1
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Patel V, Levick B, Boult S, Gibbons DC, Drysdale M, Lloyd EJ, Singh M, Birch HJ. Characteristics and outcomes of COVID-19 patients presumed to be treated with sotrovimab in NHS hospitals in England. BMC Infect Dis 2024; 24:428. [PMID: 38649824 PMCID: PMC11036565 DOI: 10.1186/s12879-024-09311-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The impact of the constantly evolving severe acute respiratory syndrome coronavirus 2 on the effectiveness of early coronavirus disease 2019 (COVID-19) treatments is unclear. Here, we report characteristics and acute clinical outcomes of patients with COVID-19 treated with a monoclonal antibody (mAb; presumed to be sotrovimab) across six distinct periods covering the emergence and predominance of Omicron subvariants (BA.1, BA.2, and BA.5) in England. METHODS Retrospective cohort study using data from the Hospital Episode Statistics database from January 1-July 31, 2022. Included patients received a mAb delivered by a National Health Service (NHS) hospital as a day-case, for which the primary diagnosis was COVID-19. Patients were presumed to have received sotrovimab based on NHS data showing that 99.98% of COVID-19-mAb-treated individuals received sotrovimab during the study period. COVID-19-attributable hospitalizations were reported overall and across six distinct periods of Omicron subvariant prevalence. Subgroup analyses were conducted in patients with severe renal disease and active cancer. RESULTS Among a total of 10,096 patients, 1.0% (n = 96) had a COVID-19-attributable hospitalization, 4.6% (n = 465) had a hospital visit due to any cause, and 0.3% (n = 27) died due to any cause during the acute period. COVID-19-attributable hospitalization rates were consistent among subgroups, and no significant differences were observed across periods of Omicron subvariant predominance. CONCLUSIONS Levels of COVID-19-attributable hospitalizations and deaths were low in mAb-treated patients and among subgroups. Similar hospitalization rates were observed whilst Omicron BA.1, BA.2, and BA.5 were predominant, despite reported reductions in in vitro neutralization activity of sotrovimab against BA.2 and BA.5.
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Affiliation(s)
- Vishal Patel
- GSK House, 980 Great West Road, TW8 9GS, Brentford, Middlesex, UK
| | | | | | - Daniel C Gibbons
- GSK House, 980 Great West Road, TW8 9GS, Brentford, Middlesex, UK
| | - Myriam Drysdale
- GSK House, 980 Great West Road, TW8 9GS, Brentford, Middlesex, UK.
| | - Emily J Lloyd
- GSK House, 980 Great West Road, TW8 9GS, Brentford, Middlesex, UK
| | - Moushmi Singh
- GSK House, 980 Great West Road, TW8 9GS, Brentford, Middlesex, UK
| | - Helen J Birch
- GSK House, 980 Great West Road, TW8 9GS, Brentford, Middlesex, UK
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2
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Tomasicchio M, Jaumdally S, Wilson L, Kotze A, Semple L, Meier S, Pooran A, Esmail A, Pillay K, Roberts R, Kriel R, Meldau R, Oelofse S, Mandviwala C, Burns J, Londt R, Davids M, van der Merwe C, Roomaney A, Kühn L, Perumal T, Scott AJ, Hale MJ, Baillie V, Mahtab S, Williamson C, Joseph R, Sigal A, Joubert I, Piercy J, Thomson D, Fredericks DL, Miller MGA, Nunes MC, Madhi SA, Dheda K. SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset. Am J Respir Crit Care Med 2024; 209:840-851. [PMID: 38226855 PMCID: PMC10995573 DOI: 10.1164/rccm.202308-1438oc] [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: 08/17/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Rationale: In the upper respiratory tract, replicating (culturable) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is recoverable for ∼4-8 days after symptom onset, but there is a paucity of data about the frequency and duration of replicating virus in the lower respiratory tract (i.e., the human lung).Objectives: We undertook lung tissue sampling (needle biopsy) shortly after death in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patients served as a control group.Methods: Lung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling, and immunohistochemistry.Measurements and Main Results: Thirty-eight percent (16 of 42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 wk) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (P < 0.05). Nasopharyngeal culture was negative in 23.1% (6 of 26) of decedents despite lung culture positivity. This hitherto undescribed biophenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary proinflammatory response but with concurrent viral culture positivity.Conclusions: Concurrent rather than sequential active viral replication continues to drive a heightened proinflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe coronavirus disease (COVID-19).
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Affiliation(s)
- Michele Tomasicchio
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Shameem Jaumdally
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Lindsay Wilson
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Andrea Kotze
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Lynn Semple
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Stuart Meier
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Anil Pooran
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Aliasgar Esmail
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Komala Pillay
- Division of Anatomical Pathology, Department of Pathology, and
| | - Riyaadh Roberts
- Division of Anatomical Pathology, Department of Pathology, and
| | - Raymond Kriel
- Division of Anatomical Pathology, Department of Pathology, and
| | - Richard Meldau
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Suzette Oelofse
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Carley Mandviwala
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Jessica Burns
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Rolanda Londt
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Malika Davids
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Charnay van der Merwe
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Aqeedah Roomaney
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Louié Kühn
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Tahlia Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | - Alex J. Scott
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sana Mahtab
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa; and
| | - Ivan Joubert
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - Jenna Piercy
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - David Thomson
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - David L. Fredericks
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - Malcolm G. A. Miller
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, University of Cape Town, Cape Town, South Africa
| | - Marta C. Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre of Excellence in Respiratory Pathogens, Hospices Civils de Lyon and Centre International de Recherche en Infectiologie, Équipe Santé Publique, Épidémiologie et Écologie Évolutive des Maladies Infectieuses, Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard – Lyon 1, Lyon, France
| | - Shabir A. Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, and
- Department of Science and Technology/National Research Foundation South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and UCT Lung Institute, Cape Town, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance
- Institute of Infectious Disease and Molecular Medicine
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom
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3
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Grannec F, Meddeb L, Tissot-Dupont H, Gentile S, Brouqui P. Pre-Hospital Management of Patients with COVID-19 and the Impact on Hospitalization. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1440. [PMID: 37629730 PMCID: PMC10456276 DOI: 10.3390/medicina59081440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/17/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
Background and Objectives: During the COVID-19 pandemic, patient care was mainly organized around the hospital. Pre-hospital care has, to our knowledge, never been evaluated. We aimed to study the impact of pre-hospital pathways on hospitalization during the last part of the pandemic. Materials and Methods: This was a monocentric, retrospective analysis of prospectively collected medical records. Data from patients admitted to our institute between 1 February and 7 March 2022 were analyzed. The primary outcomes were defined as the number of hospitalizations, resuscitations, and deaths at the time of interview and in the subsequent 30 days. The main explanatory variables were times from onset of symptoms to care, age, gender, News2 score, comorbidities, and pre-hospital pathways and their duration. Results: Three pre-hospital pathways were identified: a pathway in which the patient consults a general practitioner for a test (PHP1); a pathway in which the patient consults for care (PHP2); and no pre-hospital pathway and direct admission to hospital (PHP3). Factors independently associated with outcome (hospitalization) were being male (OR 95% CI; 2.21 (1.01-4.84), p = 0,04), News2 score (OR 95% CI; 2.04 (1.65-2.51), p < 0.001), obesity (OR 95% CI; 3.45 (1.48-8.09), p = 0.005), D-dimers > 0.5 µg/mL (OR 95% CI; 3.45 (1.47-8.12), p = 0.005), and prolonged time from symptoms to hospital care (PHP duration) (OR 95% CI; 1.07 (1.01-1.14), p = 0.03). All things being equal, patients with a "PHP2" pre-hospital pathway had a higher probability of hospitalization compared to those with a "PHP3" pre-hospital pathway (OR 95% CI; 4.31 (1.48-12.55), p = 0.007). Conclusions: Along with recognized risk factors such as gender, News 2 score, and obesity, the patient's pre-hospital pathway is an important risk factor associated with hospitalization.
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Affiliation(s)
- Floann Grannec
- IRD, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, 13005 Marseille, France;
| | - Line Meddeb
- AP-HM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.M.); (H.T.-D.); (S.G.)
| | - Herve Tissot-Dupont
- AP-HM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.M.); (H.T.-D.); (S.G.)
| | - Stephanie Gentile
- AP-HM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.M.); (H.T.-D.); (S.G.)
- EA 3279 “Santé Publique, Maladies Chroniques et Qualité de Vie”, Aix Marseille University, 13005 Marseille, France
| | - Philippe Brouqui
- IRD, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, 13005 Marseille, France;
- AP-HM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.M.); (H.T.-D.); (S.G.)
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4
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Relan P, Motaze NV, Kothari K, Askie L, Le Polain O, Van Kerkhove MD, Diaz J, Tirupakuzhi Vijayaraghavan BK. Severity and outcomes of Omicron variant of SARS-CoV-2 compared to Delta variant and severity of Omicron sublineages: a systematic review and metanalysis. BMJ Glob Health 2023; 8:e012328. [PMID: 37419502 PMCID: PMC10347449 DOI: 10.1136/bmjgh-2023-012328] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVES To compare severity and clinical outcomes from Omicron as compared with the Delta variant and to compare outcomes between Omicron sublineages. METHODS We searched the WHO COVID-19 Research database for studies that compared clinical outcomes for patients with Omicron variant and the Delta variant, and separately Omicron sublineages BA.1 and BA.2. A random-effects meta-analysis was used to pool estimates of relative risk (RR) between variants and sublineages. Heterogeneity between studies was assessed using the I2 index. Risk of bias was assessed using the tool developed by the Clinical Advances through Research and Information Translation team. RESULTS Our search identified 1494 studies and 42 met the inclusion criteria. Eleven studies were published as preprints. Of the 42 studies, 29 adjusted for vaccination status; 12 had no adjustment; and for 1, the adjustment was unclear. Three of the included studies compared the sublineages of Omicron BA.1 versus BA.2. As compared with Delta, individuals infected with Omicron had 61% lower risk of death (RR 0.39, 95% CI 0.33 to 0.46) and 56% lower risk of hospitalisation (RR 0.44, 95% CI 0.34 to 0.56). Omicron was similarly associated with lower risk of intensive care unit (ICU) admission, oxygen therapy, and non-invasive and invasive ventilation. The pooled risk ratio for the outcome of hospitalisation when comparing sublineages BA.1 versus BA.2 was 0.55 (95% 0.23 to 1.30). DISCUSSION Omicron variant was associated with lower risk of hospitalisation, ICU admission, oxygen therapy, ventilation and death as compared with Delta. There was no difference in the risk of hospitalisation between Omicron sublineages BA.1 and BA.2. PROSPERO REGISTRATION NUMBER CRD42022310880.
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Affiliation(s)
- Pryanka Relan
- Health Emergencies Programme, WHO, Geneva, Switzerland
| | - Nkengafac Villyen Motaze
- Health Emergencies Programme, WHO, Geneva, Switzerland
- Medicine Usage in South Africa, School of Pharmacy, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Kavita Kothari
- Library and Digital Information Networks, World Health Organization, Kobe, Japan
| | - Lisa Askie
- Methods and Standards Unit, Science Division, World Health Organization, Geneva, Switzerland
| | - Olivier Le Polain
- Acute Response Coordination Department, World Health Organization, Geneva, Switzerland
| | - Maria D Van Kerkhove
- COVID-19 Health Operations, World Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Janet Diaz
- Health Emergencies Programme, WHO, Geneva, Switzerland
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5
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Farahat RA, Abdelaal A, Umar TP, El-Sakka AA, Benmelouka AY, Albakri K, Ali I, Al-Ahdal T, Abdelazeem B, Sah R, Rodriguez-Morales AJ. The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends. LE INFEZIONI IN MEDICINA 2022; 30:480-494. [PMID: 36482957 PMCID: PMC9714996 DOI: 10.53854/liim-3004-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent variant of concern (VOC) established by the World Health Organization (WHO). Because of its greater infectivity and immune evasion, this variant quickly became the dominant type of circulating SARS-CoV-2 worldwide. Our literature review thoroughly explains the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, and vaccination effectiveness. The most notable difference between the three subvariants is the insufficiency of deletion (Δ69-70) in the spike protein, which results in a lower detection rate of the spike (S) gene target known as (S) gene target failure (SGTF). Furthermore, BA.2 had a stronger affinity to the human Angiotensin-converting Enzyme (hACE2) receptor than other Omicron sub-lineages. Regarding the number of mutations, BA.1.1 has the most (40), followed by BA.1, BA.3, and BA.3 with 39, 34, and 31 mutations, respectively. In addition, BA.2 and BA.3 have greater transmissibility than other sub-lineages (BA.1 and BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread and high contagiousness rates, particularly BA.2 sub-lineages.
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Affiliation(s)
| | - Abdelaziz Abdelaal
- Harvard Medical School, Boston, MA,
USA,Boston University, MA,
USA,General Practitioner, Tanta University Hospitals,
Egypt
| | | | | | | | - Khaled Albakri
- Faculty of Medicine, The Hashemite University, Zarqa,
Jordan
| | - Iftikhar Ali
- Department of Pharmacy, Paraplegic Center, Peshawar,
Pakistan
| | - Tareq Al-Ahdal
- Institute of Global Health (HIGH), Heidelberg University, Heidelberg,
Germany
| | - Basel Abdelazeem
- Department of Internal Medicine, McLaren Health Care, Flint, Michigan,
USA,Department of Internal Medicine, Michigan State University, East Lansing, Michigan,
USA
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu,
Nepal,Dr. D.Y Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra,
India
| | - Alfonso J. Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de Las Américas, Pereira, Risaralda,
Colombia,Faculty of Medicine, Institución Universitaria Vision de Las Americas, Pereira, Risaralda,
Colombia,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36,
Lebanon,Master of Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima,
Perú
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6
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Xu R, Wang W, Zhang W. As the SARS-CoV-2 virus evolves, should Omicron subvariant BA.2 be subjected to quarantine, or should we learn to live with it? Front Public Health 2022; 10:1039123. [PMID: 36504951 PMCID: PMC9730036 DOI: 10.3389/fpubh.2022.1039123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
It has been nearly 35 months since the COVID-19 outbreak. The pathogen SARS-CoV-2 has evolved into several variants. Among them, Omicron is the fifth variant of concern which have rapidly spread globally during the past 8 months. Omicron variant shows different characteristics from previous variants, which is highly infectious, highly transmissible, minimally pathogenic, vaccine and antibody tolerant; however, it is less likely to cause severe illness, resulting in fewer deaths. Omicron has evolved into five main lineages, including BA.1, BA.2, BA.3, BA.4, and BA.5. Before BA.5, Omicron BA.2 sublineage was the dominant strain all over the world for several months. The experience of prevention and treatment against BA.2 is worth studying and learning for overcoming other Omicron subvariants. Although the Omicron subvariant BA.2 is significantly less severe than that caused by ancestral strains, it is still far more dangerous than influenza, and its long-term sequelae are unknown. Effective treatments are currently limited; therefore, effective defense may be the key to controlling the epidemic today, rather than just "living with" the virus.
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Affiliation(s)
- Ren Xu
- Pulmonary and Critical Care Medicine Department, First Hospital of Jilin University, Changchun, China
| | - Wanning Wang
- Nephrology Department, First Hospital of Jilin University, Changchun, China
| | - Wenlong Zhang
- Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, China
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7
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Yuasa S, Nakajima J, Takatsuki Y, Takahashi Y, Tani‐Sassa C, Iwasaki Y, Nagano K, Sonobe K, Yoshimoto T, Nukui Y, Takeuchi H, Tanimoto K, Tanaka Y, Kimura A, Ichimura N, Tohda S. Viral load of SARS-CoV-2 Omicron is not high despite its high infectivity. J Med Virol 2022; 94:5543-5546. [PMID: 35790476 PMCID: PMC9349670 DOI: 10.1002/jmv.27974] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 12/15/2022]
Abstract
Patients infected with the Omicron variant of severe acute respiratory syndrome coronavirus 2 has increased worldwide since the beginning of 2022 and the variant has spread more rapidly than the Delta variant, which spread in the summer of 2021. It is important to clarify the cause of the strong transmissibility of the Omicron variant to control its spread. In 694 patients with coronavirus disease 2019, the copy numbers of virus in nasopharyngeal swab-soaked samples and the viral genotypes were examined using quantitative polymerase chain reaction (PCR) and PCR-based melting curve analysis, respectively. Whole-genome sequencing was also performed to verify the viral genotyping data. There was no significant difference (p = 0.052) in the copy numbers between the Delta variant cases (median 1.5 × 105 copies/μl, n = 174) and Omicron variant cases (median 1.2 × 105 copies/μl, n = 328). During this study, Omicron BA.1 cases (median 1.1 ×105 copies/μl, n = 275) began to be replaced by BA.2 cases (median 2.3 × 105 copies/μl, n = 53), and there was no significant difference between the two groups (p = 0.33). Our results suggest that increased infectivity of the Omicron variant and its derivative BA.2 is not caused by higher viral loads but by other factors, such as increased affinity to cell receptors or immune escape.
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Affiliation(s)
- Sonoka Yuasa
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Jun Nakajima
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yuna Takatsuki
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yuta Takahashi
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Chihiro Tani‐Sassa
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yumi Iwasaki
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Katsutoshi Nagano
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Kazunari Sonobe
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Tomoyo Yoshimoto
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yoko Nukui
- Infection Control and PreventionTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Hiroaki Takeuchi
- Department of Molecular VirologyTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Kousuke Tanimoto
- Genome Laboratory, Medical Research InstituteTokyo Medical and Dental University (TMDU)TokyoJapan,Research Core, Institute of ResearchTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Yukie Tanaka
- Department of Molecular MicrobiologyTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Akinori Kimura
- Institute of ResearchTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Naoya Ichimura
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Shuji Tohda
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
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Colnago M, Benvenuto GA, Casaca W, Negri RG, Fernandes EG, Cuminato JA. Risk Factors Associated with Mortality in Hospitalized Patients with COVID-19 during the Omicron Wave in Brazil. Bioengineering (Basel) 2022; 9:bioengineering9100584. [PMID: 36290552 PMCID: PMC9598428 DOI: 10.3390/bioengineering9100584] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/03/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Considering the imminence of new SARS-CoV-2 variants and COVID-19 vaccine availability, it is essential to understand the impact of the disease on the most vulnerable groups and those at risk of death from the disease. To this end, the odds ratio (OR) for mortality and hospitalization was calculated for different groups of patients by applying an adjusted logistic regression model based on the following variables of interest: gender, booster vaccination, age group, and comorbidity occurrence. A massive number of data were extracted and compiled from official Brazilian government resources, which include all reported cases of hospitalizations and deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Brazil during the “wave” of the Omicron variant (BA.1 substrain). Males (1.242; 95% CI 1.196–1.290) aged 60–79 (3.348; 95% CI 3.050–3.674) and 80 years or older (5.453; 95% CI 4.966–5.989), and hospitalized patients with comorbidities (1.418; 95% CI 1.355–1.483), were more likely to die. There was a reduction in the risk of death (0.907; 95% CI 0.866–0.951) among patients who had received the third dose of the anti-SARS-CoV-2 vaccine (booster). Additionally, this big data investigation has found statistical evidence that vaccination can support mitigation plans concerning the current scenario of COVID-19 in Brazil since the Omicron variant and its substrains are now prevalent across the entire country.
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Affiliation(s)
- Marilaine Colnago
- Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, Brazil
| | - Giovana A. Benvenuto
- Faculty of Science and Technology (FCT), São Paulo State University (UNESP), Presidente Prudente 19060-900, Brazil
| | - Wallace Casaca
- Institute of Biosciences, Letters and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto 15054-000, Brazil
- Correspondence:
| | - Rogério G. Negri
- Science and Technology Institute, São Paulo State University (UNESP), São José dos Campos 12247-004, Brazil
| | - Eder G. Fernandes
- Immunization Division—Centre of Epidemiology Surveillance of the São Paulo State Health Department, São Paulo 01246-000, Brazil
| | - José A. Cuminato
- Institute of Mathematics and Computer Science, São Paulo University (USP), São Carlos 13566-590, Brazil
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Circulating Dynamics of SARS-CoV-2 Variants between April 2021 and February 2022 in Turkey. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:4677720. [PMID: 36284529 PMCID: PMC9588334 DOI: 10.1155/2022/4677720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/19/2022] [Accepted: 09/24/2022] [Indexed: 11/18/2022]
Abstract
The diagnosis of new variants and monitoring their potential effects on diagnosis, therapeutics, and vaccines by genomic sequencing is essential to manage global public crises. In the current study, spike-genome next-generation sequencing was generated from 492 SARS-CoV-2 isolates to evaluate the mutations in Turkey from April 2021 to February 2022. The variant analysis was performed using (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). We revealed that the lineages Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), Eta (B.1.525), variant of interest (VOI), lota (B.1.526), Zeta (P.2), Omicron (B.1.1.529), and Omicron BA.1 (B.1.1.529.1) were in the circulation in Turkey during the given period. The most common lineages were B.1.1.7, B.1.617.2, B.1.1.529, and B.1.1.529.1 SARS-CoV-2 variant circulation in Turkey seems highly heterogenetic; however, quite similar to the global epidemiologic analysis. The existence of globally circulating variants in the same chronological order in Turkey can be a guide for precautions, treatment, and vaccine options to be taken in the future.
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Blann AD, Heitmar R. SARS-CoV-2 and COVID-19: A Narrative Review. Br J Biomed Sci 2022; 79:10426. [PMID: 36148046 PMCID: PMC9486701 DOI: 10.3389/bjbs.2022.10426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022]
Abstract
The World Health Organisation has reported that the viral disease known as COVID-19, caused by SARS-CoV-2, is the leading cause of death by a single infectious agent. This narrative review examines certain components of the pandemic: its origins, early clinical data, global and UK-focussed epidemiology, vaccination, variants, and long COVID.
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Kurup D, Myers J, Schnell MJ. Current vaccine strategies against SARS-CoV-2: Promises and challenges. J Allergy Clin Immunol 2022; 150:17-21. [PMID: 35618046 PMCID: PMC9126615 DOI: 10.1016/j.jaci.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 01/31/2023]
Abstract
In the years since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic began and spread across the globe, lessons have been learned about the challenges and opportunities that a pandemic brings to humankind. Researchers have produced many vaccines at unprecedented speed to protect people, but they have also been cognizant of the challenges presented by a new and unexpected infectious disease. The scope of this review is to examine the path of vaccine discovery so far and identify potential targets. Here, we provide insight into the leading vaccines and their advantages and challenges. We discuss the emerging mutations within the SARS-CoV-2 spike protein and other issues that need to be addressed to overcome coronavirus disease 2019 (COVID-19) completely. Future research is needed to develop a cheap, temperature-stable vaccine providing long-term immunity that protects the upper respiratory tract.
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Affiliation(s)
- Drishya Kurup
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Philadelphia, Pa
| | - Jacob Myers
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Philadelphia, Pa
| | - Matthias J Schnell
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Philadelphia, Pa; Jefferson Vaccine Center, Thomas Jefferson University, Philadelphia, Pa.
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Tiecco G, Storti S, Arsuffi S, Degli Antoni M, Focà E, Castelli F, Quiros-Roldan E. Omicron BA.2 Lineage, the "Stealth" Variant: Is It Truly a Silent Epidemic? A Literature Review. Int J Mol Sci 2022; 23:7315. [PMID: 35806320 PMCID: PMC9266794 DOI: 10.3390/ijms23137315] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/10/2022] [Accepted: 06/27/2022] [Indexed: 12/29/2022] Open
Abstract
The epidemic curve of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is silently rising again. Worldwide, the dominant SARS-CoV-2 variant of concern (VOC) is Omicron, and its virological characteristics, such as transmissibility, pathogenicity, and resistance to both vaccine- and infection-induced immunity as well as antiviral drugs, are an urgent public health concern. The Omicron variant has five major sub-lineages; as of February 2022, the BA.2 lineage has been detected in several European and Asian countries, becoming the predominant variant and the real antagonist of the ongoing surge. Hence, although global attention is currently focused on dramatic, historically significant events and the multi-country monkeypox outbreak, this new epidemic is unlikely to fade away in silence. Many aspects of this lineage are still unclear and controversial, but its apparent replication advantage and higher transmissibility, as well as its ability to escape neutralizing antibodies induced by vaccination and previous infection, are rising global concerns. Herein, we review the latest publications and the most recent available literature on the BA.2 lineage of the Omicron variant.
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Affiliation(s)
| | | | | | | | | | | | - Eugenia Quiros-Roldan
- Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, ASST Spedali Civili di Brescia, University of Brescia, 25123 Brescia, Italy; (G.T.); (S.S.); (S.A.); (M.D.A.); (E.F.); (F.C.)
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Peng J, Li Q, Dong J, Yuan G, Wang D. Case Report: The Experience of Managing a Moderate ARDS Caused by SARS-CoV-2 Omicron BA.2 Variant in Chongqing, China: Can We Do Better? Front Med (Lausanne) 2022; 9:921135. [PMID: 35755038 PMCID: PMC9218179 DOI: 10.3389/fmed.2022.921135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
Background The severe coronavirus disease 2019 (COVID-19) pandemic is still raging worldwide, and the Omicron BA.2 variant has become the new circulating epidemic strain. However, our understanding of the Omicron BA.2 variant is still scarce. This report aims to present a case of a moderate acute respiratory distress syndrome (ARDS) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron BA.2 variant and to discuss some management strategies that may benefit this type of case. Case Presentation A 78-year-old man, who had four negative nucleic acid tests and a fifth positive, was admitted to our hospital. This patient was generally good upon admission and tested negative for anti-SARS-CoV-2 antibodies even after receiving two doses of the COVID-19 vaccine. On the 7th day of hospitalization, he developed a moderate ARDS. Improved inflammatory index and decreased oxygen index were primarily found in this patient, and a series of treatments, including anti-inflammation and oxygen therapies, were used. Then this patient’s condition improved soon and reached two negative results of nucleic acid tests on the 18th day of hospitalization. Conclusion At-home COVID-19 rapid antigen test could be complementary to existing detection methods, and the third booster dose of COVID-19 vaccine may be advocated in the face of the omicron BA.2 variant. Anti-inflammatory and oxygen therapies are still essential treatments for ARDS patients infected with SARS-CoV-2 Omicron BA.2 variant.
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Affiliation(s)
- Junnan Peng
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qiaoli Li
- Department of Intensive Care Medicine, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Dong
- Department of Intensive Care Medicine, Chongqing Public Health Medical Center, Chongqing, China
| | - Guodan Yuan
- Department of Intensive Care Medicine, Chongqing Public Health Medical Center, Chongqing, China
- *Correspondence: Guodan Yuan,
| | - Daoxin Wang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Daoxin Wang,
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