRs ranging from 0.42 to 0.68). Moreover, all COVID-19 cohorts had compared with the LRTI cohort more DAAH after compared with before the critical illness. CONCLUSION Overall, COVID-19 critical was associated with an increased hazard of in-hospital mortality, but among those discharged alive from the hospital, less severe long-term outcomes were observed compared with other LRTIs.
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Affiliation(s)
- Pontus Hedberg
- Department of Medicine, Huddinge, Karolinska Institutet, H7 Medicin, Huddinge, H7 Infektion och Hud Sönnerborg, 171 77, Stockholm, Sweden.
| | - Nicholas Baltzer
- Division of Infectious Diseases, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Granath
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Michael Fored
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Johan Mårtensson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Pontus Nauclér
- Division of Infectious Diseases, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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Seghezzo G, Nash SG, Aziz NA, Hope R, Bernal JL, Gallagher E, Dabrera G, Thelwall S. Risk of severe outcomes among Omicron sub-lineages BA.4.6, BA.2.75, and BQ.1 compared to BA.5 in England. Epidemiol Infect 2023; 151:e189. [PMID: 37905583 PMCID: PMC10728974 DOI: 10.1017/s0950268823001760] [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: 07/14/2023] [Revised: 09/19/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023] Open
Abstract
Since the emergence of Omicron variant of SARS-CoV-2 in late 2021, a number of sub-lineages have arisen and circulated internationally. Little is known about the relative severity of Omicron sub-lineages BA.2.75, BA.4.6, and BQ.1. We undertook a case-control analysis to determine the clinical severity of these lineages relative to BA.5, using whole genome sequenced, PCR-confirmed infections, between 1 August 2022 and 27 November 2022, among those who presented to emergency care in England 14 days after and up to one day prior to the positive specimen. A total of 10,375 episodes were included in the analysis; of which, 5,207 (50.2%) were admitted to the hospital or died. Multivariable conditional regression analyses found no evidence of greater odds of hospital admission or death among those with BA.2.75 (odds ratio (OR) = 0.96, 95% confidence interval (CI): 0.84-1.09) and BA.4.6 (OR = 1.02, 95% CI: 0.88- 1.17) or BQ.1 (OR = 1.03, 95% CI: 0.94-1.13) compared to BA.5. Future lineages may not follow the same trend and there remains a need for continued surveillance of COVID-19 variants and their clinical outcomes to inform the public health response.
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Affiliation(s)
- Giulia Seghezzo
- COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, UK
| | - Sophie G. Nash
- COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, UK
| | - Nurin A. Aziz
- COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, UK
| | - Russell Hope
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK
| | - Jamie L. Bernal
- COVID-19 Surveillance Cell, UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit for Respiratory Infections, London, UK
| | - Eileen Gallagher
- Genomics and Public Health Analysis, UK Health Security Agency, London, UK
| | - Gavin Dabrera
- COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, UK
| | - Simon Thelwall
- COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, UK
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9
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de Prost N, Audureau E, Préau S, Favory R, Guigon A, Bay P, Heming N, Gault E, Pham T, Chaghouri A, Voiriot G, Morand-Joubert L, Jochmans S, Pitsch A, Meireles S, Contou D, Henry A, Joseph A, Chaix ML, Uhel F, Descamps D, Emery M, Garcia-Sanchez C, Luyt CE, Marot S, Pène F, Lhonneur AS, Gaudry S, Brichler S, Picard L, Mekontso Dessap A, Rodriguez C, Pawlotsky JM, Fourati S. Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variants BA.2, BA.5 and BQ.1.1 in critically ill patients with COVID-19: a prospective, multicenter cohort study. Intensive Care Med Exp 2023; 11:48. [PMID: 37544942 PMCID: PMC10404579 DOI: 10.1186/s40635-023-00536-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Despite current broad natural and vaccine-induced protection, a substantial number of patients infected with emerging SARS-CoV-2 variants (e.g., BF.7 and BQ.1.1) still experience severe COVID-19. Real-life studies investigating the impact of these variants on clinical outcomes of severe cases are currently not available. We performed a prospective multicenter observational cohort study. Adult patients with acute respiratory failure admitted between December 7, 2021 and December 15, 2022, in one of the 20 participating intensive care units (17 from the Greater Paris area and 3 from the North of France) were eligible for inclusion if they had SARS-CoV-2 infection confirmed by a positive reverse transcriptase-polymerase chain reaction (RT-PCR). Full-length SARS-CoV-2 genomes from all included patients were sequenced by means of next-generation sequencing. The primary endpoint of the study was day-28 mortality. RESULTS The study included 158 patients infected with three groups of Omicron sublineages, including (i) BA.2 variants and their early sublineages referred as "BA.2" (n = 50), (ii) early BA.4 and BA.5 sublineages (including BA.5.1 and BA.5.2, n = 61) referred as "BA.4/BA.5", and (iii) recent emerging BA.5 sublineages (including BQ.1, BQ.1.1, BF.7, BE.1 and CE.1, n = 47) referred as "BQ.1.1". The clinical phenotype of BQ1.1-infected patients compared to earlier BA.2 and BA.4/BA.5 sublineages, showed more frequent obesity and less frequent immunosuppression. There was no significant difference between Omicron sublineage groups regarding the severity of the disease at ICU admission, need for organ failure support during ICU stay, nor day 28 mortality (21.7%, n = 10/47 in BQ.1.1 group vs 26.7%, n = 16/61 in BA.4/BA.5 vs 22.0%, n = 11/50 in BA.2, p = 0.791). No significant relationship was found between any SARS-CoV-2 substitution and/or deletion on the one hand and survival on the other hand over hospital follow-up. CONCLUSIONS Critically-ill patients with Omicron BQ.1.1 infection showed a different clinical phenotype than other patients infected with earlier Omicron sublineage but no day-28 mortality difference.
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Affiliation(s)
- Nicolas de Prost
- Service de Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France.
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France.
- Université Paris-Est-Créteil (UPEC), Créteil, France.
| | - Etienne Audureau
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Public Health, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
- IMRB INSERM U955, Team CEpiA, Créteil, France
| | - Sébastien Préau
- U1167, RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, 59000, Lille, France
| | - Raphaël Favory
- U1167, RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, 59000, Lille, France
| | - Aurélie Guigon
- Service de Virologie, CHU de Lille, 59000, Lille, France
| | - Pierre Bay
- Service de Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Nicholas Heming
- Médecine Intensive Réanimation, Hôpital Raymond Poincaré, Assistance Publique, Hôpitaux de Paris (AP-HP), Garches, France
| | - Elyanne Gault
- Laboratoire de Virologie, Hôpital Ambroise Paré, Assistance Publique, Hôpitaux de Paris (AP-HP), Boulogne, France
| | - Tài Pham
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
- Service de Médecine Intensive-Réanimation, Assistance Publique, Hôpitaux de Paris, Hôpital de Bicêtre, DMU 4 CORREVE Maladies du Cœur et Des Vaisseaux, FHU Sepsis, Le Kremlin-Bicêtre, France
- Inserm U1018, Equipe d'Epidémiologie Respiratoire Intégrative, CESP, 94807, Villejuif, France
| | - Amal Chaghouri
- Laboratoire de Virologie, Hôpital Paul Brousse, Assistance Publique, Hôpitaux de Paris, Villejuif, France
| | - Guillaume Voiriot
- Sorbonne Université, Centre de Recherche Saint-Antoine INSERM, Médecine Intensive Réanimation, Hôpital Tenon, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
- Laboratoire de Virologie, Hôpital Saint-Antoine, Assistance Publique, Hôpitaux de Paris, 75012, Paris, France
| | | | - Aurélia Pitsch
- Laboratoire de Microbiologie, Hôpital Marc Jacquet, Melun, France
| | - Sylvie Meireles
- Service de Réanimation Médico-Chirurgicale, Assistance Publique, Hôpitaux de Paris, Hôpital Ambroise Paré, Boulogne, France
| | - Damien Contou
- Service de Réanimation, Hôpital Victor Dupouy, Argenteuil, France
| | - Amandine Henry
- Service de Virologie, Hôpital Victor Dupouy, Argenteuil, France
| | - Adrien Joseph
- Médecine Intensive Réanimation, Hôpital Saint-Louis, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Marie-Laure Chaix
- Université de Paris, Inserm HIPI, 75010, Paris, France
- Laboratoire de Virologie, Hôpital Saint-Louis, Assistance Publique, Hôpitaux de Paris, 75010, Paris, France
| | - Fabrice Uhel
- n, Université de Paris, APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimatio, Colombes, France
- INSERM U1151, CNRS UMR 8253, Institut Necker-Enfants Malades (INEM), Department of Immunology, Infectiology and Hematology, Paris, France
| | - Diane Descamps
- Université de Paris, IAME INSERM UMR 1137, Service de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Malo Emery
- Service de Réanimation, Hôpital Saint-Camille, Bry-Sur-Marne, France
| | | | - Charles-Edouard Luyt
- Sorbonne Université, Assistance Publique, Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Médecine Intensive Réanimation, Paris, France
- INSERM UMRS_1166-iCAN, Institute of Cardiometabolism and Nutrition, Paris, France
| | - Stéphane Marot
- Département de Virologie, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Frédéric Pène
- Médecine Intensive Réanimation, Hôpital Cochin, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Anne-Sophie Lhonneur
- Laboratoire de Virologie, Hôpital Cochin, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Stéphane Gaudry
- Service de Réanimation, Hôpital Avicenne, Assistance Publique, Hôpitaux de Paris, Bobigny, France
| | - Ségolène Brichler
- Laboratoire de Virologie, Hôpital Avicenne, Assistance Publique, Hôpitaux de Paris, Bobigny, France
| | - Lucile Picard
- Département d'Anesthésie Réanimations Chirurgicales, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
| | - Armand Mekontso Dessap
- Service de Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
- Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris, Créteil, France
- INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris, Créteil, France
- INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Slim Fourati
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris, Créteil, France
- INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
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Almalki SSR, Izhari MA, Alyahyawi HE, Alatawi SK, Klufah F, Ahmed WAM, Alharbi R. Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia. J Multidiscip Healthc 2023; 16:2117-2136. [PMID: 37529147 PMCID: PMC10389082 DOI: 10.2147/jmdh.s419859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023] Open
Abstract
Purpose Omicron (B.1.1.529) is one of the highly mutated variants of concern of SARS-CoV-2. Lineages of Omicron bear a remarkable degree of mutations leading to enhanced pathogenicity and upward transmission trajectory. Mutating Omicron lineages may trigger a fresh COVID-19 wave at any time in any region. We aimed at the whole-genome sequencing of SARS-CoV-2 to determine variants/subvariants and significant mutations which can foster virus evolution, monitoring of disease spread, and outbreak management. Methods We used Illumina-NovaSeq 6000 for SARS-CoV-2 genome sequencing, MEGA 10.2 and nextstrain tools for phylogeny; CD-HIT program (version 4.8.1) and MUSCLE program for clustering and alignment. At the same time, UCSF Chimera was employed for protein visualization. Results Predominant Omicron pango lineages in Al-Baha were BA.5.2/B22 (n=4, 57%), and other lineages were BA.2.12/21L (n=1, 14.28%), BV.1/22B (n=1, 14.28%) and BA.5.2.18/22B (n=1, 14.28%). 22B nextstrain clade was predominant, while only one lineage showed 21L. BA.5.2/22B, BA.5.2/22B harbored a maximum of n=24 mutations in the spike region. Twelve crucial RBD mutations: D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, and Y505H were identified except the lineage BA.5.2/22B in which F486V mutation was not observed. Critical deletions S106 in membrane protein NSP6, E31in nucleocapsid, and L24 in spike region were observed in all the lineages. Furthermore, we identified common mutations of Omicron variants of SARS-CoV-2 in therapeutic hot spot spike region: T19I, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, A653V, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, D1146D, L452R, F486V, N679K and D796Y. The effect of RBD-targeted mutations on neutralizing (NAbs) binding was considerable. Conclusion The outcome of this first report on SARS-CoV-2 variants identification and mutation in the Al-Baha region could be used to lay down the policies to manage and impede the regional outbreak of COVID-19 effectively.
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Affiliation(s)
- Shaia S R Almalki
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Mohammad Asrar Izhari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Hanan E Alyahyawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Saleha Keder Alatawi
- Department of Optometry, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Faisal Klufah
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Waled A M Ahmed
- Department of Nursing, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Raed Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
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11
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Zhang L, Wang Z, Lyu F, Liu C, Li C, Liu W, Ma X, Zhou J, Qian X, Qian Z, Lu Y. Characterizing distinct profiles of immune and inflammatory response with age to Omicron infection. Front Immunol 2023; 14:1189482. [PMID: 37457688 PMCID: PMC10348361 DOI: 10.3389/fimmu.2023.1189482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Background Understanding inflammatory and immune responses to Omicron infection based on age is crucial when addressing this global health threat. However, the lacking of comprehensive elucidation hinders the development of distinct treatments tailored to different age populations. Methods 1299 cases of Omicron infection in Shanghai were enrolled between April 10, 2022 and June 3, 2022, dividing into three groups by ages: Adult group (18-59 years), Old group (60-79 years), and Elder group (≥ 80 years). Laboratory data including inflammatory cytokines, cellular, and humoral immunity were collected and analyzed. Results The mean age of Adult, Old, and Elder groups were 44.14, 69.98, and 89.35 years, respectively, with 40.9% being men. The Elder group patients exhibited higher white blood cell (WBC) counts and elevated levels of inflammatory cytokines, but their lymphocyte counts were relatively lower. In comparison to the Old group patients, the Elder group patients demonstrated significantly lower CD3+ T-cell counts, CD3+ T-cell proportion, CD4+ T-cell counts, CD8+ T-cell counts, and CD19+ B-cell counts, while the NK-cell counts were higher. Omicron negative patients displayed a higher proportion of CD19+ B-cells and higher levels of Complement-3 and IL-17 compared to the positive patients in the Old group. Omicron negative patients had lower WBC counts, CD3+CD8+ T-cells proportion, and the levels of serum amyloid A and IgA in the Elder group, but the CD4+/CD8+ ratio was higher. Conclusions Our study identified the distinct profiles of inflammatory and immune responses to Omicron infection varying with age and highlighted the diverse correlations between the levels of various biomarkers and Omicron infected/convalescent patients.
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Affiliation(s)
- Lina Zhang
- Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Provincial Clinical Research Center for Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhanwen Wang
- Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Provincial Clinical Research Center for Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Feng Lyu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Chun Liu
- Respiratory and Critical Care Medicine Department, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chunhui Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Liu
- Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Provincial Clinical Research Center for Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinhua Ma
- Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Provincial Clinical Research Center for Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jieyu Zhou
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Xinyu Qian
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Zhaoxin Qian
- Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Provincial Clinical Research Center for Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yong Lu
- Department of Radiology, Ruijin Hospital Luwan Branch, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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Kurtz P, Bastos LSL, Ranzani OT, Soares M, Zampieri F, Hamacher S, Salluh J, Bozza FA. Variants of concern and clinical outcomes in critically ill COVID-19 patients. Intensive Care Med 2023; 49:697-699. [PMID: 37067557 PMCID: PMC10108805 DOI: 10.1007/s00134-023-07039-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2023] [Indexed: 04/18/2023]
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13
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Wu Y, Pan Y, Su K, Zhang Y, Jia Z, Yi J, Lv H, Zhang L, Xue M, Cao D, Jiang J. Elder and booster vaccination associates with decreased risk of serious clinical outcomes in comparison of Omicron and Delta variant: A meta-analysis of SARS-CoV-2 infection. Front Microbiol 2023; 14:1051104. [PMID: 37125157 PMCID: PMC10140352 DOI: 10.3389/fmicb.2023.1051104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Background The COVID-19 pandemic brings great pressure to the public health systems. This meta-analysis aimed to compare the clinical outcomes among different virus variants, to clarify their impact on medical resources and to provide evidence for the formulation of epidemic prevention policies. Methods A systematic literature search was performed in the PubMed, Embase, and Cochrane Library databases using the key words "Omicron" and "Delta." The adjusted Risk ratios (RRs), Odds ratios (ORs) and Hazard ratios (HRs) were extracted, and RRs and Rate difference % (RD%) were used to interpret the risk estimates of the outcomes ultimately. Results Forty-three studies were included, with 3,812,681 and 14,926,841 individuals infected with SARS-CoV-2 Delta and Omicron variant, respectively. The relative risks of hospitalization, death, ICU admission, and mechanical ventilation use after infection with the Omicron variant were all significantly reduced compared those after infection with the Delta variant (RRhospitalization = 0.45, 95%CI: 0.40-0.52; RRdeath = 0.37, 95%CI: 0.30-0.45; RRICU = 0.35, 95%CI: 0.29-0.42; RRmechanical ventilation = 0.33, 95%CI: 0.25-0.44). The change of both absolute and relative risks for hospitalization was more evident (RR = 0.47, 95%CI: 0.42-0.53;RD% =10.61, 95%CI: 8.64-12.59) and a significant increase was observed for the absolute differences in death in the elderly (RD% = 5.60, 95CI%: 4.65-6.55); the change of the absolute differences in the risk of hospitalization and death were most markedly observed in the patients with booster vaccination (RD%hospitalization = 8.60, 95CI%: 5.95-11.24; RD%death = 3.70, 95CI%: 0.34-7.06). Conclusion The ability of the Omicron variant to cause severe clinical events has decreased significantly, as compared with the Delta variant, but vulnerable populations still need to be vigilant. There was no interaction between the vaccination doses and different variants.
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Affiliation(s)
- Yanhua Wu
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yuchen Pan
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Kaisheng Su
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yangyu Zhang
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Zhifang Jia
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Jiaxin Yi
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Haiyong Lv
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Lihuan Zhang
- The Second Hospital of Jilin University, Changchun, China
| | - Mingyang Xue
- School of Public Health, Jilin University, Changchun, China
| | - Donghui Cao
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Jing Jiang
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
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14
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Piralla A, Mojoli F, Pellegrinelli L, Ceriotti F, Valzano A, Grasselli G, Gismondo MR, Micheli V, Castelli A, Farina C, Arosio M, Lorini FL, Fanti D, Busni A, Laratta M, Maggi F, Novazzi F, Cabrini L, Callegaro AP, Keim R, Remuzzi G, Cavallero A, Malandrin SMI, Rona R, Giardina F, Ferrari G, Zavaglio F, D'angelo P, Galli C, Bubba L, Binda S, Oggioni M, Uceda Renteria SC, Bono P, Baj A, Ferrante FD, Guarneri D, Tonelli M, Napolitano G, Nava A, Romeo L, Nicolini E, Valaperta R, Varisano L, Mele C, Liguori L, Raggi M, Mongodi S, Pagani M, Severgnini P, Gasberti D, Bonanomi E, Gritti P, Marrazzo F, Giovannini I, Sacchi N, Sagliocco O, Cereda D, Buoro S, Baldanti F, Pariani E. Impact of SARS-CoV-2 Omicron and Delta variants in patients requiring intensive care unit (ICU) admission for COVID-19, Northern Italy, December 2021 to January 2022. Respir Med Res 2023; 83:100990. [PMID: 36871459 PMCID: PMC9984278 DOI: 10.1016/j.resmer.2023.100990] [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: 06/13/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 03/06/2023]
Abstract
This multicenter observational study included 171 COVID-19 adult patients hospitalized in the ICUs of nine hospitals in Lombardy (Northern Italy) from December, 1st 2021, to February, 9th 2022. During the study period, the Delta/Omicron variant ratio of cases decreased with a delay of two weeks in ICU patients compared to that in the community; a higher proportion of COVID-19 unvaccinated patients was infected by Delta than by Omicron whereas a higher rate of COVID-19 boosted patients was Omicron-infected. A higher number of comorbidities and a higher comorbidity score in ICU critically COVID-19 inpatients was positively associated with the Omicron infection as well in vaccinated individuals. Although people infected by Omicron have a lower risk of severe disease than those infected by Delta variant, the outcome, including the risk of ICU admission and the need for mechanical ventilation due to infection by Omicron versus Delta, remains uncertain. The continuous monitoring of the circulating SARS-CoV-2 variants remains a milestone to counteract this pandemic.
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Affiliation(s)
- Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - Francesco Mojoli
- Anaesthesia and Intensive Care, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Ferruccio Ceriotti
- Clinical Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonia Valzano
- Clinical Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giacomo Grasselli
- Department of Anesthesia, Critical Care and Emergency, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria Rita Gismondo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Valeria Micheli
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Antonio Castelli
- Division of Anesthesiology and Intensive Care, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", Bergamo, Italy
| | - Marco Arosio
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", Bergamo, Italy
| | | | - Diana Fanti
- Laboratory of Clinical Microbiology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Andrea Busni
- Laboratory of Clinical Microbiology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Matteo Laratta
- Department of Anesthesia and Intensive Care Ospedale Niguarda, Università degli studi Milano Bicocca, Milan, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Federica Novazzi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Luca Cabrini
- Intensive Care and Anesthesia Unit, Ospedale di Circolo e Fondazione Macchi, Varese, Italy
| | | | | | | | | | | | - Roberto Rona
- Department of Anesthesia and Intensive Care Medicine, San Gerardo Hospital ASST Monza, Monza, Italy
| | - Federica Giardina
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Zavaglio
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Piera D'angelo
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Laura Bubba
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Massimo Oggioni
- Clinical Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Patrizia Bono
- Clinical Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | - Davide Guarneri
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", Bergamo, Italy
| | - Marco Tonelli
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", Bergamo, Italy
| | - Gavino Napolitano
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", Bergamo, Italy
| | - Alice Nava
- Laboratory of Clinical Microbiology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Lorenzo Romeo
- Residency in Microbiology and Virology, Università degli Studi di Milano, Milan
| | - Elena Nicolini
- Residency in Microbiology and Virology, Università degli Studi di Milano, Milan
| | | | | | - Caterina Mele
- Laboratory of Immunology and Genetics of Rare Diseases, Istituto di Ricerche Farmacologiche Mario Negri IRCCS
| | - Lucia Liguori
- Laboratory of Immunology and Genetics of Rare Diseases, Istituto di Ricerche Farmacologiche Mario Negri IRCCS
| | - Monica Raggi
- Microbiology Laboratory San Gerardo Hospital, Monza, Italy
| | - Silvia Mongodi
- Anaesthesia and Intensive Care, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Michele Pagani
- Anaesthesia and Intensive Care, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Paolo Severgnini
- Department of Biotechnology and Life, Ospedale di Circolo e Fondazione Macchi, University of Insubria, Varese, Italy
| | - Dario Gasberti
- Intensive Care and Anesthesia Unit, Ospedale di Circolo e Fondazione Macchi, Varese, Italy
| | - Ezio Bonanomi
- Department of Emergency and ICU, ASST "Papa Giovanni XXIII", Bergamo, Italy
| | - Paolo Gritti
- Department of Emergency and ICU, ASST "Papa Giovanni XXIII", Bergamo, Italy
| | - Francesco Marrazzo
- Department of Anesthesia and Intensive Care Ospedale Niguarda, Università degli studi Milano Bicocca, Milan, Italy
| | - Ilaria Giovannini
- Department of Anesthesia and Intensive Care Ospedale Niguarda, Università degli studi Milano Bicocca, Milan, Italy
| | | | | | - Danilo Cereda
- Direzione Generale Welfare, Regione Lombardia, Milan, Italy
| | - Sabrina Buoro
- Direzione Generale Welfare, Regione Lombardia, Milan, Italy
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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15
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SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19. Diagnostics (Basel) 2023; 13:diagnostics13030559. [PMID: 36766664 PMCID: PMC9913917 DOI: 10.3390/diagnostics13030559] [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: 01/06/2023] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
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16
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de Prost N, Audureau E, Heming N, Gault E, Pham T, Chaghouri A, de Montmollin N, Voiriot G, Morand-Joubert L, Joseph A, Chaix ML, Préau S, Favory R, Guigon A, Luyt CE, Burrel S, Mayaux J, Marot S, Roux D, Descamps D, Meireles S, Pène F, Rozenberg F, Contou D, Henry A, Gaudry S, Brichler S, Timsit JF, Kimmoun A, Hartard C, Jandeaux LM, Fafi-Kremer S, Gabarre P, Emery M, Garcia-Sanchez C, Jochmans S, Pitsch A, Annane D, Azoulay E, Mekontso Dessap A, Rodriguez C, Pawlotsky JM, Fourati S. Clinical phenotypes and outcomes associated with SARS-CoV-2 variant Omicron in critically ill French patients with COVID-19. Nat Commun 2022; 13:6025. [PMID: 36224216 PMCID: PMC9555693 DOI: 10.1038/s41467-022-33801-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Infection with SARS-CoV-2 variant Omicron is considered to be less severe than infection with variant Delta, with rarer occurrence of severe disease requiring intensive care. Little information is available on comorbid factors, clinical conditions and specific viral mutational patterns associated with the severity of variant Omicron infection. In this multicenter prospective cohort study, patients consecutively admitted for severe COVID-19 in 20 intensive care units in France between December 7th 2021 and May 1st 2022 were included. Among 259 patients, we show that the clinical phenotype of patients infected with variant Omicron (n = 148) is different from that in those infected with variant Delta (n = 111). We observe no significant relationship between Delta and Omicron variant lineages/sublineages and 28-day mortality (adjusted odds ratio [95% confidence interval] = 0.68 [0.35–1.32]; p = 0.253). Among Omicron-infected patients, 43.2% are immunocompromised, most of whom have received two doses of vaccine or more (85.9%) but display a poor humoral response to vaccination. The mortality rate of immunocompromised patients infected with variant Omicron is significantly higher than that of non-immunocompromised patients (46.9% vs 26.2%; p = 0.009). In patients infected with variant Omicron, there is no association between specific sublineages (BA.1/BA.1.1 (n = 109) and BA.2 (n = 21)) or any viral genome polymorphisms/mutational profile and 28-day mortality. SARS-CoV-2 variant Omicron has been suggested to cause less severe disease. This prospective study shows that the clinical phenotype in patients infected with Omicron differs from patients infected with Delta but no association between Delta and Omicron including sublineages and mortality was observed.
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Affiliation(s)
- Nicolas de Prost
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France.,Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France.,Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Etienne Audureau
- Université Paris-Est-Créteil (UPEC), Créteil, France.,Department of Public Health, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France.,IMRB INSERM U955, Team CEpiA, Créteil, France
| | - Nicholas Heming
- Médecine Intensive Réanimation, Hôpital Raymond Poincaré, Assistance Publique-Hôpitaux de Paris (AP-HP), Garches, France
| | - Elyanne Gault
- Laboratoire de Virologie, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris (AP-HP), Boulogne, France
| | - Tài Pham
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France.,Service de Médecine Intensive-Réanimation, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, DMU 4 CORREVE Maladies du Cœur et des Vaisseaux, FHU Sepsis, Le Kremlin-Bicêtre, France.,Inserm U1018, Equipe d'Epidémiologie respiratoire intégrative, CESP, 94807, Villejuif, France
| | - Amal Chaghouri
- Laboratoire de Virologie, Hôpital Paul Brousse, Assistance Publique-Hôpitaux de Paris, Villejuif, France
| | - Nina de Montmollin
- Sorbonne Université, Centre de Recherche Saint-Antoine INSERM, Médecine Intensive Réanimation, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guillaume Voiriot
- Sorbonne Université, Centre de Recherche Saint-Antoine INSERM, Médecine Intensive Réanimation, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,Laboratoire de virologie, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, F-75012, Paris, France
| | - Adrien Joseph
- Médecine Intensive Réanimation, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Marie-Laure Chaix
- Université de Paris, Inserm HIPI, F-75010, Paris, France.,Laboratoire de Virologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Sébastien Préau
- U1167-RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, F-59000, Lille, France
| | - Raphaël Favory
- U1167-RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, F-59000, Lille, France
| | - Aurélie Guigon
- Service de virologie, CHU de Lille, F-59000, Lille, France
| | - Charles-Edouard Luyt
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Médecine Intensive Réanimation, Paris, France.,INSERM UMRS_1166-iCAN, Institute of Cardiometabolism and Nutrition, Paris, France
| | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,Département de Virologie, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Julien Mayaux
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Médecine Intensive Réanimation, Paris, France
| | - Stéphane Marot
- Département de Virologie, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Damien Roux
- Université de Paris, APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimation, Colombes, France.,INSERM U1151, CNRS UMR 8253, Institut Necker-Enfants Malades (INEM), Department of Immunology, Infectiology and Hematology, Paris, France
| | - Diane Descamps
- Université de Paris, IAME INSERM UMR 1137, Service de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sylvie Meireles
- Service de Réanimation médico-chirurgicale, Assistance Publique-Hôpitaux de Paris, Hôpital Ambroise Paré, Boulogne, France
| | - Frédéric Pène
- Médecine Intensive Réanimation, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Flore Rozenberg
- Laboratoire de Virologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Damien Contou
- Service de Réanimation, Hôpital Victor Dupouy, Argenteuil, France
| | - Amandine Henry
- Service de Virologie, Hôpital Victor Dupouy, Argenteuil, France
| | - Stéphane Gaudry
- Service de Réanimation, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Ségolène Brichler
- Laboratoire de Virologie, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Jean-François Timsit
- Service de Médecine Intensive Réanimation, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Antoine Kimmoun
- Université de Lorraine, CHRU de Nancy, Médecine Intensive et Réanimation Brabois, Vandœuvre-lès-Nancy, France.,INSERM U942 and U1116, F-CRIN-INIC RCT, Vandœuvre-lès-Nancy, France
| | - Cédric Hartard
- Service de Virologie, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Louise-Marie Jandeaux
- INSERM (French National Institute of Health and Medical Research), UMR 1260, Regenerative Nanomedicine (RNM), CRBS (Centre de Recherche en Biomédecine de Strasbourg), FMTS (Fédération de Médecine Translationnelle de Strasbourg), University of Strasbourg, Strasbourg, France.,Department of Intensive Care (Service de Médecine Intensive - Réanimation), Nouvel Hôpital Civil, Hôpital Universitaire de Strasbourg, Strasbourg, France
| | - Samira Fafi-Kremer
- Service de Virologie, Nouvel Hôpital Civil, Hôpital Universitaire de Strasbourg, Strasbourg, France
| | - Paul Gabarre
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Médecine Intensive Réanimation, 75571, Paris, Cedex 12, France
| | - Malo Emery
- Service de Réanimation, Hôpital Saint-Camille, Bry-sur-Marne, France
| | | | | | - Aurélia Pitsch
- Laboratoire de Microbiologie, Hôpital Marc Jacquet, Melun, France
| | - Djillali Annane
- Médecine Intensive Réanimation, Hôpital Raymond Poincaré, Assistance Publique-Hôpitaux de Paris (AP-HP), Garches, France
| | - Elie Azoulay
- Médecine Intensive Réanimation, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Armand Mekontso Dessap
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France.,Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France.,Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France.,Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France.,INSERM U955, Team « Viruses, Hepatology, Cancer », Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France.,Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France.,INSERM U955, Team « Viruses, Hepatology, Cancer », Créteil, France
| | - Slim Fourati
- Université Paris-Est-Créteil (UPEC), Créteil, France. .,Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France. .,INSERM U955, Team « Viruses, Hepatology, Cancer », Créteil, France.
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17
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Corriero A, Ribezzi M, Mele F, Angrisani C, Romaniello F, Daleno A, Loconsole D, Centrone F, Chironna M, Brienza N. COVID-19 Variants in Critically Ill Patients: A Comparison of the Delta and Omicron Variant Profiles. Infect Dis Rep 2022; 14:492-500. [PMID: 35735762 PMCID: PMC9222818 DOI: 10.3390/idr14030052] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Coronavirus disease is a pandemic that has disrupted many human lives, threatening people's physical and mental health. Each pandemic wave struck in different ways, infectiveness-wise and mortality-wise. This investigation focuses on critically ill patients affected by the last two variants, Delta and Omicron, and aims to analyse if any difference exists between the two groups. METHODS intensive care unit (ICU) COVID-19 consecutive admissions between 1 October 2021 and 31 March 2022 were recorded daily, and data concerning the patients' demographics, variants, main comorbidities, ICU parameters on admission, and the outcome were analysed by a univariate procedure and by a multivariate analysis. RESULTS 65 patients were enrolled, 31 (47.69%) belonging to the Omicron versus 34 (52.31%) to the Delta group. The mortality rate was 52.94% for the Omicron group versus 41.9% for the Delta group. A univariate analysis showed that the Omicron variant was associated with total comorbidities number, Charlson Comorbidity Index (CCI), pre-existing pulmonary disease, vaccination status, and acute kidney injury (AKI). In stepwise multivariate analysis, the total number of comorbidities was positively associated with the Omicron group, while pulmonary embolism was negatively correlated with the Omicron group. CONCLUSION Omicron appears to have lost some of the hallmarks of the Delta variant, such as endothelialitis and more limited cellular tropism when it comes to the patients in the ICU. Further studies are encouraged to explore different therapeutic approaches to treat critical patients with COVID-19.
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Affiliation(s)
- Alberto Corriero
- Unit of Anesthesia and Resuscitation, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
- Correspondence: (A.C.); (N.B.)
| | - Mario Ribezzi
- Department of Interdisciplinary Medicine—Intensive Care Unit Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Federica Mele
- Department of Interdisciplinary Medicine—Section of Legal Medicine, Policlinico di Bari Hospital, University of Bari, 70124 Bari, Italy; (F.M.); (C.A.)
| | - Carmelinda Angrisani
- Department of Interdisciplinary Medicine—Section of Legal Medicine, Policlinico di Bari Hospital, University of Bari, 70124 Bari, Italy; (F.M.); (C.A.)
| | - Fabio Romaniello
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Antonio Daleno
- Hospital Direction, Azienda Universitaria Ospedaliera Consorziale Policlinico Bari, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Daniela Loconsole
- Department of Interdisciplinary Medicine—Hygiene Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.C.)
| | - Francesca Centrone
- Department of Interdisciplinary Medicine—Hygiene Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.C.)
| | - Maria Chironna
- Department of Interdisciplinary Medicine—Hygiene Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.C.)
| | - Nicola Brienza
- Department of Interdisciplinary Medicine—Intensive Care Unit Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Correspondence: (A.C.); (N.B.)
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Riou B, Freund Y. Histoire exceptionnelle d’un article peu banal. ANNALES FRANCAISES DE MEDECINE D URGENCE 2022. [DOI: 10.3166/afmu-2022-0406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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