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DostΓ‘lkovΓ‘ A, ZdeΕkovΓ‘ K, BartΓ‘ΔkovΓ‘ J, ΔermΓ‘kovΓ‘ E, Kapisheva M, Lopez Marin MA, Kouba V, SΓ½kora P, Chmel M, BartoΕ‘ O, Dresler J, DemnerovΓ‘ K, RumlovΓ‘ M, BartΓ‘Δek J. Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing. CHEMOSPHERE 2024; 351:141162. [PMID: 38218235 DOI: 10.1016/j.chemosphere.2024.141162] [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: 06/30/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.
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Affiliation(s)
- AlΕΎbΔta DostΓ‘lkovΓ‘
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Kamila ZdeΕkovΓ‘
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic.
| | - Jana BartΓ‘ΔkovΓ‘
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - EliΕ‘ka ΔermΓ‘kovΓ‘
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Marina Kapisheva
- National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Marco A Lopez Marin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - VojtΔch Kouba
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Petr SΓ½kora
- PVK a.s., Prague Water Supply and Sewerage Company, Czech Republic
| | - Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic; Military Health Institute, Military Medical Agency, Czech Republic
| | - OldΕich BartoΕ‘
- Military Health Institute, Military Medical Agency, Czech Republic
| | - JiΕΓ Dresler
- Military Health Institute, Military Medical Agency, Czech Republic
| | - KateΕina DemnerovΓ‘
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Michaela RumlovΓ‘
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Jan BartΓ‘Δek
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
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Sheng WH, Lin PH, Cheng YC, Wu YY, Hsieh MJ, Yang HC, Chang SY, Chang SC. Immunogenicity and safety of heterologous booster with protein-based COVID-19 vaccine (NVX-CoV2373) in healthy adults: A comparative analysis with mRNA vaccines. J Formos Med Assoc 2024; 123:340-346. [PMID: 37996322 DOI: 10.1016/j.jfma.2023.10.012] [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: 05/11/2023] [Revised: 08/07/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Information on the protein-based severe acute respiratory syndrome (SARS-CoV-2) vaccine-NVX-CoV2373 (Novavax), as a heterologous booster remains limited. We investigated the immunogenicity and adverse events of NVX-CoV2373 as a second booster and compared them with those of mRNA vaccines in healthy adults. METHODS Healthcare workers who had received an mRNA vaccine (mRNA-1273 or BNT-162b2) as the first booster (third dose) 12 weeks prior were recruited. Participants voluntarily received either NVX-CoV2373 or an mRNA vaccine as a second booster. Participants with a history of SARS-CoV-2 infection were excluded. The primary outcomes included serum anti-SARS-CoV-2 spike protein (SP) and neutralizing antibody titers against B.1.1.7 (Alpha), B.1.1.529 (Omicron) BA2, and BA5 variants on the 28th day after the boost. Secondary outcomes included new SARS-CoV-2 infections and adverse events reported during the study period. RESULTS A total of 160 participants were enrolled in this study. Compared with the mRNA vaccination group (nΒ =Β 59), the NVX-CoV2373 vaccination group (nΒ =Β 101) had significantly lower anti-SARS-CoV-2 SP antibody titers and neutralizing antibody titers against all variants tested after the boost. During the study period, higher rates of new SARS-CoV-2 infections and a lower incidence of adverse events were observed in the NVX-CoV2373 vaccination group. No significant differences in cellular immune responses were observed between the two groups. CONCLUSION Compared to a homologous mRNA booster vaccination, heterologous boosters with NVX-CoV2373 showed lower antibody responses, a higher incidence of new SARS-CoV-2 infections, and fewer adverse events.
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Affiliation(s)
- Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan; School of Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan
| | - Pin-Hung Lin
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Chen Cheng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Yun Wu
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Ju Hsieh
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan; Occupational Safety and Health Office, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Chih Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan; Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei City, Taiwan
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan; School of Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan.
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53
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Pei Y, Li T, Chen C, Huang Y, Yang Y, Zhou T, Shi M. Clinical features that predict the mortality risk in older patients with Omicron pneumonia: the MLWAP score. Intern Emerg Med 2024; 19:465-475. [PMID: 38104038 PMCID: PMC10954909 DOI: 10.1007/s11739-023-03506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
In December 2022, the Chinese suffered widespread Omicron of SARS-CoV-2 with variable symptom severity and outcome. We wanted to develop a scoring model to predict the mortality risk of older Omicron pneumonia patients by analyzing admission data. We enrolled 227 Omicron pneumonia patients aged 60Β years and older, admitted to our hospital from December 15, 2022, to January 16, 2023, and divided them randomly into a 70% training set and a 30% test set. The former were used to identify predictors and develop a model, the latter to verify the model, using the area under the receiver operating characteristic curve (AUC), the Hosmer-Lemeshow goodness-of-fit test, a calibration curve to test its performance and comparing it to the existing scores. The MLWAP score was calculated based on a multivariate logistic regression model to predict mortality with a weighted score that included immunosuppression, lactateββ₯β2.4, white blood cell countββ₯β6.70βΓβ109/L, ageββ₯β77Β years, and PaO2/FiO2Β β€Β 211. The AUC for the model in the training and test sets was 0.852 (95% CI, 0.792-0.912) and 0.875 (95% CI, 0.789-0.961), respectively. The calibration curves showed a good fit. We grouped the risk scores into low (score 0-7 points), medium (8-10 points), and high (11-13 points). This model had a sensitivity of 0.849, specificity of 0.714, and better predictive ability than the CURB-65 and PSI scores (AUROCβ=β0.859 vs. 0.788 vs. 0.801, respectively). The MLWAP-mortality score may help clinicians to stratify hospitalized older Omicron pneumonia patients into relevant risk categories, rationally allocate medical resources, and reduce the mortality.
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Affiliation(s)
- Yongjian Pei
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, 1055 SanXiang Road, Gusu District, Suzhou, 215004, Jiangsu, China
| | - Ting Li
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, 1055 SanXiang Road, Gusu District, Suzhou, 215004, Jiangsu, China
| | - Chen Chen
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, 1055 SanXiang Road, Gusu District, Suzhou, 215004, Jiangsu, China
| | - Yongkang Huang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, 1055 SanXiang Road, Gusu District, Suzhou, 215004, Jiangsu, China
| | - Yun Yang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, 1055 SanXiang Road, Gusu District, Suzhou, 215004, Jiangsu, China
| | - Tong Zhou
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, 1055 SanXiang Road, Gusu District, Suzhou, 215004, Jiangsu, China
| | - Minhua Shi
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, 1055 SanXiang Road, Gusu District, Suzhou, 215004, Jiangsu, China.
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Park JS, Jeon J, Um J, Choi YY, Kim MK, Lee KS, Sung HK, Jang HC, Chin B, Kim CK, Oh MD, Lee CS. Magnitude and Duration of Serum Neutralizing Antibody Titers Induced by a Third mRNA COVID-19 Vaccination against Omicron BA.1 in Older Individuals. Infect Chemother 2024; 56:25-36. [PMID: 38014726 PMCID: PMC10990888 DOI: 10.3947/ic.2023.0057] [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: 05/26/2023] [Accepted: 08/21/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) is dominating coronavirus disease 2019 (COVID-19) worldwide. The waning protective effect of available vaccines against the Omicron variant is a critical public health issue. This study aimed to assess the impact of the third COVID-19 vaccination on immunity against the SARS-CoV-2 Omicron BA.1 strain in older individuals. MATERIALS AND METHODS Adults aged β₯60 years who had completed two doses of the homologous COVID-19 vaccine with either BNT162b2 (Pfizer/BioNTech, New York, NY, USA, BNT) or ChAdOx1 nCoV (SK bioscience, Andong-si, Gyeongsangbuk-do, Korea, ChAd) were registered to receive the third vaccination. Participants chose either BNT or mRNA-1273 (Moderna, Norwood, MA, USA, m1273) mRNA vaccine for the third dose and were categorized into four groups: ChAd/ChAd/BNT, ChAd/ChAd/m1273, BNT/BNT/BNT, and BNT/BNT/m1273. Four serum specimens were obtained from each participant at 0, 4, 12, and 24 weeks after the third dose (V1, V2, V3, and V4, respectively). Serum-neutralizing antibody (NAb) activity against BetaCoV/Korea/KCDC03/2020 (NCCP43326, ancestral strain) and B.1.1.529 (NCCP43411, Omicron BA.1 variant) was measured using plaque reduction neutralization tests. A 50% neutralizing dilution (ND50) >10 was considered indicative of protective NAb titers. RESULTS In total, 186 participants were enrolled between November 24, 2021, and June 30, 2022. The respective groups received the third dose at a median (interquartile range [IQR]) of 132 (125 - 191), 123 (122 - 126), 186 (166 - 193), and 182 (175 - 198) days after the second dose. Overall, ND50 was lower at V1 against Omicron BA.1 than against the ancestral strain. NAb titers against the ancestral strain and Omicron BA.1 variant at V2 were increased at least 30-fold (median [IQR], 1235.35 [1021.45 - 2374.65)] and 129.8 [65.3 - 250.7], respectively). ND50 titers against the ancestral strain and Omicron variant did not differ significantly among the four groups (P = 0.57). NAb titers were significantly lower against the Omicron variant than against the ancestral strain at V3 (median [IQR], 36.4 (17.55 - 75.09) vs. 325.9 [276.07 - 686.97]; P = 0.012). NAb titers against Omicron at V4 were 16 times lower than that at V3. Most sera exhibited a protective level (ND50 >10) at V4 (75.0% [24/32], 73.0% [27/37], 73.3% [22/30], and 70.6% [12/17] in the ChAd/ChAd/BNT, ChAd/ChAd/m1273, BNT/BNT/BNT, and BNT/BNT/m1273 groups, respectively), with no significant differences among groups (P = 0.99). CONCLUSION A third COVID-19 mRNA vaccine dose restored waning NAb titers against Omicron BA.1. Our findings support a third-dose vaccination program to prevent the waning of humoral immunity to SARS-CoV-2.
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Affiliation(s)
- Jun-Sun Park
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Jaehyun Jeon
- Department of Infectious Diseases, National Medical Center, Seoul, Korea
| | - Jihye Um
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Youn Young Choi
- Department of Pediatrics, National Medical Center, Seoul, Korea
| | - Min-Kyung Kim
- Department of Infectious Diseases, National Medical Center, Seoul, Korea
| | - Kyung-Shin Lee
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Ho Kyung Sung
- Research Institute for Public Healthcare, National Medical Center, Seoul, Korea
| | - Hee-Chang Jang
- National Institute of Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Korea
| | - BumSik Chin
- Department of Infectious Diseases, National Medical Center, Seoul, Korea
| | - Choon Kwan Kim
- Division of Infectious Diseases, VHS Medical Center, Seoul, Korea
| | - Myung-don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Chang-Seop Lee
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
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Vermeulen M, Mhlanga L, Sykes W, Cable R, Coleman C, Pietersen N, Swanevelder R, Glatt TN, Bingham J, van den Berg K, Grebe E, Welte A. The evolution and interpretation of seroprevalence of SARS-CoV-2 antibodies among South African blood donors from the Beta to Omicron variant-driven waves. Vox Sang 2024; 119:242-251. [PMID: 38156504 DOI: 10.1111/vox.13571] [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: 08/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND AND OBJECTIVES Confirmed COVID-19 diagnoses underestimate the total number of infections. Blood donors can provide representative seroprevalence estimates, which can be leveraged into reasonable estimates of total infection counts and infection fatality rate (IFR). MATERIALS AND METHODS Blood donors who donated after each of three epidemic waves (Beta, Delta and first Omicron waves) were tested for anti-SARS-CoV-2 nucleocapsid antibodies using the Roche Elecsys anti-SARS-CoV-2 total immunoglobulin assay. Roche Elecsys anti-spike antibody testing was done for the post-Omicron sampling. Prevalence of antibodies was estimated by age, sex, race and province and compared to official case reporting. Province and age group-specific IFRs were estimated using external excess mortality estimates. RESULTS The nationally weighted anti-nucleocapsid seroprevalence estimates after the Beta, Delta and Omicron waves were 47% (46.2%-48.6%), 71% (68.8%-73.5%) and 87% (85.5%-88.4%), respectively. There was no variation by age and sex, but there were statistically and epidemiologically significant differences by province (except at the latest time point) and race. There was a 13-fold higher seroprevalence than confirmed case counts at the first time point. Age-dependent IFR roughly doubled for every 10βyears of age increase over 6 decades from 0.014% in children to 6.793% in octogenarians. CONCLUSION Discrepancies were found between seroprevalence and confirmed case counts. High seroprevalence rates found among Black African donors can be ascribed to historical inequities. Our IFR estimates were useful in refining previous large disagreements about the severity of the epidemic in South Africa. Blood donor-based serosurveys provided a valuable and efficient way to provide near real-time monitoring of the ongoing SARS-CoV-2 outbreak.
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Affiliation(s)
- Marion Vermeulen
- South African National Blood Service, Johannesburg, South Africa
- University of the Free State, Bloemfontein, South Africa
| | - Laurette Mhlanga
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- Northwestern University, Chicago, Illinois, USA
| | - Wendy Sykes
- South African National Blood Service, Johannesburg, South Africa
| | | | - Charl Coleman
- South African National Blood Service, Johannesburg, South Africa
| | | | | | - Tanya Nadia Glatt
- South African National Blood Service, Johannesburg, South Africa
- University of Johannesburg, Johannesburg, South Africa
| | - Jeremy Bingham
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Karin van den Berg
- South African National Blood Service, Johannesburg, South Africa
- University of the Free State, Bloemfontein, South Africa
- University of Cape Town, Rondebosch, South Africa
| | - Eduard Grebe
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- Vitalant Research Institute, San Francisco, California, USA
- University of California San Francisco, San Francisco, California, USA
| | - Alex Welte
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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Teixeira DG, Rodrigues-Neto JF, da Cunha DCS, Jeronimo SMB. Understanding SARS-CoV-2 spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105556. [PMID: 38242186 DOI: 10.1016/j.meegid.2024.105556] [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: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
SARS-CoV-2 genome underwent mutations since it started circulating within the human population. The aim of this study was to understand the fluctuation of the spike clusters concomitant to the population immunity either due to natural infection and/or vaccination in a state of Brazil that had both high rate of natural infection and vaccination coverage. A total of 1725 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and to correlate with circulating variants. From March 2020 to June 2022, the state of Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across the three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta (AY.*), which circulated in Brazil in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma (P.1Β +Β P.1.*)) dominated the first half of 2021. Late 2021 had two new clusters, Cluster 2 (Omicron, (B.1.1.529Β +Β BA.*)), and Cluster 3 (BA.*) with the most unique epitopes, in addition to Cluster 4 (Delta sub lineages) which emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome.
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Affiliation(s)
- Diego Gomes Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - JoΓ£o Firmino Rodrigues-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Escola Multicampi de CiΓͺncias MΓ©dicas do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, CaicΓ³, Rio Grande do Norte, Brazil
| | - Dayse Caroline Severiano da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Selma Maria Bezerra Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Departmento de BioquΓmica, Centro de BiociΓͺncias, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil; Instituto Nacional de CiΓͺncia e Tecnologia de DoenΓ§as Tropicais, Natal, Rio Grande do Norte, Brazil.
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Zang P, Xu Q, Li C, Tao M, Zhang Z, Li J, Zhang W, Li S, Li C, Yang Q, Guo Z, Yao J, Zhou L. Self-correction of cycle threshold values by a normal distribution-based process to improve accuracy of quantification in real-time digital PCR. Anal Bioanal Chem 2024:10.1007/s00216-024-05208-w. [PMID: 38400940 DOI: 10.1007/s00216-024-05208-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: 11/22/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
TheΒ digital polymerase chain reaction (dPCR) is a new and developing nucleic acid detection technology with high sensitivity that can realize the absolute quantitative analysis of samples. In order to improve the accuracy of quantitative results, real-time digital PCR emphasizes the kinetic information during amplification to identify prominent abnormal data. However, it is challenging to use a unified standard to accurately classify the amplification curve of each well as negative and positive, due to the interference caused by various factors in the experiment. In this work, a normal distribution-based cycle threshold value self-correcting model (NCSM) was established, which focused on the feature of the cycle threshold values in amplification curves and conducted continuous detection and correction on the whole. The cycle threshold value distribution was closer to the ideal normal distribution to avoid the influence of interference. Thus, the model achieves a more accurate classification between positive and negative results. The corrective process was applied to plasmid samples and resulted in an accuracy improvement from 92 to 99%. The coefficient of variation was below 5% when considering the quantitation of a range between 100 and 10,000 copies. At the same time, by utilizing this model, the distribution of cycle threshold values at the endpoint can be predicted with fewer thermal cycles, which can reduce the cycling time by around 25% while maintaining a consistency of more than 98%. Therefore, using the NCSM can effectively enhance the quantitative accuracy and increase the detection efficiency based on the real-time dPCR platform.
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Affiliation(s)
- Peilin Zang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Qi Xu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chuanyu Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Mingli Tao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqi Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
- Suzhou CASENS Co., Ltd, Suzhou, 215163, China
| | - Jinze Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
- Suzhou CASENS Co., Ltd, Suzhou, 215163, China
| | - Shuli Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chao Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Qi Yang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhen Guo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Jia Yao
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Lianqun Zhou
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
- Suzhou CASENS Co., Ltd, Suzhou, 215163, China.
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SoΔan M, Mrzel M, Prosenc K, Korva M, AvΕ‘iΔ-Ε½upanc T, Poljak M, Lunar MM, ZupaniΔ T. Comparing COVID-19 severity in patients hospitalized for community-associated Delta, BA.1 and BA.4/5 variant infection. Front Public Health 2024; 12:1294261. [PMID: 38450129 PMCID: PMC10915065 DOI: 10.3389/fpubh.2024.1294261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Background Despite decreasing COVID-19 disease severity during the Omicron waves, a proportion of patients still require hospitalization and intensive care. Objective To compare demographic characteristics, comorbidities, vaccination status, and previous infections in patients hospitalized for community-associated COVID-19 (CAC) in predominantly Delta, Omicron BA.1 and BA.4/5 SARS-CoV-2 waves. Methods Data were extracted from three national databases-the National COVID-19 Database, National Vaccination Registry and National Registry of Hospitalizations. Results Among the hospitalized CAC patients analyzed in this study, 5,512 were infected with Delta, 1,120 with Omicron BA.1, and 1,143 with the Omicron BA.4/5 variant. The age and sex structure changed from Delta to BA.4/5, with the proportion of women (9.5% increase), children and adolescents (10.4% increase), and octa- and nonagenarians increasing significantly (24.5% increase). Significantly more patients had comorbidities (measured by the Charlson Comorbidity Index), 30.3% in Delta and 43% in BA.4/5 period. The need for non-invasive ventilatory support (NiVS), ICU admission, mechanical ventilation (MV), and in-hospital mortality (IHM) decreased from Delta to Omicron BA.4/5 period for 12.6, 13.5, 11.5, and 6.3%, respectively. Multivariate analysis revealed significantly lower odds for ICU admission (OR 0.68, CI 0.54-0.84, p < 0.001) and IHM (OR 0.74, CI 0.58-0.93, p = 0.011) during the Delta period in patients who had been fully vaccinated or boosted with a COVID-19 vaccine within the previous 6 months. In the BA.1 variant period, patients who had less than 6 months elapsed between the last vaccine dose and SARS-CoV-2 positivity had lower odds for MV (OR 0.38, CI 0.18-0.72, p = 0.005) and IHM (OR 0.56, CI 0.37- 0.83, p = 0.005), but not for NIVS or ICU admission. Conclusion The likelihood of developing severe CAC in hospitalized patients was higher in those with the Delta and Omicron BA.1 variant compared to BA.4/5.
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Affiliation(s)
- Maja SoΔan
- National Institute of Public Health, Ljubljana, Slovenia
| | - Maja Mrzel
- National Institute of Public Health, Ljubljana, Slovenia
| | - Katarina Prosenc
- National Institute of Health, Environment and Food, Ljubljana, Slovenia
| | - MiΕ‘a Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana AvΕ‘iΔ-Ε½upanc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja M. Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tina ZupaniΔ
- National Institute of Public Health, Ljubljana, Slovenia
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Zhong J, Zhong Q, Xiong H, Wu D, Zheng C, Liu S, Zhong Q, Chen Y, Zhang D. Public acceptance of COVID-19 control measures and associated factors during Omicron-dominant period in China: a cross-sectional survey. BMC Public Health 2024; 24:543. [PMID: 38383375 PMCID: PMC10882874 DOI: 10.1186/s12889-024-17646-3] [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: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/23/2024] Open
Abstract
OBJECTIVES This study aims to evaluate the public acceptance of coronavirus disease 2019 (COVID-19) control measures during the Omicron-dominant period and its associated factors. METHODS A cross-sectional design was conducted and 1391 study participants were openly recruited to participate in the questionnaire survey. Logistic regression model was performed to assess the association between the public acceptance and potential factors more specifically. RESULTS By August 26, 2022, 58.9% of the study participants were less acceptive of the control measures while 41.1% expressed higher acceptance. Factors associated with lower acceptance included young age, such as <β18 (ORβ=β8.251, 95% CI: 2.009 to 33.889) and 18-29 (ORβ=β2.349, 95% CI: 1.564 to 3.529), and household per capita monthly income lower than 5000 yuan (ORβ=β1.512, 95% CI: 1.085 to 2.105). Furthermore, individuals who perceived that the case fatality rate (CFR) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was very low (ORβ=β6.010, 95% CI: 2.475 to 14.595) and that the restrictions could be eased once the CFR dropped to 2-3 times of the influenza (ORβ=β2.792, 95% CI: 1.939 to 4.023) showed greater oppositional attitudes. Likewise, respondents who were dissatisfied with control measures (ORβ=β9.639, 95% CI: 4.425 to 20.998) or preferred fully relaxation as soon as possible (ORβ=β13.571, 95% CI: 7.751 to 23.758) had even lower acceptability. By contrast, rural residents (ORβ=β0.683, 95% CI: 0.473 to 0.987), students (ORβ=β0.510, 95% CI: 0.276 to 0.941), public (ORβ=β0.417, 95% CI: 0.240 to 0.727) and private (ORβ=β0.562, 95% CI: 0.320 to 0.986) employees, and vaccinated participants (ORβ=β0.393, 95% CI: 0.204 to 0.756) were more compliant with control measures. CONCLUSION More than half of the Chinese public were less supportive of COVID-19 control measures during Omicron-dominant period, which varied based on their different demographic characteristics, cognition and overall attitude towards SARS-CoV-2 infection. Control measures that struck a balance between public safety and individual freedom would be more acceptable during the pandemic.
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Affiliation(s)
- Jiayi Zhong
- School of Public Health, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Qianhong Zhong
- Department of Tuberculosis Control, The Fourth People's Hospital of Foshan city, 528000, Foshan, Guangdong, China
| | - Husheng Xiong
- School of Public Health, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Dawei Wu
- School of Public Health, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Caiyun Zheng
- School of Public Health, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Shuang Liu
- School of Public Health, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Qinyi Zhong
- School of Law, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Yan Chen
- Medical College of Shaoguan University, 512026, Shaoguan, Guangdong, China.
| | - Dingmei Zhang
- School of Public Health, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China.
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60
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Zhang M, Cao L, Zhang L, Li X, Chen S, Zhang Y. SARS-CoV-2 reinfection with Omicron variant in Shaanxi Province, China: December 2022 to February 2023. BMC Public Health 2024; 24:496. [PMID: 38365671 PMCID: PMC10870596 DOI: 10.1186/s12889-024-17902-6] [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: 07/04/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Prior to December 2022, there were no reports of reinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Shaanxi province, China. Since then, China has refined its strategy in response to coronaviruses. The purpose of this study was to determine the incidence of SARS-CoV-2 reinfections and its contributing factors, as well as to compare clinical characteristics between first and second episodes of infection in Shaanxi Province, China between December 2022 and February 2023. METHODS We conducted a cross-sectional study using an epidemiological survey system and electronic questionnaires to investigate the incidence of SARS-CoV-2 reinfection among previously infected individuals during the epidemic wave owing to the Omicron variant that began in December 2022. A logistic regression model was used to determine those factors influencing SARS-CoV-2 reinfections. RESULTS According to the virus variant that caused the first infection, the rate of reinfection for the Omicron variants was 1.28%, 1.96%, and 5.92% at 2-3 months, 4-5 months, and 7-9 months after the primary infection, respectively. The rate of reinfection for the Delta variants was 25.10% 11-12 months after the primary infection. Females, adults between 18 and 38 years and being a medical worker were associated with an increased risk of reinfection. Fever, cough, sore throat and fatigue were the four most common clinical symptoms during both first and second COVID-19 infections. CONCLUSIONS In our study, the rate of SARS-CoV-2 reinfection increased over time during epidemic waves predominantly involving the Omicron variant in Shaanxi province, China. Large-scale infections are less likely in subsequent Omicron epidemic waves. Nevertheless, it is essential to continuously monitor cases of infection as well as continue surveillance for emerging SARS-CoV-2 variants.
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Affiliation(s)
- Mengyan Zhang
- Shaanxi Provincial Centre for Disease Prevention and Control, Xi'an, People's Republic of China
| | - Lei Cao
- Shaanxi Provincial Centre for Disease Prevention and Control, Xi'an, People's Republic of China
| | - Luqian Zhang
- Shaanxi Provincial Centre for Disease Prevention and Control, Xi'an, People's Republic of China
| | - Xinxin Li
- Shaanxi Provincial Centre for Disease Prevention and Control, Xi'an, People's Republic of China
| | - Sa Chen
- Shaanxi Provincial Centre for Disease Prevention and Control, Xi'an, People's Republic of China
| | - Yi Zhang
- Shaanxi Provincial Centre for Disease Prevention and Control, Xi'an, People's Republic of China.
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Planas D, Staropoli I, Michel V, Lemoine F, Donati F, Prot M, Porrot F, Guivel-Benhassine F, Jeyarajah B, Brisebarre A, Dehan O, Avon L, Boland WH, Hubert M, Buchrieser J, Vanhoucke T, Rosenbaum P, Veyer D, PΓ©rΓ© H, Lina B, Trouillet-Assant S, Hocqueloux L, Prazuck T, Simon-Loriere E, Schwartz O. Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567873. [PMID: 38045308 PMCID: PMC10690205 DOI: 10.1101/2023.11.20.567873] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolated and characterized XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicated in IGROV-1 but no longer in Vero E6 and were not markedly fusogenic. They potently infected nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remained active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals were markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhanced NAb responses against both XBB and BA.2.86 variants. JN.1 displayed lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.
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Affiliation(s)
- Delphine Planas
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
- Vaccine Research Institute, CrΓ©teil, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
| | - Vincent Michel
- Pathogenesis of Vascular Infections Unit, Institut Pasteur, INSERM, Paris, France
| | - Frederic Lemoine
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, UniversitΓ© Paris CitΓ©, Paris, France
- Bioinformatics and Biostatistics Hub, Paris, France
| | - Flora Donati
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, UniversitΓ© Paris CitΓ©, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, UniversitΓ© Paris CitΓ©, Paris, France
| | - Francoise Porrot
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
| | | | - Banujaa Jeyarajah
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Angela Brisebarre
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - OcΓ©ane Dehan
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - LΓ©a Avon
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - William Henry Boland
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
| | - Thibault Vanhoucke
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
| | - Pierre Rosenbaum
- Humoral Immunology Laboratory, Institut Pasteur, UniversitΓ© Paris CitΓ©, INSERM U1222, Paris, France
| | - David Veyer
- Laboratoire de Virologie, Service de Microbiologie, HΓ΄pital EuropΓ©en Georges Pompidou, Paris, France
- Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, INSERM, UniversitΓ© de Paris, Sorbonne UniversitΓ©, Paris, France
| | - Hélène Péré
- Laboratoire de Virologie, Service de Microbiologie, HΓ΄pital EuropΓ©en Georges Pompidou, Paris, France
- Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, INSERM, UniversitΓ© de Paris, Sorbonne UniversitΓ©, Paris, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Centre National de RΓ©fΓ©rence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, UniversitΓ© Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Sophie Trouillet-Assant
- Laboratoire de Virologie, Institut des Agents Infectieux, Centre National de RΓ©fΓ©rence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, UniversitΓ© Claude Bernard Lyon 1, CNRS, Lyon, France
| | | | | | - Thierry Prazuck
- CHU dβOrlΓ©ans, Service de Maladies Infectieuses, OrlΓ©ans, France
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, UniversitΓ© Paris CitΓ©, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, UniversitΓ© Paris CitΓ©, CNRS UMR3569, Paris, France
- Vaccine Research Institute, CrΓ©teil, France
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Elko EA, Mead HL, Nelson GA, Zaia JA, Ladner JT, Altin JA. Recurrent SARS-CoV-2 mutations at Spike D796 evade antibodies from pre-Omicron convalescent and vaccinated subjects. Microbiol Spectr 2024; 12:e0329123. [PMID: 38189279 PMCID: PMC10871546 DOI: 10.1128/spectrum.03291-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/03/2023] [Indexed: 01/09/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages of the Omicron variant rapidly became dominant in early 2022 and frequently cause human infections despite vaccination or prior infection with other variants. In addition to antibody-evading mutations in the receptor-binding domain, Omicron features amino acid mutations elsewhere in the Spike protein; however, their effects generally remain ill defined. The Spike D796Y substitution is present in all Omicron sub-variants and occurs at the same site as a mutation (D796H) selected during viral evolution in a chronically infected patient. Here, we map antibody reactivity to a linear epitope in the Spike protein overlapping position 796. We show that antibodies binding this region arise in pre-Omicron SARS-CoV-2 convalescent and vaccinated subjects but that both D796Y and D796H abrogate their binding. These results suggest that D796Y contributes to the fitness of Omicron in hosts with pre-existing immunity to other variants of SARS-CoV-2 by evading antibodies targeting this site.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved substantially through the coronavirus disease 2019 (COVID-19) pandemic: understanding the drivers and consequences of this evolution is essential for projecting the course of the pandemic and developing new countermeasures. Here, we study the immunological effects of a particular mutation present in the Spike protein of all Omicron strains and find that it prevents the efficient binding of a class of antibodies raised by pre-Omicron vaccination and infection. These findings reveal a novel consequence of a poorly understood Omicron mutation and shed light on the drivers and effects of SARS-CoV-2 evolution.
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Affiliation(s)
- Evan A. Elko
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Heather L. Mead
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - Georgia A. Nelson
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - John A. Zaia
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - John A. Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
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Wei J, Stoesser N, Matthews PC, Khera T, Gethings O, Diamond I, Studley R, Taylor N, Peto TEA, Walker AS, Pouwels KB, Eyre DW. Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population. Nat Commun 2024; 15:1008. [PMID: 38307854 PMCID: PMC10837445 DOI: 10.1038/s41467-024-44973-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/10/2024] [Indexed: 02/04/2024] Open
Abstract
SARS-CoV-2 reinfections increased substantially after Omicron variants emerged. Large-scale community-based comparisons across multiple Omicron waves of reinfection characteristics, risk factors, and protection afforded by previous infection and vaccination, are limited. Here we studied ~45,000 reinfections from the UK's national COVID-19 Infection Survey and quantified the risk of reinfection in multiple waves, including those driven by BA.1, BA.2, BA.4/5, and BQ.1/CH.1.1/XBB.1.5 variants. Reinfections were associated with lower viral load and lower percentages of self-reporting symptoms compared with first infections. Across multiple Omicron waves, estimated protection against reinfection was significantly higher in those previously infected with more recent than earlier variants, even at the same time from previous infection. Estimated protection against Omicron reinfections decreased over time from the most recent infection if this was the previous or penultimate variant (generally within the preceding year). Those 14-180βdays after receiving their most recent vaccination had a lower risk of reinfection than those >180βdays from their most recent vaccination. Reinfection risk was independently higher in those aged 30-45βyears, and with either low or high viral load in their most recent previous infection. Overall, the risk of Omicron reinfection is high, but with lower severity than first infections; both viral evolution and waning immunity are independently associated with reinfection.
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Affiliation(s)
- Jia Wei
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Francis Crick Institute, 1 Midland Road, London, UK
- Division of infection and immunity, University College London, London, UK
| | | | | | | | | | | | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - Koen B Pouwels
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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64
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Richard L, Nisenbaum R, Colwill K, Mishra S, Dayam RM, Liu M, Pedersen C, Gingras AC, Hwang SW. Enhancing detection of SARS-CoV-2 re-infections using longitudinal sero-monitoring: demonstration of a methodology in a cohort of people experiencing homelessness in Toronto, Canada. BMC Infect Dis 2024; 24:125. [PMID: 38302878 PMCID: PMC10835952 DOI: 10.1186/s12879-024-09013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Accurate estimation of SARS-CoV-2 re-infection is crucial to understanding the connection between infection burden and adverse outcomes. However, relying solely on PCR testing results in underreporting. We present a novel approach that includes longitudinal serologic data, and compared it against testing alone among people experiencing homelessness. METHODS We recruited 736 individuals experiencing homelessness in Toronto, Canada, between June and September 2021. Participants completed surveys and provided saliva and blood serology samples every three months over 12 months of follow-up. Re-infections were defined as: positive PCR or rapid antigen test (RAT) resultsβ>β90 days after initial infection; new serologic evidence of infection among individuals with previous infection who sero-reverted; or increases in anti-nucleocapsid in seropositive individuals whose levels had begun to decrease. RESULTS Among 381 participants at risk, we detected 37 re-infections through PCR/RAT and 98 re-infections through longitudinal serology. The comprehensive method identified 37.4 re-infection events per 100 person-years, more than four-fold more than the rate detected through PCR/RAT alone (9.0 events/100 person-years). Almost all test-confirmed re-infections (85%) were also detectable by longitudinal serology. CONCLUSIONS Longitudinal serology significantly enhances the detection of SARS-CoV-2 re-infections. Our findings underscore the importance and value of combining data sources for effective research and public health surveillance.
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Affiliation(s)
- Lucie Richard
- MAP Centre for Urban Health Solutions, Unity Health Toronto, 30 Bond St, M5B1W8, Toronto, ON, Canada.
| | - Rosane Nisenbaum
- MAP Centre for Urban Health Solutions, Unity Health Toronto, 30 Bond St, M5B1W8, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, 155 College St, Toronto, Canada
| | - Karen Colwill
- Sinai Health, Lunenfeld-Tanenbaum Research Institute, 600 University Ave, Toronto, ON, Canada
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, Unity Health Toronto, 30 Bond St, M5B1W8, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, 155 College St, Toronto, Canada
- Department of Medicine, University of Toronto, 1 King's College Circle, Toronto, Canada
| | - Roya M Dayam
- Sinai Health, Lunenfeld-Tanenbaum Research Institute, 600 University Ave, Toronto, ON, Canada
| | - Michael Liu
- MAP Centre for Urban Health Solutions, Unity Health Toronto, 30 Bond St, M5B1W8, Toronto, ON, Canada
- Harvard Medical School, 25 Shattuck St, Boston, MA, USA
| | - Cheryl Pedersen
- MAP Centre for Urban Health Solutions, Unity Health Toronto, 30 Bond St, M5B1W8, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Sinai Health, Lunenfeld-Tanenbaum Research Institute, 600 University Ave, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Canada
| | - Stephen W Hwang
- MAP Centre for Urban Health Solutions, Unity Health Toronto, 30 Bond St, M5B1W8, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, 155 College St, Toronto, Canada
- Department of Medicine, University of Toronto, 1 King's College Circle, Toronto, Canada
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65
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Zou F, Xiao J, Jin Y, Jian R, Hu Y, Liang X, Ma W, Zhu S. Multilayer factors associated with excess all-cause mortality during the omicron and non-omicron waves of the COVID-19 pandemic: time series analysis in 29 countries. BMC Public Health 2024; 24:350. [PMID: 38308279 PMCID: PMC10835930 DOI: 10.1186/s12889-024-17803-8] [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: 10/08/2023] [Accepted: 01/18/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has resulted in significant excess mortality globally. However, the differences in excess mortality between the Omicron and non-Omicron waves, as well as the contribution of local epidemiological characteristics, population immunity, and social factors to excess mortality, remain poorly understood. This study aims to solve the above problems. METHODS Weekly all-cause death data and covariates from 29 countries for the period 2015-2022 were collected and used. The Bayesian Structured Time Series Model predicted expected weekly deaths, stratified by gender and age groups for the period 2020-2022. The quantile-based g-computation approach accounted for the effects of factors on the excess all-cause mortality rate. Sensitivity analyses were conducted using alternative Omicron proportion thresholds. RESULTS From the first week of 2021 to the 30th week of 2022, the estimated cumulative number of excess deaths due to COVID-19 globally was nearly 1.39Β million. The estimated weekly excess all-cause mortality rate in the 29 countries was approximately 2.17 per 100,000 (95% CI: 1.47 to 2.86). Weekly all-cause excess mortality rates were significantly higher in both male and female groups and all age groups during the non-Omicron wave, except for those younger than 15 years (Pβ<β0.001). Sensitivity analysis confirmed the stability of the results. Positive associations with all-cause excess mortality were found for the constituent ratio of non-Omicron in all variants, new cases per million, positive rate, cardiovascular death rate, people fully vaccinated per hundred, extreme poverty, hospital patients per million humans, people vaccinated per hundred, and stringency index. Conversely, other factors demonstrated negative associations with all-cause excess mortality from the first week of 2021 to the 30th week of 2022. CONCLUSION Our findings indicate that the COVID-19 Omicron wave was associated with lower excess mortality compared to the non-Omicron wave. This study's analysis of the factors influencing excess deaths suggests that effective strategies to mitigate all-cause mortality include improving economic conditions, promoting widespread vaccination, and enhancing overall population health. Implementing these measures could significantly reduce the burden of COVID-19, facilitate coexistence with the virus, and potentially contribute to its elimination.
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Affiliation(s)
- Fengjuan Zou
- Department of Epidemiology, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Jianpeng Xiao
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, 511430, China
| | - Yingying Jin
- Department of Epidemiology, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Ronghua Jian
- Department of Epidemiology, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Yijun Hu
- Department of Epidemiology, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
| | - Xiaofeng Liang
- Disease Control and Prevention Institute, Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China
- Chinese Preventive Medicine Association, Beijing, 100062, China
| | - Wenjun Ma
- Department of Epidemiology, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China.
| | - Sui Zhu
- Department of Epidemiology, School of Medicine, Jinan University, No.601 Huangpu Road West, Guangzhou, Guangdong, 510632, China.
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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Liu P, Xing Z, Peng X, Zhang M, Shu C, Wang C, Li R, Tang L, Wei H, Ran X, Qiu S, Gao N, Yeo YH, Liu X, Ji F. Machine learning versus multivariate logistic regression for predicting severe COVID-19 in hospitalized children with Omicron variant infection. J Med Virol 2024; 96:e29447. [PMID: 38305064 DOI: 10.1002/jmv.29447] [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: 05/08/2023] [Revised: 01/02/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
With the emergence of the Omicron variant, the number of pediatric Coronavirus Disease 2019Β (COVID-19) cases requiring hospitalization and developing severe or critical illness has significantly increased. Machine learning and multivariate logistic regression analysis were used to predict risk factors and develop prognostic models for severe COVID-19 in hospitalized children with the Omicron variant in this study. Of the 544 hospitalized children including 243 and 301 in the mild and severe groups, respectively. Fever (92.3%) was the most common symptom, followed by cough (79.4%), convulsions (36.8%), and vomiting (23.2%). The multivariate logistic regression analysis showed that age (1-3 years old, odds ratio (OR): 3.193, 95% confidence interval (CI): 1.778-5.733], comorbidity (OR: 1.993, 95%Β CI:1.154-3.443), cough (OR: 0.409, 95%Β CI:0.236-0.709), and baseline neutrophil-to-lymphocyte ratio (OR: 1.108, 95%Β CI: 1.023-1.200), lactate dehydrogenase (OR: 1.993, 95%Β CI: 1.154-3.443), blood urea nitrogen (OR: 1.002, 95%Β CI: 1.000-1.003) and total bilirubin (OR: 1.178, 95%Β CI: 1.005-3.381) were independent risk factors for severe COVID-19. The area under the curve (AUC) of the prediction models constructed by multivariate logistic regression analysis and machine learning (RandomForestβ+βTomekLinks) were 0.7770 and 0.8590, respectively. The top 10 most important variables of random forest variables were selected to build a prediction model, with an AUC of 0.8210. Compared with multivariate logistic regression, machine learning models could more accurately predict severe COVID-19 in children with Omicron variant infection.
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Affiliation(s)
- Pan Liu
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Zixuan Xing
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaokang Peng
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Mengyi Zhang
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, China
| | - Chang Shu
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Ce Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Ruina Li
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Li Tang
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Huijing Wei
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Xiaoshan Ran
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Sikai Qiu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Ning Gao
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yee Hui Yeo
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Xiaoguai Liu
- Department of Infectious Diseases, Xi'an Jiaotong University Affiliated Children's Hospital, Xi'an, Shaanxi, China
| | - Fanpu Ji
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Shaanxi Provincial Clinical Medical Research Center of Infectious Diseases, Xi'an, China
- Key Laboratory of Surgical Critical Care and Life Support (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China
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Ghafari M, Hall M, Golubchik T, Ayoubkhani D, House T, MacIntyre-Cockett G, Fryer HR, Thomson L, Nurtay A, Kemp SA, Ferretti L, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith DL, Bashton M, Nelson A, Crown M, McCann C, Young GR, Santos RAND, Richards Z, Tariq MA, Cahuantzi R, Barrett J, Fraser C, Bonsall D, Walker AS, Lythgoe K. Prevalence of persistent SARS-CoV-2 in a large community surveillance study. Nature 2024; 626:1094-1101. [PMID: 38383783 PMCID: PMC10901734 DOI: 10.1038/s41586-024-07029-4] [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: 01/29/2023] [Accepted: 01/04/2024] [Indexed: 02/23/2024]
Abstract
Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1-5, give rise to highly divergent lineages6-8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as 'persistent infections' as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1-0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11-14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.
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Affiliation(s)
- Mahan Ghafari
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Daniel Ayoubkhani
- Office for National Statistics, Newport, UK
- Leicester Real World Evidence Unit, Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Helen R Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Steven A Kemp
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lorne J Lonie
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | - Darren L Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Matthew Crown
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Clare McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Gregory R Young
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Rui Andre Nunes Dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Mohammad Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | | | | | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Science Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - Katrina Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Pandemic Science Institute, University of Oxford, Oxford, UK.
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Chen YH, Lee CY, Cheng HY, Chen CM, Cheuh YN, Lee CL, Kuo HW. Risk factors and mortality of SARS-CoV-2 reinfection during the Omicron era in Taiwan: A nationwide population-based cohort study. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:30-37. [PMID: 37978019 DOI: 10.1016/j.jmii.2023.10.013] [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: 03/30/2023] [Revised: 10/17/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Prior to 2022, Taiwan had effectively contained the domestic COVID-19 epidemic. However, during 2022, the country encountered multiple large outbreaks of COVID-19, with patients experiencing their first or second infection (reinfection) were both predominantly caused by the Omicron variant. Data are lacking on the risk factors and mortality of COVID-19 reinfection in Omicron era. METHODS In this retrospective population-based cohort study, we recruited COVID-19 patients with their first episode confirmed between April 1, 2022 and June 11, 2022. A reinfection patient was defined as an individual who infected again by SARS-CoV-2 with an interval of more than 90 days. Demographic characteristics, severity of underlying diseases, and vaccination status were adjusted to identify risk factors for reinfection and to further evaluate the hazard of all-cause mortality within 30 days between reinfection and non-reinfection patients. RESULTS There were 28,588 reinfection patients matched with 142,940 non-reinfection patients included in this study. We found that being female, younger in age, having more severe underlying diseases, and not being fully vaccinated against COVID-19 were risk factors for reinfection. After adjusting for confounding factors, reinfection patients were at a significantly higher risk of all-cause mortality within 30 days (aHRΒ =Β 4.29, 95% CI: 3.00-6.12, pΒ <Β 0.001) comparing with non-reinfection patients. CONCLUSION During the SARS-CoV-2 Omicron era, reinfection patients were observed to have an increased risk of all-cause mortality. To reduce the disease burden and minimize the risk of reinfection, it is crucial for vulnerable patients to receive full vaccination and adhere to recommended precautions.
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Affiliation(s)
- Yi-Hsuan Chen
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Cheng-Yi Lee
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Hao-Yuan Cheng
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Chiu-Mei Chen
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Yu-Neng Cheuh
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Chia-Lin Lee
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
| | - Hung-Wei Kuo
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan.
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70
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Ciubotariu II, Wilkes RP, Kattoor JJ, Christian EN, Carpi G, Kitchen A. Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population. Microb Genom 2024; 10:001194. [PMID: 38334271 PMCID: PMC10926704 DOI: 10.1099/mgen.0.001194] [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: 11/08/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome sequences collected over an entire academic year in a university population in Indiana, USA. We clearly captured the rapidity with which Delta variant was wholly replaced by Omicron variant across the West Lafayette campus over the length of two academic semesters in a community with high vaccination rates. This mirrored the emergence of Omicron throughout the state of Indiana and the USA. Further, phylogenetic analyses demonstrated that there was a more diverse set of potential geographic origins for Omicron viruses introduction into campus when compared to Delta. Lastly, statistics indicated that there was a more significant role for international and out-of-state migration in the establishment of Omicron variants at Purdue. This surveillance workflow, coupled with viral genomic sequencing and phylogeographic analyses, provided critical insights into SARS-CoV-2 transmission dynamics and variant arrival.
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Affiliation(s)
- Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Rebecca P. Wilkes
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Jobin J. Kattoor
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Erin N. Christian
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana 47907, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, Iowa, USA
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Reuschl AK, Thorne LG, Whelan MVX, Ragazzini R, Furnon W, Cowton VM, De Lorenzo G, Mesner D, Turner JLE, Dowgier G, Bogoda N, Bonfanti P, Palmarini M, Patel AH, Jolly C, Towers GJ. Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants. Nat Microbiol 2024; 9:451-463. [PMID: 38228858 PMCID: PMC10847042 DOI: 10.1038/s41564-023-01588-4] [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: 07/22/2022] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human adaptation resulted in distinct lineages with enhanced transmissibility called variants of concern (VOCs). Omicron is the first VOC to evolve distinct globally dominant subvariants. Here we compared their replication in human cell lines and primary airway cultures and measured host responses to infection. We discovered that subvariants BA.4 and BA.5 have improved their suppression of innate immunity when compared with earlier subvariants BA.1 and BA.2. Similarly, more recent subvariants (BA.2.75 and XBB lineages) also triggered reduced innate immune activation. This correlated with increased expression of viral innate antagonists Orf6 and nucleocapsid, reminiscent of VOCs Alpha to Delta. Increased Orf6 levels suppressed host innate responses to infection by decreasing IRF3 and STAT1 signalling measured by transcription factor phosphorylation and nuclear translocation. Our data suggest that convergent evolution of enhanced innate immune antagonist expression is a common pathway of human adaptation and link Omicron subvariant dominance to improved innate immune evasion.
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Affiliation(s)
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
- Department of Infectious Diseases, St Mary's Medical School, Imperial College London, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L E Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Giulia Dowgier
- Division of Infection and Immunity, University College London, London, UK
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Nathasha Bogoda
- Division of Infection and Immunity, University College London, London, UK
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | | | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, UK.
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK.
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72
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Shi G, Li T, Lai KK, Johnson RF, Yewdell JW, Compton AA. Omicron Spike confers enhanced infectivity and interferon resistance to SARS-CoV-2 in human nasal tissue. Nat Commun 2024; 15:889. [PMID: 38291024 PMCID: PMC10828397 DOI: 10.1038/s41467-024-45075-8] [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: 05/30/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
Omicron emerged following COVID-19 vaccination campaigns, displaced previous SARS-CoV-2 variants of concern worldwide, and gave rise to lineages that continue to spread. Here, we show that Omicron exhibits increased infectivity in primary adult upper airway tissue relative to Delta. Using recombinant forms of SARS-CoV-2 and nasal epithelial cells cultured at the liquid-air interface, we show that mutations unique to Omicron Spike enable enhanced entry into nasal tissue. Unlike earlier variants of SARS-CoV-2, our findings suggest that Omicron enters nasal cells independently of serine transmembrane proteases and instead relies upon metalloproteinases to catalyze membrane fusion. Furthermore, we demonstrate that this entry pathway unlocked by Omicron Spike enables evasion from constitutive and interferon-induced antiviral factors that restrict SARS-CoV-2 entry following attachment. Therefore, the increased transmissibility exhibited by Omicron in humans may be attributed not only to its evasion of vaccine-elicited adaptive immunity, but also to its superior invasion of nasal epithelia and resistance to the cell-intrinsic barriers present therein.
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Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Reed F Johnson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alex A Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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73
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Ali EA, Al-Sadi A, Al-maharmeh Q, Subahi EA, Bellamkonda A, Kalavar M, Panigrahi K, Alshurafa A, Yassin MA. SARS-CoV-2 and chronic myeloid leukemia: a systematic review. Front Med (Lausanne) 2024; 10:1280271. [PMID: 38327268 PMCID: PMC10847560 DOI: 10.3389/fmed.2023.1280271] [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: 08/19/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus causing the coronavirus disease of 2019. The disease has caused millions of deaths since the first pandemic at the end of 2019. Immunocompromised individuals are more likely to develop severe infections. Numerous mutations had developed in SARS-CoV-2, resulting in strains (Alfa Beta Delta Omicron) with varying degrees of virulence disease severity. In CML (chronic myeloid leukemia) patients, there is a lot of controversy regarding the effect of the treatment on the patient outcome. Some reports suggested potential better outcomes among patients with CML, likely due to the use of TKI; other reports showed no significant effects. Additionally, it is unknown how much protection immunization provides for cancer patients. Method In accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) standards, we conducted a systematic review. Retrospective, prospective studies, reviews, case series, and case reports of chronic myeloid leukemia patients aged above 18βyears who had SARS-CoV-2 infection were included. English literature was screened using PubMed, SCOPUS, and Google Scholar. Search terms include chronic myeloid leukemia, chronic myelogenous leukemia, and SARS-CoV-2 and Coronavirus disease 2019 (COVID-19). We searched the reference lists of the included studies for any new articles. The search included all articles published up to April 20, 2023. The review is registered in PROSPERO (registration number CRD42022326674). Results We reviewed 33 articles of available published literature up to April 2023 and collected data from a total of 682 CML patients with COVID-19. Most patients were in the chronic phase, seven were in the accelerated phase, and eight were in the blast phase. Disease severity was classified according to WHO criteria. Mortality was seen in 45 patients, and there were no reports of thrombotic events. Two hundred seventy-seven patients were in the era before vaccination; among them, eight were in the intensive care unit (ICU), and mortality was 30 (11%). There were 405 patients after the era of vaccination; among them, death was reported in 15 (4%) patients and ICU in 13 patients. Limitations and conclusion The major limitation of this review is the lack of details about the use or hold of TKIs during SARS-CoV-2 infection. Additionally, after the appearance of the different variants of the SARS-CoV-2 virus, few studies mentioned the variant of the virus, which makes it difficult to compare the outcome of the other variants of the SARS-CoV-2 virus in patients with CML. Despite the limitations of the study, CML patients with COVID-19 have no significant increase in mortality compared to other hematological malignancy. Hematological cancers are associated with an increased risk of thrombosis, which is expected to increase in patients with COVID-19. However, patient with CML has not been reported to have a significant increase in thrombosis risk. The available data indicates that COVID-19's effect on patients with chronic myeloid leukemia (CML) still needs to be better understood due to the limited data. Systematic review registration https://www.crd.york.ac.uk/PROSPERO/display_record.php? RecordID:326674.
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Affiliation(s)
- Elrazi A. Ali
- Internal Medicine Department, Interfaith Medical Center/One Brooklyn Health, Brooklyn, NY, United States
| | - Anas Al-Sadi
- Internal Medicine Department, Hamad Medical Corporation, Doha, Qatar
| | - Qusai Al-maharmeh
- Internal Medicine Department, Saint Michael's Medical Center, Newark, CA, United States
| | - Eihab A. Subahi
- Internal Medicine Department, Hamad Medical Corporation, Doha, Qatar
| | - Amulya Bellamkonda
- Internal Medicine Department, Interfaith Medical Center/One Brooklyn Health, Brooklyn, NY, United States
| | - Madhumati Kalavar
- Internal Medicine Department, Interfaith Medical Center/One Brooklyn Health, Brooklyn, NY, United States
| | - Kalpana Panigrahi
- Internal Medicine Department, Interfaith Medical Center/One Brooklyn Health, Brooklyn, NY, United States
| | - Awni Alshurafa
- Department of Oncology-Hematology, National Center for Cancer Care and Research β Hamad Medical Corporation, Doha, Qatar
| | - Mohamed A. Yassin
- Department of Oncology-Hematology, National Center for Cancer Care and Research β Hamad Medical Corporation, Doha, Qatar
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74
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Horbach IS, de Souza Azevedo A, Schwarcz WD, Alves NDS, de Moura Dias B, Setatino BP, da Cruz Moura L, de Souza AF, Denani CB, da Silva SA, Pimentel TG, de Oliveira Silva Ferreira V, Azamor T, Ano Bom APD, da Penha Gomes Gouvea M, Mill JG, Valim V, Polese J, Campi-Azevedo AC, Peruhype-MagalhΓ£es V, Teixeira-Carvalho A, Martins-Filho OA, de Lima SMB, de Sousa Junior IP. Plaque Reduction Neutralization Test (PRNT) Accuracy in Evaluating Humoral Immune Response to SARS-CoV-2. Diseases 2024; 12:29. [PMID: 38248380 PMCID: PMC10814169 DOI: 10.3390/diseases12010029] [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: 12/12/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Massive vaccination positively impacted the SARS-CoV-2 pandemic, being a strategy to increase the titers of neutralizing antibodies (NAbs) in the population. Assessing NAb levels and understanding the kinetics of NAb responses is critical for evaluating immune protection. In this study, we optimized and validated a PRNT50 assay to assess 50% virus neutralization and evaluated its accuracy to measure NAbs to the original strain or variant of SARS-CoV-2. The optimal settings were selected, such as the cell (2 Γ 105 cells/well) and CMC (1.5%) concentrations and the viral input (~60 PFU/well) for PRNT-SARS-CoV-2 with cut-off point = 1.64 log5 based on the ROC curve (AUC = 0.999). The validated PRNT-SARS-CoV-2 assay presented high accuracy with an intraassay precision of 100% for testing samples with different NAb levels (low, medium, and high titers). The method displays high selectivity without cross-reactivity with dengue (DENV), measles (MV), zika (ZIKV), and yellow fever (YFV) viruses. In addition, the standardized PRNT-SARS-CoV-2 assay presented robustness when submitted to controlled variations. The validated PRNT assay was employed to test over 1000 specimens from subjects with positive or negative diagnoses for SARS-CoV-2 infection. Patients with severe COVID-19 exhibited higher levels of NAbs than those presenting mild symptoms for both the Wuhan strain and Omicron. In conclusion, this study provides a detailed description of an optimized and validated PRNT50 assay to monitor immune protection and to subsidize surveillance policies applied to epidemiologic studies of COVID-19.
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Affiliation(s)
- Ingrid Siciliano Horbach
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
- Programa de Pós-Graduação em Medicina Tropical, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Adriana de Souza Azevedo
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
| | - Waleska Dias Schwarcz
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
| | - Nathalia dos Santos Alves
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
| | - Brenda de Moura Dias
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
| | - Bruno Pimenta Setatino
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
| | - Luma da Cruz Moura
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
| | - Ariane Faria de Souza
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
| | - Caio Bidueira Denani
- Laboratório de AnÑlise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (I.S.H.); (A.d.S.A.); (W.D.S.); (N.d.S.A.); (B.d.M.D.); (B.P.S.); (L.d.C.M.); (A.F.d.S.); (C.B.D.)
- Programa de Pós-Graduação em Medicina Tropical, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Stephanie Almeida da Silva
- Laboratório de Tecnologia Virológica, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Thiago Goes Pimentel
- Núcleo de Apoio Administrativo VDINV, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Victor de Oliveira Silva Ferreira
- Seção de Validação AnalΓtica, Instituto de Tecnologia em ImunobiolΓ³gicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Tamiris Azamor
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (T.A.); (A.P.D.A.B.)
| | - Ana Paula Dinis Ano Bom
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (T.A.); (A.P.D.A.B.)
| | - Maria da Penha Gomes Gouvea
- Hospital UniversitΓ‘rio Cassiano AntΓ΄nio Moraes, Universidade Federal do EspΓrito Santo (HUCAM-UFES/EBSERH), VitΓ³ria 29041-295, Brazil; (M.d.P.G.G.); (J.G.M.); (V.V.)
| | - JosΓ© Geraldo Mill
- Hospital UniversitΓ‘rio Cassiano AntΓ΄nio Moraes, Universidade Federal do EspΓrito Santo (HUCAM-UFES/EBSERH), VitΓ³ria 29041-295, Brazil; (M.d.P.G.G.); (J.G.M.); (V.V.)
| | - ValΓ©ria Valim
- Hospital UniversitΓ‘rio Cassiano AntΓ΄nio Moraes, Universidade Federal do EspΓrito Santo (HUCAM-UFES/EBSERH), VitΓ³ria 29041-295, Brazil; (M.d.P.G.G.); (J.G.M.); (V.V.)
| | - Jessica Polese
- Programa de PΓ³s-Graduação em CiΓͺncias FisiolΓ³gicas da Universidade Federal do EspΓrito Santo, VitΓ³ria 29500-000, Brazil;
| | - Ana Carolina Campi-Azevedo
- Grupo Integrado de Pesquisa em Biomarcadores, Instituto RenΓ© Rachou, FIOCRUZ-Minas, Belo Horizonte 30190-002, Brazil; (A.C.C.-A.); (V.P.-M.); (A.T.-C.); (O.A.M.-F.)
| | - Vanessa Peruhype-MagalhΓ£es
- Grupo Integrado de Pesquisa em Biomarcadores, Instituto RenΓ© Rachou, FIOCRUZ-Minas, Belo Horizonte 30190-002, Brazil; (A.C.C.-A.); (V.P.-M.); (A.T.-C.); (O.A.M.-F.)
| | - AndrΓ©a Teixeira-Carvalho
- Grupo Integrado de Pesquisa em Biomarcadores, Instituto RenΓ© Rachou, FIOCRUZ-Minas, Belo Horizonte 30190-002, Brazil; (A.C.C.-A.); (V.P.-M.); (A.T.-C.); (O.A.M.-F.)
| | - Olindo Assis Martins-Filho
- Grupo Integrado de Pesquisa em Biomarcadores, Instituto RenΓ© Rachou, FIOCRUZ-Minas, Belo Horizonte 30190-002, Brazil; (A.C.C.-A.); (V.P.-M.); (A.T.-C.); (O.A.M.-F.)
| | - Sheila Maria Barbosa de Lima
- Departamento de Desenvolvimento Experimental e PrΓ©-clΓnico (DEDEP), Instituto de Tecnologia em ImunobiolΓ³gicos Bio-Manguinhos, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
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BΓΈΓ₯s H, Storm ML, Tapia G, Kristoffersen AB, LΓΈvlie AL, StΓΈrdal K, Lyngstad TM, Bragstad K, Hungnes O, Veneti L. Frequency and risk of SARS-CoV-2 reinfections in Norway: a nation-wide study, February 2020 to January 2022. BMC Public Health 2024; 24:181. [PMID: 38225588 PMCID: PMC10789014 DOI: 10.1186/s12889-024-17695-8] [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: 08/08/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND SARS-CoV-2 reinfection rates have been shown to vary depending on the circulating variant, vaccination status and background immunity, as well as the time interval used to identify reinfections. This study describes the frequency of SARS-CoV-2 reinfections in Norway using different time intervals and assesses potential factors that could impact the risk of reinfections during the different variant waves. METHODS We used linked individual-level data from national registries to conduct a retrospective cohort study including all cases with a positive test for SARS-CoV-2 from February 2020 to January 2022. Time intervals of 30, 60, 90 or 180 days between positive tests were used to define potential reinfections. A multivariable Cox regression model was used to assess the risk of reinfection in terms of variants adjusting for vaccination status, demographic factors, and underlying comorbidities. RESULTS The reinfection rate varied between 0.2%, 0.6% and 5.9% during the Alpha, Delta and early Omicron waves, respectively. In the multivariable model, younger age groups were associated with a higher risk of reinfection compared to older age groups, whereas vaccination was associated with protection against reinfection. Moreover, the risk of reinfection followed a pattern similar to risk of first infection. Individuals infected early in the pandemic had higher risk of reinfection than individuals infected in more recent waves. CONCLUSIONS Reinfections increased markedly during the Omicron wave. Younger individuals, and primary infections during earlier waves were associated with an increased reinfection risk compared to primary infections during more recent waves, whereas vaccination was a protective factor. Our results highlight the importance of age and post infection waning immunity and are relevant when evaluating vaccination polices.
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Affiliation(s)
- HΓ₯kon BΓΈΓ₯s
- Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Lovisenberggata 8, 0456, Oslo, Norway.
| | | | - German Tapia
- Department of Chronic Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Astrid Louise LΓΈvlie
- Department of Infectious Disease Registries, Norwegian Institute of Public Health, Oslo, Norway
| | - Ketil StΓΈrdal
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Trude Marie Lyngstad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Karoline Bragstad
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Olav Hungnes
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Lamprini Veneti
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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76
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An G, Mi Z, Hong D, Ou D, Cao X, Liu Q, Xiong L, Li C. Nomogram to predict the incidence of delirium in elderly patients with non-severe SARS-CoV-2 infection. Front Psychiatry 2024; 14:1288948. [PMID: 38274422 PMCID: PMC10808537 DOI: 10.3389/fpsyt.2023.1288948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Objective To construct and validate nomogram models that predict the incidence of delirium in elderly patients with non-severe SARS-CoV-2 infection. Methods Elderly patients (β₯65y) tested positive for SARS-CoV-2 infection at the hospital were included. We used the 3-min diagnostic Confusion Assessment Method for delirium diagnosis. Least absolute shrinkage and selection operator (LASSO) logistical regression analysis was performed to explore potential independent influencing factors of delirium. A predict model visualized by nomogram was constructed based on the confirmed variables. The predictive accuracy and clinical value of the model were evaluated using receiver operating characteristic (ROC) curves. Results The data of 311 elderly patients were analyzed, of whom 73 (23.47%) patients were diagnosed with delirium. Three independent influencing factors of delirium were confirmed: age (OR1.16,1.11-1.22), Glomerular filtration rate (OR 0.98,0.97-0.99), platelet-large cell ratio (1.06,1.02-1.10). These parameters were used to create a nomogram to predict the development of delirium, which showed good predictive accuracy confirmed by the ROC curves (AUC 0.82,0.76-0.88). Conclusion We construct a credible nomogram to predict the development of delirium in elderly patients with Non-severe SARS-CoV-2 infection. Our finding may be useful to physicians in early prevention and treatment of delirium.
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Affiliation(s)
| | | | | | | | | | - Qidong Liu
- Department of Anesthesiology and Perioperative Medicine, Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lize Xiong
- Department of Anesthesiology and Perioperative Medicine, Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Cheng Li
- Department of Anesthesiology and Perioperative Medicine, Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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77
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Johnston TS, Li SH, Painter MM, Atkinson RK, Douek NR, Reeg DB, Douek DC, Wherry EJ, Hensley SE. Immunological imprinting shapes the specificity of human antibody responses against SARS-CoV-2 variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.08.24301002. [PMID: 38260304 PMCID: PMC10802657 DOI: 10.1101/2024.01.08.24301002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The spike glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to accumulate substitutions, leading to breakthrough infections of vaccinated individuals and prompting the development of updated booster vaccines. Here, we determined the specificity and functionality of antibody and B cell responses following exposure to BA.5 and XBB variants in individuals who received ancestral SARS-CoV-2 mRNA vaccines. BA.5 exposures elicited antibody responses that primarily targeted epitopes conserved between the BA.5 and ancestral spike, with poor reactivity to the XBB.1.5 variant. XBB exposures also elicited antibody responses that targeted epitopes conserved between the XBB.1.5 and ancestral spike. However, unlike BA.5, a single XBB exposure elicited low levels of XBB.1.5-specific antibodies and B cells in some individuals. Pre-existing cross-reactive B cells and antibodies were correlated with stronger overall responses to XBB but weaker XBB-specific responses, suggesting that baseline immunity influences the activation of variant-specific SARS-CoV-2 responses.
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Affiliation(s)
- Timothy S. Johnston
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- Vaccine Research Center, NIAID, NIH; Bethesda, MD
- These authors contributed equally
| | - Shuk Hang Li
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- These authors contributed equally
| | - Mark M. Painter
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- These authors contributed equally
| | - Reilly K. Atkinson
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Naomi R. Douek
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - David B. Reeg
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | | | - E. John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Scott E. Hensley
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
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78
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Kahn R, Feikin DR, Wiegand RE, Lipsitch M. EXAMINING BIAS FROM DIFFERENTIAL DEPLETION OF SUSCEPTIBLES IN VACCINE EFFECTIVENESS ESTIMATES IN SETTINGS OF WANING. Am J Epidemiol 2024; 193:232-234. [PMID: 37771045 PMCID: PMC10773472 DOI: 10.1093/aje/kwad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/13/2023] [Accepted: 09/26/2023] [Indexed: 09/30/2023] Open
Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Center for Forecasting and Outbreak Analytics, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Daniel R Feikin
- Department of Immunizations, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland
| | - Ryan E Wiegand
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Center for Forecasting and Outbreak Analytics, Centers for Disease Control and Prevention, Atlanta, GA, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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Mei S, Zou Y, Jiang S, Xue L, Wang Y, Jing H, Yang P, Niu MM, Li J, Yuan K, Zhang Y. Highly potent dual-targeting angiotensin-converting enzyme 2 (ACE2) and Neuropilin-1 (NRP1) peptides: A promising broad-spectrum therapeutic strategy against SARS-CoV-2 infection. Eur J Med Chem 2024; 263:115908. [PMID: 37981444 DOI: 10.1016/j.ejmech.2023.115908] [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: 05/22/2023] [Revised: 10/12/2023] [Accepted: 10/21/2023] [Indexed: 11/21/2023]
Abstract
The efficacy of approved vaccines has been diminishing due to the increasing advent of SARS-CoV-2 variants with diverse mutations that favor sneak entry. Nonetheless, these variants recognize the conservative host receptors angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1) for entry, rendering the dual blockade of ACE2 and NRP1 an advantageous pan-inhibition strategy. Here, we identified a highly potent dual-targeting peptide AP-1 using structure-based virtual screening protocol. AP-1 had nanoscale binding affinities for ACE2 (KdΒ =Β 6.1Β Β±Β 0.2Β nM) and NRP1 (KdΒ =Β 13.4Β Β±Β 1.2Β nM) and approximately 102- and 8-fold stronger than positive inhibitors S471-503 and NMTP-5, respectively. Further evidence in pseudovirus cell infection and cytotoxicity assays demonstrated that AP-1 exhibited remarkable entry inhibition of variants of concern (VOCs) of SARS-CoV-2 without impairing host cell viability. Together, our findings suggest that AP-1 with dual-targeting ACE2/NRP1 efficacy could be a promising broad-spectrum agent for treating SARS-CoV-2 emerging VOCs.
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Affiliation(s)
- Shuang Mei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Yunting Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Su Jiang
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Lu Xue
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Yuting Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Han Jing
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Miao-Miao Niu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Jindong Li
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yan Zhang
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
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Baker SJC, Nfonsam LE, Leto D, Rutherford C, Smieja M, McArthur AG. Chronic COVID-19 infection in an immunosuppressed patient shows changes in lineage over time: a case report. Virol J 2024; 21:8. [PMID: 38178158 PMCID: PMC10768205 DOI: 10.1186/s12985-023-02278-7] [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: 08/01/2023] [Accepted: 12/25/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 virus, emerged in late 2019 and spready globally. Many effects of infection with this pathogen are still unknown, with both chronic and repeated COVID-19 infection producing novel pathologies. CASE PRESENTATION An immunocompromised patient presented with chronic COVID-19 infection. The patient had history of Hodgkin's lymphoma, treated with chemotherapy and stem cell transplant. During the course of their treatment, eleven respiratory samples from the patient were analyzed by whole-genome sequencing followed by lineage identification. Whole-genome sequencing of the virus present in the patient over time revealed that the patient at various timepoints harboured three different lineages of the virus. The patient was initially infected with the B.1.1.176 lineage before coinfection with BA.1. When the patient was coinfected with both B.1.1.176 and BA.1, the viral populations were found in approximately equal proportions within the patient based on sequencing read abundance. Upon further sampling, the lineage present within the patient during the final two timepoints was found to be BA.2.9. The patient eventually developed respiratory failure and died. CONCLUSIONS This case study shows an example of the changes that can happen within an immunocompromised patient who is infected with COVID-19 multiple times. Furthermore, this case demonstrates how simultaneous coinfection with two lineages of COVID-19 can lead to unclear lineage assignment by standard methods, which are resolved by further investigation. When analyzing chronic COVID-19 infection and reinfection cases, care must be taken to properly identify the lineages of the virus present.
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Affiliation(s)
- Sheridan J C Baker
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
| | - Landry E Nfonsam
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Daniela Leto
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Candy Rutherford
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
| | - Marek Smieja
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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81
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Sankhala RS, Lal KG, Jensen JL, Dussupt V, Mendez-Rivera L, Bai H, Wieczorek L, Mayer SV, Zemil M, Wagner DA, Townsley SM, Hajduczki A, Chang WC, Chen WH, Donofrio GC, Jian N, King HAD, Lorang CG, Martinez EJ, Rees PA, Peterson CE, Schmidt F, Hart TJ, Duso DK, Kummer LW, Casey SP, Williams JK, Kannan S, Slike BM, Smith L, Swafford I, Thomas PV, Tran U, Currier JR, Bolton DL, Davidson E, Doranz BJ, Hatziioannou T, Bieniasz PD, Paquin-Proulx D, Reiley WW, Rolland M, Sullivan NJ, Vasan S, Collins ND, Modjarrad K, Gromowski GD, Polonis VR, Michael NL, Krebs SJ, Joyce MG. Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques. Nat Commun 2024; 15:200. [PMID: 38172512 PMCID: PMC10764318 DOI: 10.1038/s41467-023-44265-0] [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: 05/22/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
The repeat emergence of SARS-CoV-2 variants of concern (VoC) with decreased susceptibility to vaccine-elicited antibodies highlights the need to develop next-generation vaccine candidates that confer broad protection. Here we describe the antibody response induced by the SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine candidate adjuvanted with the Army Liposomal Formulation including QS21 (ALFQ) in non-human primates. By isolating and characterizing several monoclonal antibodies directed against the Spike Receptor Binding Domain (RBD), N-Terminal Domain (NTD), or the S2 Domain, we define the molecular recognition of vaccine-elicited cross-reactive monoclonal antibodies (mAbs) elicited by SpFN. We identify six neutralizing antibodies with broad sarbecovirus cross-reactivity that recapitulate serum polyclonal antibody responses. In particular, RBD mAb WRAIR-5001 binds to the conserved cryptic region with high affinity to sarbecovirus clades 1 and 2, including Omicron variants, whileΒ mAb WRAIR-5021 offers complete protection from B.1.617.2 (Delta) in a murine challenge study. Our data further highlight the ability of SpFN vaccination to stimulate cross-reactive B cells targeting conserved regions of the Spike with activity against SARS CoV-1 and SARS-CoV-2 variants.
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Affiliation(s)
- Rajeshwer S Sankhala
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kerri G Lal
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jaime L Jensen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Vincent Dussupt
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Letzibeth Mendez-Rivera
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Hongjun Bai
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsay Wieczorek
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sandra V Mayer
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michelle Zemil
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Danielle A Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samantha M Townsley
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - William C Chang
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gina C Donofrio
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ningbo Jian
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Hannah A D King
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Cynthia G Lorang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth J Martinez
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Phyllis A Rees
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caroline E Peterson
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | | | | | | | | | | | - Bonnie M Slike
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lauren Smith
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Isabella Swafford
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Paul V Thomas
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ursula Tran
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Diane L Bolton
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Dominic Paquin-Proulx
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Morgane Rolland
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sandhya Vasan
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Natalie D Collins
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Vaccine Research and Development, Pfizer, Pearl River, New York, NY, USA
| | - Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nelson L Michael
- Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Shelly J Krebs
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - M Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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Ryu B, Shin E, Kim DH, Lee H, Choi SY, Kim SS, Kim IH, Kim EJ, Lee S, Jeon J, Kwon D, Cho S. Changes in the intrinsic severity of severe acute respiratory syndrome coronavirus 2 according to the emerging variant: a nationwide study from February 2020 to June 2022, including comparison with vaccinated populations. BMC Infect Dis 2024; 24:1. [PMID: 38166696 PMCID: PMC10759357 DOI: 10.1186/s12879-023-08869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND As the population acquires immunity through vaccination and natural infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the intrinsic severity of coronavirus disease (COVID-19) is becoming challenging. We aimed to evaluate the intrinsic severity regarding circulating variants of SARS-CoV-2 and to compare this between vaccinated and unvaccinated individuals. METHODS With unvaccinated and initially infected confirmed cases of COVID-19, we estimated the case severity rate (CSR); case fatality rate (CFR); and mortality rate (MR), including severe/critical cases and deaths, stratified by age and compared by vaccination status according to the period regarding the variants of COVID-19 and vaccination. The overall rate was directly standardized with age. RESULTS The age-standardized CSRs (aCSRs) of the unvaccinated group were 2.12%, 5.51%, and 0.94% in the pre-delta, delta, and omicron period, respectively, and the age-standardized CFRs (aCFRs) were 0.60%, 2.49%, and 0.63% in each period, respectively. The complete vaccination group had lower severity than the unvaccinated group over the entire period showing under 1% for the aCSR and 0.5% for the aCFR. The age-standardized MR of the unvaccinated group was 448 per million people per month people in the omicron period, which was 11 times higher than that of the vaccinated group. In terms of age groups, the CSR and CFR sharply increased with age from the 60Β s and showed lower risk reduction in the 80Β s when the period changed to the omicron period. CONCLUSIONS The intrinsic severity of COVID-19 was the highest in the delta period, with over 5% for the aCSR, whereas the completely vaccinated group maintained below 1%. This implies that when the population is vaccinated, the impact of COVID-19 will be limited, even if a new mutation appears. Moreover, considering the decreasing intrinsic severity, the response to COVID-19 should prioritize older individuals at a higher risk of severe disease.
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Affiliation(s)
- Boyeong Ryu
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - Eunjeong Shin
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - Dong Hwi Kim
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - HyunJu Lee
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - So Young Choi
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - Seong-Sun Kim
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - Sangwon Lee
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea
| | - Jaehyun Jeon
- Department of Infectious Diseases, Clinical Infectious Disease Research Center, National Medical Center, 245, Eulji-ro, Jung-gu, Seoul, Korea
| | - Donghyok Kwon
- Epidemiological Investigation and Analysis Task Force, Central Disease Control Headquarters, Korea Disease Control and Prevention Agency (KDCA), 187, Osongsaengmyeong 2-Ro, Osong-Eup, Heungdeok-Gu, Cheongju, Korea.
| | - Sungil Cho
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea.
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Abdoli A, Jamshidi H, Taqavian M, Baghal ML, Jalili H. Omicron-specific and bivalent omicron-containing vaccine candidates elicit potent virus neutralisation in the animal model. Sci Rep 2024; 14:268. [PMID: 38168473 PMCID: PMC10762194 DOI: 10.1038/s41598-023-50822-w] [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: 03/27/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
Omicron variant (B.1.1.529) is able to escape from naturally acquired and vaccine-induced immunity, which mandates updating the current COVID-19 vaccines. Here, we investigated and compared the neutralising antibody induction of the ancestral variant-based BIV1-CovIran vaccine, the Omicron variant-based BIV1-CovIran Plus vaccine, and the novel bivalent vaccine candidate, BBIV1-CovIran, against the Omicron and ancestral Wuhan variants on the rat model. After inactivating the viral particles, the viruses were purified and formulated. Bivalent vaccines were a composition of 2.5 Β΅g (5 Β΅g total) or 5 Β΅g (10 Β΅g total) doses of each ansectral-based and Omicron-based monovalent vaccine. Subsequently, the potency of the monovalent and bivalent vaccines was investigated using the virus neutralisation test (VNT). The group that received three doses of the Omicron-specific vaccine demonstrated neutralisation activity against the Omicron variant with a geometric mean titer of 337.8. However, three doses of the Wuhan variant-specific vaccine could neutralise the Omicron variant at a maximum of 1/32 serum dilution. The neutralisation activity of the Omicron-specific vaccine, when administered as the booster dose after two doses of the Wuhan variant-specific vaccine, was 100% against the Omicron variant and the Wuhan variant at 1/64 and 1/128 serum dilution, respectively. Three doses of 5 Β΅g bivalent vaccine could effectively neutralise both variants at the minimum of 1/128 serum dilution. The 10 Β΅g bivalent vaccine at three doses showed even higher neutralisation titers: the geometric mean of 388 (95% CI 242.2-621.7) against Omicron and 445.7 (95% CI 303.3-655.0) against Wuhan. It is shown that the candidate bivalent and Omicron-specific vaccines could elicit a potent immune response against both Wuhan-Hu-1 and Omicron BA.1 variants.
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Affiliation(s)
- Asghar Abdoli
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
- Amirabad Virology Laboratory, Vaccine Unit, Tehran, Iran
| | - Hamidreza Jamshidi
- Department of Pharmacology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | | | - Hasan Jalili
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran.
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Liu S, Anzai A, Nishiura H. Reconstructing the COVID-19 incidence in India using airport screening data in Japan. BMC Infect Dis 2024; 24:12. [PMID: 38166666 PMCID: PMC10763058 DOI: 10.1186/s12879-023-08882-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND A major epidemic of COVID-19 caused by the Delta variant (B.1.617.2) occurred in India from March to July 2021, resulting in 19 million documented cases. Given the limited healthcare and testing capacities, the actual number of infections is likely to have been greater than reported, and several modelling studies and excess mortality research indicate that this epidemic involved substantial morbidity and mortality. METHODS To estimate the incidence during this epidemic, we used border entry screening data in Japan to estimate the daily incidence and cumulative incidence of COVID-19 infection in India. Analysing the results of mandatory testing among non-Japanese passengers entering Japan from India, we calculated the prevalence and then backcalculated the incidence in India from February 28 to July 3, 2021. RESULTS The estimated number of infections ranged from 448 to 576 million people, indicating that 31.8% (95% confidence interval (CI): 26.1, 37.7) - 40.9% (95% CI: 33.5, 48.4) of the population in India had experienced COVID-19 infection from February 28 to July 3, 2021. In addition to obtaining cumulative incidence that was consistent with published estimates, we showed that the actual incidence of COVID-19 infection during the 2021 epidemic in India was approximately 30 times greater than that based on documented cases, giving a crude infection fatality risk of 0.47%. Adjusting for test-negative certificate before departure, the quality control of which was partly questionable, the cumulative incidence can potentially be up to 2.3-2.6 times greater than abovementioned estimates. CONCLUSIONS Our estimate of approximately 32-41% cumulative infection risk from February 28 to July 3, 2021 is roughly consistent with other published estimates, and they can potentially be greater, given an exit screening before departure. The present study results suggest the potential utility of border entry screening data to backcalculate the incidence in countries with limited surveillance capacity owing to a major surge in infections.
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Affiliation(s)
- Shiqi Liu
- Kyoto University School of Public Health, Yoshidakonoe cho, Sakyo ku, Kyoto City, 6068501, Japan
| | - Asami Anzai
- Kyoto University School of Public Health, Yoshidakonoe cho, Sakyo ku, Kyoto City, 6068501, Japan
| | - Hiroshi Nishiura
- Kyoto University School of Public Health, Yoshidakonoe cho, Sakyo ku, Kyoto City, 6068501, Japan.
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Krammer F. The role of vaccines in the COVID-19 pandemic: what have we learned? Semin Immunopathol 2024; 45:451-468. [PMID: 37436465 PMCID: PMC11136744 DOI: 10.1007/s00281-023-00996-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/24/2023] [Indexed: 07/13/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged late in 2019 and caused the coronavirus disease 2019 (COVID-19) pandemic that has so far claimed approximately 20 million lives. Vaccines were developed quickly, became available in the end of 2020, and had a tremendous impact on protection from SARS-CoV-2 mortality but with emerging variants the impact on morbidity was diminished. Here I review what we learned from COVID-19 from a vaccinologist's perspective.
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Affiliation(s)
- Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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86
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Zhang H, Liu Y, Liu Z. Nanomedicine approaches against SARS-CoV-2 and variants. J Control Release 2024; 365:101-111. [PMID: 37951476 DOI: 10.1016/j.jconrel.2023.11.004] [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: 07/26/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
The world is grappling with the ongoing crisis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a global pandemic that continues to have a detrimental impact on public health and economies worldwide. The virus's relentless mutation has led to more transmissible, immune-evasive strains, thereby escalating the incidence of reinfection. This underscores the urgent need for highly effective and safe countermeasures against SARS-CoV-2 and its evolving variants. In the current context, nanomedicine presents an innovative and promising alternative to mitigate the impacts of this pandemic wave. It does so by harnessing the structural and functional properties at a nanoscale in a straightforward and adaptable manner. This review emphasizes the most recent progress in the development of nanovaccines, nanodecoys, and nanodisinfectants to tackle SARS-CoV-2 and its variants. Notably, the insights gained and strategies implemented in managing the ongoing pandemic may also offer invaluable guidance for the development of potent nanomedicines to combat future pandemics.
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Affiliation(s)
- Han Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China.
| | - Yanbin Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China.
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87
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Das R, Hyer RN, Burton P, Miller JM, Kuter BJ. Emerging heterologous mRNA-based booster strategies within the COVID-19 vaccine landscape. Hum Vaccin Immunother 2023; 19:2153532. [PMID: 36629006 PMCID: PMC9980456 DOI: 10.1080/21645515.2022.2153532] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Messenger RNA (mRNA)-based vaccine platforms used for the development of mRNA-1273 and BNT162b2 have provided a robust adaptable approach to offer protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, as variants of concern (VoCs), such as omicron and associated sub-variants, emerge, boosting strategies must also adapt to keep pace with the changing landscape. Heterologous vaccination regimens involving the administration of booster vaccines different than the primary vaccination series offer a practical, effective, and safe approach to continue to reduce the global burden of coronavirus disease 2019 (COVID-19). To understand the immunogenicity, effectiveness, and safety of heterologous mRNA-based vaccination strategies, relevant clinical and real-world observational studies were identified and summarized. Overall, heterologous boosting strategies with mRNA-based vaccines that are currently available and those in development will play an important global role in protecting individuals from COVID-19 caused by emerging VoCs.
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Affiliation(s)
- Rituparna Das
- Infectious Diseases, Moderna, Inc., Cambridge, MA, USA,CONTACT Rituparna Das Moderna, Inc., 200 Technology Square, Cambridge, MA02139, USA
| | - Randall N. Hyer
- Experimental Therapeutics, Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Paul Burton
- Infectious Diseases, Moderna, Inc., Cambridge, MA, USA
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88
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Holdenrieder S, Dos Santos Ferreira CE, Izopet J, Theel ES, Wieser A. Clinical and laboratory considerations: determining an antibody-based composite correlate of risk for reinfection with SARS-CoV-2 or severe COVID-19. Front Public Health 2023; 11:1290402. [PMID: 38222091 PMCID: PMC10788057 DOI: 10.3389/fpubh.2023.1290402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024] Open
Abstract
Much of the global population now has some level of adaptive immunity to SARS-CoV-2 induced by exposure to the virus (natural infection), vaccination, or a combination of both (hybrid immunity). Key questions that subsequently arise relate to the duration and the level of protection an individual might expect based on their infection and vaccination history. A multi-component composite correlate of risk (CoR) could inform individuals and stakeholders about protection and aid decision making. This perspective evaluates the various elements that need to be accommodated in the development of an antibody-based composite CoR for reinfection with SARS-CoV-2 or development of severe COVID-19, including variation in exposure dose, transmission route, viral genetic variation, patient factors, and vaccination status. We provide an overview of antibody dynamics to aid exploration of the specifics of SARS-CoV-2 antibody testing. We further discuss anti-SARS-CoV-2 immunoassays, sample matrices, testing formats, frequency of sampling and the optimal time point for such sampling. While the development of a composite CoR is challenging, we provide our recommendations for each of these key areas and highlight areas that require further work to be undertaken.
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Affiliation(s)
- Stefan Holdenrieder
- Institute of Laboratory Medicine, German Heart Centre Munich, Technical University Munich, Munich, Germany
| | | | - Jacques Izopet
- Laboratory of Virology, Toulouse University Hospital and INFINITY Toulouse Institute for Infections and Inflammatory Diseases, INSERM UMR 1291 CNRS UMR 5051, University Toulouse III, Toulouse, France
| | - Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
- Faculty of Medicine, Max Von Pettenkofer Institute, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Munich, Germany
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89
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Li L, Xie Z, Li Y, Luo M, Zhang L, Feng C, Tang G, Huang H, Hou R, Xu Y, Jia S, Shi J, Fan Q, Gan Q, Yu N, Hu F, Li Y, Lan Y, Tang X, Li F, Deng X. Immune response and severity of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants. Front Cell Infect Microbiol 2023; 13:1277880. [PMID: 38188634 PMCID: PMC10766752 DOI: 10.3389/fcimb.2023.1277880] [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: 08/15/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction COVID-19 continues to spread worldwide, with an increasing number of individuals experiencing reinfection after recovering from their primary infection. However, the nature and progression of this infection remain poorly understood. We aimed to investigate the immune response, severity and outcomes of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants. Methods We enrolled 432 COVID-19 cases who had experienced prior infection with the ancestral SARS-CoV-2 virus, Delta variant or Omicron BA.2 variant between January 2020 and May 2022 in Guangzhou, China. All cases underwent follow-up from March to April, 2023 through telephone questionnaires and clinical visits. Nasal lavage fluid and peripheral blood were collected to assess anti-RBD IgA, anti-RBD IgG and virus-specific IFN-Ξ³ secreting T cells. Results Our study shows that 73.1%, 56.7% and 12.5% of individuals with a prior infection of the ancestral virus, Delta or Omicron BA.2 variant experienced reinfection with the BA.5 variant, respectively. Fever, cough and sore throat were the most common symptoms of BA.5 reinfection, with most improving within one week and none progressing to a critical condition. Compared with individuals without reinfection, reinfected patients with a prior Delta infection exhibited elevated levels of nasal anti-RBD IgA, serum anti-RBD IgG and IFN-Ξ³ secreting T cells, whereas there was no noticeable change in reinfected individuals with a prior BA.2 infection. Conclusion These results suggest that BA.5 reinfection is common but severe outcomes are relatively rare. Reinfection with a novel SARS-CoV-2 variant different from the prior infection may induce a more robust immune protection, which should be taken into account during vaccine development.
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Affiliation(s)
- Lu Li
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhiwei Xie
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Youxia Li
- Department of Critical Care Medicine, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Minhan Luo
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lieguang Zhang
- Department of Radiology, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chengqian Feng
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Guofang Tang
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Huang Huang
- Department of Critical Care Medicine, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ruitian Hou
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yujuan Xu
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shijie Jia
- Department of Traditional Chinese Medicine, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jingrong Shi
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qinghong Fan
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qingxin Gan
- Department of Radiology, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Na Yu
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fengyu Hu
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Yueping Li
- Department of Infectious Critical Care Medicine, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yun Lan
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoping Tang
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Feng Li
- Institute of Infectious Diseases, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Xilong Deng
- Department of Critical Care Medicine, Guangzhou Eighth Peopleβs Hospital, Guangzhou Medical University, Guangzhou, China
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90
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Penetra SLS, Santos HFP, Resende PC, Bastos LS, da Silva MFB, Pina-Costa A, Lopes RS, Saboia-Vahia L, de Oliveira ACA, Pereira EC, Filho FM, Wakimoto MD, Calvet GA, Fuller TL, Whitworth J, Smith C, Nielsen-Saines K, Carvalho MS, EspΓndola OM, Guaraldo L, Siqueira MM, Brasil P. SARS-CoV-2 Reinfection Cases in a Household-Based Prospective Cohort in Rio de Janeiro. J Infect Dis 2023; 228:1680-1689. [PMID: 37571849 PMCID: PMC11032242 DOI: 10.1093/infdis/jiad336] [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: 03/23/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023] Open
Abstract
This was a household-based prospective cohort study conducted in Rio de Janeiro, in which people with laboratory-confirmed coronavirus disease 2019 (COVID-19) and their household contacts were followed from April 2020 through June 2022. Ninety-eight reinfections were identified, with 71 (72.5%) confirmed by genomic analyses and lineage definition in both infections. During the pre-Omicron period, 1 dose of any COVID-19 vaccine was associated with a reduced risk of reinfection, but during the Omicron period not even booster vaccines had this effect. Most reinfections were asymptomatic or milder in comparison with primary infections, a justification for continuing active surveillance to detect infections in vaccinated individuals. Our findings demonstrated that vaccination may not prevent infection or reinfection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Therefore we highlight the need to continuously update the antigenic target of SARS CoV-2 vaccines and administer booster doses to the population regularly, a strategy well established in the development of vaccines for influenza immunization programs.
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Affiliation(s)
- Stephanie L S Penetra
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heloisa F P Santos
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Soares Bastos
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michele F B da Silva
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anielle Pina-Costa
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata Serrano Lopes
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Saboia-Vahia
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Any Caroline Alves de Oliveira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisa Cavalcante Pereira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Medeiros Filho
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mayumi D Wakimoto
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme A Calvet
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Trevon L Fuller
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- University of California, Los Angeles, Los Angeles, California, USA
| | - Jimmy Whitworth
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher Smith
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | | | - Marilia SΓ‘ Carvalho
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - OtΓ‘vio M EspΓndola
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lusiele Guaraldo
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Brasil
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
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91
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Jin J, Wang X, Li Y, Yang X, Wang H, Han X, Sun J, Ma Z, Duan J, Zhang G, Huang T, Zhang T, Wu H, Zhang X, Su B. Weak SARS-CoV-2-specific responses of TIGIT-expressing CD8 + T cells in people living with HIV after a third dose of a SARS-CoV-2 inactivated vaccine. Chin Med J (Engl) 2023; 136:2938-2947. [PMID: 37963586 PMCID: PMC10752475 DOI: 10.1097/cm9.0000000000002926] [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: 05/30/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND T-cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibition motif domains (TIGIT), an inhibitory receptor expressed on T cells, plays a dysfunctional role in antiviral infection and antitumor activity. However, it is unknown whether TIGIT expression on T cells influences the immunological effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inactivated vaccines. METHODS Forty-five people living with HIV (PLWH) on antiretroviral therapy (ART) for more than two years and 31 healthy controls (HCs), all received a third dose of a SARS-CoV-2 inactivated vaccine, were enrolled in this study. The amounts, activation, proportion of cell subsets, and magnitude of the SARS-CoV-2-specific immune response of TIGIT + CD4 + and TIGIT + CD8 + T cells were investigated before the third dose but 6 months after the second vaccine dose (0W), 4 weeks (4W) and 12 weeks (12W) after the third dose. RESULTS Compared to that in HCs, the frequency of TIGIT + CD8 + T cells in the peripheral blood of PLWH increased at 12W after the third dose of the inactivated vaccine, and the immune activation of TIGIT + CD8 + T cells also increased. A decrease in the ratio of both T naΓ―ve (T N ) and central memory (T CM ) cells among TIGIT + CD8 + T cells and an increase in the ratio of the effector memory (T EM ) subpopulation were observed at 12W in PLWH. Interestingly, particularly at 12W, a higher proportion of TIGIT + CD8 + T cells expressing CD137 and CD69 simultaneously was observed in HCs than in PLWH based on the activation-induced marker assay. Compared with 0W, SARS-CoV-2-specific TIGIT + CD8 + T-cell responses in PLWH were not enhanced at 12W but were enhanced in HCs. Additionally, at all time points, the SARS-CoV-2-specific responses of TIGIT + CD8 + T cells in PLWH were significantly weaker than those of TIGIT - CD8 + T cells. However, in HCs, the difference in the SARS-CoV-2-specific responses induced between TIGIT + CD8 + T cells and TIGIT - CD8 + T cells was insignificant at 4W and 12W, except at 0W. CONCLUSIONS TIGIT expression on CD8 + T cells may hinder the T-cell immune response to a booster dose of an inactivated SARS-CoV-2 vaccine, suggesting weakened resistance to SARS-CoV-2 infection, especially in PLWH. Furthermore, TIGIT may be used as a potential target to increase the production of SARS-CoV-2-specific CD8 + T cells, thereby enhancing the effectiveness of vaccination.
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Affiliation(s)
- Junyan Jin
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Xiuwen Wang
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Yongzheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xiaodong Yang
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Hu Wang
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Xiaoxu Han
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Jin Sun
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Zhenglai Ma
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Junyi Duan
- Tian Yuan Studio, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Guanghui Zhang
- Tian Yuan Studio, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Tao Huang
- Tian Yuan Studio, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Xin Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
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92
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Plans-RubiΓ³ P. Effectiveness of Adapted COVID-19 Vaccines and Ability to Establish Herd Immunity against Omicron BA.1 and BA4-5 Variants of SARS-CoV-2. Vaccines (Basel) 2023; 11:1836. [PMID: 38140240 PMCID: PMC10747774 DOI: 10.3390/vaccines11121836] [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: 10/28/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of novel SARS-CoV-2 variants has raised concerns about the ability of COVID-19 vaccination programs to establish adequate herd immunity levels in the population. This study assessed the effectiveness of adapted vaccines in preventing SARS-CoV-2 infection and the ability of the adapted vaccines to establish herd immunity against emerging Omicron variants. A systematic literature review was conducted to estimate the absolute vaccine effectiveness (aVE) in preventing SARS-CoV-2 infection using adapted vaccines targeting Omicron variants. The ability of the adapted vaccines to establish herd immunity was assessed by taking into account the following factors: aVE, Ro values of SARS-CoV-2 and the use of non-pharmacological interventions (NPIs). This study found meta-analysis-based aVEs in preventing severe disease and SARS-CoV-2 infection of 56-60% and 36-39%, respectively. Adapted vaccines could not establish herd immunity against the Omicron BA.1 and BA.4-5 variants without using non-pharmacological interventions (NPIs). The adapted vaccines could establish herd immunity only by achieving >80% vaccination coverage, using NPIs with greater effectiveness and when 20-30% of individuals were already protected against SARS-CoV-2 in the population. New adapted COVID-19 vaccines with greater effectiveness in preventing SARS-CoV-2 infection must be developed to increase herd immunity levels against emerging SARS-CoV-2 variants in the population.
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Affiliation(s)
- Pedro Plans-RubiΓ³
- Public Health Agency of Catalonia, Department of Health of Catalonia, 08005 Barcelona, Spain;
- Ciber of Epidemiology and Public Health (CIBERESP), 28028 Madrid, Spain
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93
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Gu Y, Shunmuganathan B, Qian X, Gupta R, Tan RSW, Kozma M, Purushotorman K, Murali TM, Tan NYJ, Preiser PR, Lescar J, Nasir H, Somani J, Tambyah PA, Smith KGC, Renia L, Ng LFP, Lye DC, Young BE, MacAry PA. Employment of a high throughput functional assay to define the critical factors that influence vaccine induced cross-variant neutralizing antibodies for SARS-CoV-2. Sci Rep 2023; 13:21810. [PMID: 38071323 PMCID: PMC10710454 DOI: 10.1038/s41598-023-49231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The scale and duration of neutralizing antibody responses targeting SARS-CoV-2 viral variants represents a critically important serological parameter that predicts protective immunity for COVID-19. In this study, we describe the development and employment of a new functional assay that measures neutralizing antibodies for SARS-CoV-2 and present longitudinal data illustrating the impact of age, sex and comorbidities on the kinetics and strength of vaccine-induced antibody responses for key variants in an Asian volunteer cohort. We also present an accurate quantitation of serological responses for SARS-CoV-2 that exploits a unique set of in-house, recombinant human monoclonal antibodies targeting the viral Spike and nucleocapsid proteins and demonstrate a reduction in neutralizing antibody titres across all groups 6 months post-vaccination. We also observe a marked reduction in the serological binding activity and neutralizing responses targeting recently newly emerged Omicron variants including XBB 1.5 and highlight a significant increase in cross-protective neutralizing antibody responses following a third dose (boost) of vaccine. These data illustrate how key virological factors such as immune escape mutations combined with host demographic factors such as age and sex of the vaccinated individual influence the strength and duration of cross-protective serological immunity for COVID-19.
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Affiliation(s)
- Yue Gu
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore
| | - Bhuvaneshwari Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rashi Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rebecca S W Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mary Kozma
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tanusya M Murali
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nikki Y J Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group (AMR-IRG), Singapore-MIT Alliance in Research and Technology (SMART), Singapore, 138602, Singapore
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Julien Lescar
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Dr, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Haziq Nasir
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Jyoti Somani
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Paul A Tambyah
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Kenneth G C Smith
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - David C Lye
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Barnaby E Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Paul A MacAry
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore.
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94
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GΓ³mez-Gonzales W, Chihuantito-Abal LA, Gamarra-Bustillos C, MorΓ³n-Valenzuela J, Zavaleta-Oliver J, Gomez-Livias M, Vargas-Pancorbo L, Auqui-Canchari ME, MejΓa-Zambrano H. Risk Factors Contributing to Reinfection by SARS-CoV-2: A Systematic Review. Adv Respir Med 2023; 91:560-570. [PMID: 38131876 PMCID: PMC10740414 DOI: 10.3390/arm91060041] [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: 11/04/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
This article aims to systematize the evidence regarding risk factors associated with COVID-19 reinfection. We conducted a systematic review of all the scientific publications available until August 2022. To ensure the inclusion of the most recent and relevant information, we searched the PubMed and Scopus databases. Thirty studies were reviewed, with a significant proportion being analytical observational case-control and cohort studies. Upon qualitative analysis of the available evidence, it appears that the probability of reinfection is higher for individuals who are not fully immunized when exposed to a new variant, females, those with pre-existing chronic diseases, individuals aged over 60, and those who have previously experienced severe symptoms of the disease or are immunocompromised. In conclusion, further analytical observational case-control studies are necessary to gain a better understanding of the risk factors associated with SARS-CoV-2 (COVID-19) reinfection.
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Affiliation(s)
- Walter GΓ³mez-Gonzales
- Escuela de Medicina, Filial Ica, Universidad Privada San Juan Bautista, Ica 11001, Peru;
| | | | | | | | - Jenny Zavaleta-Oliver
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Peru; (J.Z.-O.); (H.M.-Z.)
| | - Maria Gomez-Livias
- Escuela de Medicina, Universidad Norbert Wiener, Lima 15046, Peru; (C.G.-B.); (M.G.-L.)
| | | | | | - Henry MejΓa-Zambrano
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Peru; (J.Z.-O.); (H.M.-Z.)
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95
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Khan K, Lustig G, RΓΆmer C, Reedoy K, Jule Z, Karim F, Ganga Y, Bernstein M, Baig Z, Jackson L, Mahlangu B, Mnguni A, Nzimande A, Stock N, Kekana D, Ntozini B, van Deventer C, Marshall T, Manickchund N, Gosnell BI, Lessells RJ, Karim QA, Abdool Karim SS, Moosa MYS, de Oliveira T, von Gottberg A, Wolter N, Neher RA, Sigal A. Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant. Nat Commun 2023; 14:8078. [PMID: 38057313 PMCID: PMC10700484 DOI: 10.1038/s41467-023-43703-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties in cell culture. We found that BA.2.86 does not have significantly more escape relative to Omicron XBB.1.5 from neutralizing immunity elicited by either Omicron XBB-family subvariant infection or from residual neutralizing immunity of recently collected sera from the South African population. BA.2.86 does have extensive escape relative to ancestral virus with the D614G substitution (B.1 lineage) when neutralized by sera from pre-Omicron vaccinated individuals and relative to Omicron BA.1 when neutralized by sera from Omicron BA.1 infected individuals. BA.2.86 and XBB.1.5 show similar viral infection dynamics in the VeroE6-TMPRSS2 and H1299-ACE2 cell lines. We also investigate the relationship of BA.2.86 to BA.2 sequences. The closest BA.2 sequences are BA.2 samples from Southern Africa circulating in early 2022. Similarly, many basal BA.2.86 sequences were sampled in Southern Africa. This suggests that BA.2.86 potentially evolved in this region, and that unobserved evolution led to escape from neutralizing antibodies similar in scale to recently circulating strains of SARS-CoV-2.
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Affiliation(s)
- Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Cornelius RΓΆmer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | | | - Zainab Baig
- Africa Health Research Institute, Durban, South Africa
| | | | - Boitshoko Mahlangu
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anele Mnguni
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ayanda Nzimande
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nadine Stock
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Dikeledi Kekana
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Buhle Ntozini
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | | | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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96
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Tong MZW, Sng JDJ, Carney M, Cooper L, Brown S, Lineburg KE, Chew KY, Collins N, Ignacio K, Airey M, Burr L, Joyce BA, Jayasinghe D, McMillan CLD, Muller DA, Adhikari A, Gallo LA, Dorey ES, Barrett HL, Gras S, Smith C, GoodβJacobson K, Short KR. Elevated BMI reduces the humoral response to SARS-CoV-2 infection. Clin Transl Immunology 2023; 12:e1476. [PMID: 38050635 PMCID: PMC10693902 DOI: 10.1002/cti2.1476] [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: 09/17/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Objective Class III obesity (body mass index [BMI] β₯β40 kg m-2) significantly impairs the immune response to SARS-CoV-2 vaccination. However, the effect of an elevated BMI (β₯β25 kg m-2) on humoral immunity to SARS-CoV-2 infection and COVID-19 vaccination remains unclear. Methods We collected blood samples from people who recovered from SARS-CoV-2 infection approximately 3 and 13 months of post-infection (noting that these individuals were not exposed to SARS-CoV-2 or vaccinated in the interim). We also collected blood samples from people approximately 5 months of post-second dose COVID-19 vaccination (the majority of whom did not have a prior SARS-CoV-2 infection). We measured their humoral responses to SARS-CoV-2, grouping individuals based on a BMI greater or less than 25 kg m-2. Results Here, we show that an increased BMI (β₯β25 kg m-2), when accounting for age and sex differences, is associated with reduced antibody responses after SARS-CoV-2 infection. At 3 months of post-infection, an elevated BMI was associated with reduced antibody titres. At 13 months of post-infection, an elevated BMI was associated with reduced antibody avidity and a reduced percentage of spike-positive B cells. In contrast, no significant association was noted between a BMI β₯β25 kg m-2 and humoral immunity to SARS-CoV-2 at 5 months of post-secondary vaccination. Conclusions Taken together, these data showed that elevated BMI is associated with an impaired humoral immune response to SARS-CoV-2 infection. The impairment of infection-induced immunity in individuals with a BMI β₯β25 kg m-2 suggests an added impetus for vaccination rather than relying on infection-induced immunity.
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Affiliation(s)
- Marcus ZW Tong
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Julian DJ Sng
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Meagan Carney
- School of Mathematics and PhysicsThe University of QueenslandSt LuciaQLDAustralia
| | - Lucy Cooper
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
- Immunity Program, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Samuel Brown
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Katie E Lineburg
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation ProgramQIMR Berghofer Medical Research InstituteHerstonQLDAustralia
| | - Keng Yih Chew
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Neve Collins
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Kirsten Ignacio
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Megan Airey
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Lucy Burr
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation ProgramQIMR Berghofer Medical Research InstituteHerstonQLDAustralia
- Department of Respiratory MedicineMater HealthBrisbaneQLDAustralia
| | - Briony A Joyce
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Dhilshan Jayasinghe
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
- Department of Biochemistry and ChemistryLa Trobe Institute for Molecular Science, La Trobe UniversityBundooraVICAustralia
| | - Christopher LD McMillan
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt LuciaQLDAustralia
| | - David A Muller
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt LuciaQLDAustralia
| | - Anurag Adhikari
- Department of Biochemistry and ChemistryLa Trobe Institute for Molecular Science, La Trobe UniversityBundooraVICAustralia
| | - Linda A Gallo
- School of HealthUniversity of the Sunshine CoastPetrieQLDAustralia
| | - Emily S Dorey
- Mater ResearchThe University of QueenslandSouth BrisbaneQLDAustralia
| | - Helen L Barrett
- Mater ResearchThe University of QueenslandSouth BrisbaneQLDAustralia
- University of New South Wales MedicineKensingtonNSWAustralia
- Obstetric MedicineRoyal Hospital for WomenRandwickNSWAustralia
| | - Stephanie Gras
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
- Department of Biochemistry and ChemistryLa Trobe Institute for Molecular Science, La Trobe UniversityBundooraVICAustralia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation ProgramQIMR Berghofer Medical Research InstituteHerstonQLDAustralia
| | - Kim GoodβJacobson
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
- Immunity Program, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Kirsty R Short
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLDAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt LuciaQLDAustralia
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97
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Wang L, Liu T, Yue H, Zhang J, Sheng Q, Wu L, Wang X, Zhang M, Wang J, Wang J, Yu W. Clinical characteristics and high risk factors of patients with Omicron variant strain infection in Hebei, China. Front Cell Infect Microbiol 2023; 13:1294904. [PMID: 38145047 PMCID: PMC10744887 DOI: 10.3389/fcimb.2023.1294904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Objective The Omicron variant has a weaker pathogenicity compared to the Delta variant but is highly transmissible and elderly critically ill patients account for the majority. This study has significant implications for guiding clinical personalized treatment and effectively utilizing healthcare resources. Methods The study focuses on 157 patients infected with the novel coronavirus Omicron variant, from December, 2022, to February, 2023. The objective is to analyze the baseline data, test results, imaging findings and identify risk factors associated with severe illness. Results Among the 157 included patients, there were 55 cases in the non-severe group (all were moderate cases) and 102 cases in the severe group (including severe and critical cases). Infection with the Omicron variant exhibits significant differences between non-severe and severe cases (baseline data, blood routine, coagulation, inflammatory markers, cardiac, liver, kidney functions, Chest CT, VTE score, etc.). A multifactorial logistic regression analysis showed that neutrophil percentage >75%, eosinophil percentage <0.4%, D-dimer >0.55 mg/L, PCT >0.25 ng/mL, LDH >250 U/L, albumin <40 g/L, A/G ratio <1.2, cholinesterase<5100 U/L, uric acid >357 mole/L and blood calcium<2.11 mmol/L were the most likely independent risk factors for severe novel coronavirus infection. Conclusion Advanced age, low oxygenation index, elevated neutrophil percentage, decreased eosinophil percentage, elevated PCT, elevated LDH, decreased albumin, decreased A/G ratio, elevated uric acid, decreased blood calcium, and elevated D-dimer are independent prognostic risk factors for non-severe patients progressing to severe illness. These factors should be closely monitored and actively treated to prevent or minimize the occurrence of severe illness.
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Affiliation(s)
- Lihong Wang
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ting Liu
- Department of Endoscopy Center, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hongjuan Yue
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jiaojiao Zhang
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qihong Sheng
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ling Wu
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaoyu Wang
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Mei Zhang
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jing Wang
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jia Wang
- Department of Infectious Diseases, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Weifang Yu
- Department of Endoscopy Center, The First Hospital of Hebei Medical University, Shijiazhuang, China
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98
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Kowalski EN, Wang X, Patel NJ, Kawano Y, Cook CE, Vanni KMM, Qian G, Bade KJ, Srivatsan S, Williams ZK, Wallace ZS, Sparks JA. Risk factors and outcomes for repeat COVID-19 infection among patients with systemic autoimmune rheumatic diseases: A case-control study. Semin Arthritis Rheum 2023; 63:152286. [PMID: 37913612 PMCID: PMC10842150 DOI: 10.1016/j.semarthrit.2023.152286] [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: 08/02/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
OBJECTIVE To investigate risk factors and outcomes of repeat COVID-19 infections among patients with systemic autoimmune rheumatic diseases (SARDs). METHODS We performed a case-control study investigating repeat COVID-19 infection within the Mass General Brigham Health Care System. We systematically identified all SARD patients with confirmed COVID-19 (15/Mar/2020 to 17/Oct/2022). Cases had confirmed repeat COVID-19 infections >60 days apart (index date: repeat COVID-19 date). Controls were matched to cases (up to 3:1) by calendar date of first infection and duration between first COVID-19 infection and index dates. We collected demographics, lifestyle, comorbidities, SARD features, and COVID-19 characteristics at initial infection and index date by medical record review. We used conditional logistic regression to identify associations with repeat COVID-19 infection, adjusting for potential confounders. We described the severity of repeat COVID-19 infection among cases. RESULTS Among 2203 SARD patients with COVID-19, we identified 76 cases with repeat COVID-19 infection (80.3Β % female) and matched to 207 matched controls (77.8Β % female) with no repeat infection. At first infection, cases were younger (mean 49.5 vs. 60.3 years, pΒ <Β 0.0001), less likely to have hypertension (32.9Β % vs. 45.9Β %, pΒ =Β 0.050), and less likely to have been hospitalized for COVID-19 (13.2Β % vs. 24.6Β %, pΒ =Β 0.037) than controls. At index date, cases were more likely than controls to be rituximab users (18.4Β % vs. 6.3Β %, pΒ =Β 0.0021). In the multivariable model, younger age (OR 0.67 per 10 years, 95Β %CI 0.54-0.82), rituximab use vs. non-use (OR 3.38, 95Β %CI 1.26-9.08), and methotrexate use vs. non-use (OR 2.24, 95Β %CI 1.08-4.61) were each associated with repeat COVID-19 infection. Among those with repeat COVID-19 infection, 5/76 (6.6Β %) were hospitalized and there were no deaths. CONCLUSION Younger age, rituximab, and methotrexate were each associated with repeat COVID-19 infection risk among patients with SARDs. Reassuringly, there were no deaths, and the hospitalization rate was low among those with repeat COVID-19 infection.
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Affiliation(s)
- Emily N Kowalski
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Xiaosong Wang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Naomi J Patel
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Rheumatology Associates, 55 Fruit Street, Boston, MA, 02114, USA; Harvard Medical School, Boston, MA, USA
| | - Yumeko Kawano
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, USA
| | - Claire E Cook
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Rheumatology Associates, 55 Fruit Street, Boston, MA, 02114, USA; Rheumatology and Allergy Clinical Epidemiology Research Center, Mongan Institute, Department of Medicine, Massachusetts General Hospital, 100 Cambridge Street, Suite 1600, Boston, MA, 02114, USA
| | - Kathleen M M Vanni
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Grace Qian
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Katarina J Bade
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Shruthi Srivatsan
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Rheumatology Associates, 55 Fruit Street, Boston, MA, 02114, USA; Rheumatology and Allergy Clinical Epidemiology Research Center, Mongan Institute, Department of Medicine, Massachusetts General Hospital, 100 Cambridge Street, Suite 1600, Boston, MA, 02114, USA
| | - Zachary K Williams
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Rheumatology Associates, 55 Fruit Street, Boston, MA, 02114, USA; Rheumatology and Allergy Clinical Epidemiology Research Center, Mongan Institute, Department of Medicine, Massachusetts General Hospital, 100 Cambridge Street, Suite 1600, Boston, MA, 02114, USA
| | - Zachary S Wallace
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Rheumatology Associates, 55 Fruit Street, Boston, MA, 02114, USA; Harvard Medical School, Boston, MA, USA; Rheumatology and Allergy Clinical Epidemiology Research Center, Mongan Institute, Department of Medicine, Massachusetts General Hospital, 100 Cambridge Street, Suite 1600, Boston, MA, 02114, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, USA.
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99
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Zhang Y, Zhao Y, Liang H, Xu Y, Zhou C, Yao Y, Wang H, Yang X. Innovation-driven trend shaping COVID-19 vaccine development in China. Front Med 2023; 17:1096-1116. [PMID: 38102402 DOI: 10.1007/s11684-023-1034-6] [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: 05/22/2023] [Accepted: 09/15/2023] [Indexed: 12/17/2023]
Abstract
Confronted with the Coronavirus disease 2019 (COVID-19) pandemic, China has become an asset in tackling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and mutation, with several innovative platforms, which provides various technical means in this persisting combat. Derived from collaborated researches, vaccines based on the spike protein of SARS-CoV-2 or inactivated whole virus are a cornerstone of the public health response to COVID-19. Herein, we outline representative vaccines in multiple routes, while the merits and plights of the existing vaccine strategies are also summarized. Likewise, new technologies may provide more potent or broader immunity and will contribute to fight against hypermutated SARS-CoV-2 variants. All in all, with the ultimate aim of delivering robust and durable protection that is resilient to emerging infectious disease, alongside the traditional routes, the discovery of innovative approach to developing effective vaccines based on virus properties remains our top priority.
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Affiliation(s)
- Yuntao Zhang
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Yuxiu Zhao
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Hongyang Liang
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Ying Xu
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Chuge Zhou
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Yuzhu Yao
- China National Biotec Group Company Limited, Beijing, 100029, China
| | - Hui Wang
- China National Biotec Group Company Limited, Beijing, 100029, China.
| | - Xiaoming Yang
- China National Biotec Group Company Limited, Beijing, 100029, China.
- National Engineering Technology Research Center of Combined Vaccines, Wuhan, 430207, China.
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Li J, Liu Y, Wei X, Liu Z, Yang Z, Liu L, Zhou M, Xu G, Chen L, Ding Y, Lei H, Yang Z, Chen S, Zhang X, Tang Y, Fu H, He S, Guo B, Liang X, Zhang L, Zhang W, Wu J, Wang C, Hu C, Hu R, Luo X, Quan X, Zeng C, Liang S, Liu T, Lv J, Luo Q, Qi Q, Xu L, Xiong Y, Liu J, Huang D, Xiao C, Liu J, Yang T, Xiang Y, Li Q, Nan Y, Li J, Zhang Y, Wu Y, Liu Y. Antibody responses to SARS-CoV-2 Omicron infection in patients with hematological malignancies: A multicenter, prospective cohort study. J Med Virol 2023; 95:e29300. [PMID: 38063070 DOI: 10.1002/jmv.29300] [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: 08/13/2023] [Revised: 10/15/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023]
Abstract
Little is known about antibody responses to natural Omicron infection and the risk factors for poor responders in patients with hematological malignancies (HM). We conducted a multicenter, prospective cohort study during the latest Omicron wave in Chongqing, China, aiming to compare the antibody responses, as assessed by IgG levels of anti-receptor binding domain of spike protein (anti-S-RBD), to Omicron infection in the HM cohort (HMC) with healthy control cohort (HCC), and solid cancer cohort (SCC). In addition, we intend to explore the risk factors for poor responders in the HMC. Among the 466 HM patients in this cohort, the seroconversion rate was 92.7%, no statistically difference compared with HCC (98.2%, pβ=β0.0513) or SCC (100%, pβ=β0.1363). The median anti-S-RBD IgG titer was 29.9βng/mL, significantly lower than that of HCC (46.9βng/mL, pβ<β0.0001) or SCC (46.2βng/mL, pβ<β0.0001). Risk factors associated with nonseroconversion included no COVID-19 vaccination history (odds ratio [OR]β=β4.58, 95% confidence interval [CI]: 1.75-12.00, pβ=β0.002), clinical course of COVID-19ββ€β7 days (ORβ=β2.86, 95% CI: 1.31-6.25, pβ=β0.008) and severe B-cell reduction (0-10/ΞΌL) (ORβ=β3.22, 95% CI: 1.32-7.88, pβ=β0.010). Risk factors associated with low anti-S-RBD IgG titer were clinical course of COVID-19ββ€β7 days (ORβ=β2.58, 95% CI: 1.59-4.18, pβ<β0.001) and severe B-cell reduction (0-10/ΞΌL) (ORβ=β2.87, 95% CI: 1.57-5.24, pβ<β0.001). This study reveals a poor antibody responses to Omicron (BA.5.2.48) infection in HM patients and identified risk factors for poor responders. Highlights that HM patients, especially those with these risk factors, may be susceptible to SARS-CoV-2 reinfection, and the postinfection vaccination strategies for these patients should be tailored. Clinical trial: ChiCTR2300071830.
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Affiliation(s)
- Jun Li
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yi Liu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Xia Wei
- Department of Hematology, the Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhanshu Liu
- Department of Hematology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Zailiang Yang
- Department of Hematology and Medical Oncology, Chongqing University Fuling Hospital, Chongqing, China
| | - Ling Liu
- Department of Medical Laboratory, People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Meiyu Zhou
- Department of Hematology and Medical Oncology, Chongqing University Fuling Hospital, Chongqing, China
| | - Guofa Xu
- Department of Hematology and Medical Oncology, Chongqing University Fuling Hospital, Chongqing, China
| | - Lanting Chen
- Department of Hematology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yao Ding
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Haike Lei
- Department of Chongqing Cancer Multi-omics Big Data Application Engineering Research Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Zailin Yang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Shuang Chen
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiaomei Zhang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yifeng Tang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Huihui Fu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Sanxiu He
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Bingling Guo
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiping Liang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Lingqian Zhang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Wenjun Zhang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jing Wu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Chaoyu Wang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Chongling Hu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Renzhi Hu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Xin Luo
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Xi Quan
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Chensi Zeng
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Shunsi Liang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Tingting Liu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jing Lv
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Qin Luo
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Qin Qi
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Luxiang Xu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yan Xiong
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jueyin Liu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Dehong Huang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Chunyan Xiao
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jun Liu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Tao Yang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Ying Xiang
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Qiying Li
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yingyu Nan
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jieping Li
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yong Zhang
- Department of Hematology, the Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongzhong Wu
- Department of Radiation Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yao Liu
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
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