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Arantes I, Gomes M, Ito K, Sarafim S, Gräf T, Miyajima F, Khouri R, de Carvalho FC, de Almeida WAF, Siqueira MM, Resende PC, Naveca FG, Bello G. Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023. Microbiol Spectr 2024; 12:e0383123. [PMID: 38315011 PMCID: PMC10913747 DOI: 10.1128/spectrum.03831-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n = 11,065 sequences) with epidemiological data of severe acute respiratory infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB* + F486P, XBB* + F486P + F456L, and XBB* + F486P + F456L + L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil's epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB* + F486P + F456L + L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead. IMPORTANCE Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.
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Affiliation(s)
- Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marcelo Gomes
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Sharbilla Sarafim
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | | | | | - Felipe Cotrim de Carvalho
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Walquiria Aparecida Ferreira de Almeida
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - COVID-19 Fiocruz Genomic Surveillance Network
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
- Fiocruz, Fortaleza, Brazil
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
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Wang Y, Yao Y, Zhang Q, Chen H, He Y, Hu K. Clinical courses and outcomes of COVID-19 associated pulmonary aspergillosis in 168 patients with the SARS-CoV-2 omicron variant. BMC Infect Dis 2024; 24:117. [PMID: 38263011 PMCID: PMC10804746 DOI: 10.1186/s12879-023-08971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024] Open
Abstract
PURPOSE We aimed to analyze the clinical features of COVID-19-associated pulmonary aspergillosis (CAPA) during the SARS-CoV-2 Omicron variant pandemic and to reveal the risk factors for CAPA and death. METHODS A retrospective cohort study was conducted on 168 CAPA patients from December 8, 2022 to January 31, 2023. 168 COVID-19 patients without secondary fungal infection during this period were matched 1:1 using propensity score matching as controls. RESULTS The incidence of CAPA was 3.8% (168/4421). Compared with patients without fungal infection, CAPA patients had a higher mortality (43.5% vs. 10.1%, P < 0.001). Patients in the death group (n = 73) were more likely to be admitted to ICU (91.8% vs. 26.3%, p < 0.001), had a shorter ICU length of hospitalization (10 (IQR, 6 ~ 16.5) days vs. 14 (IQR, 8 ~ 37) days, p = 0.012). Immunocompromised status (p = 0.023), NLR ≥ 5.7 (p = 0.004), CRP ≥ 50 mg/L (p = 0.043), and the number of antibiotics ≥ 3 (p < 0.001) were all risk factors for CAPA; NLR ≥ 5.7 (p = 0.009) and the number of antibiotics ≥ 3 (p = 0.018) were all independent risk factors for death. CONCLUSIONS During the Omicron variant pandemic, CAPA increased death and ICU length of hospitalization. The risk factors of CAPA and death obtained from the study can help us further understand the disease characteristics of CAPA and better guide our clinical decision-making.
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Affiliation(s)
- Yixuan Wang
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yan Yao
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Qingfeng Zhang
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hao Chen
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ke Hu
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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You R, Wu R, Wang X, Fu R, Xia N, Chen Y, Yang K, Chen J. Systematic Genomic Surveillance of SARS-CoV-2 at Xiamen International Airport and the Port of Xiamen Reveals the Importance of Incoming Travelers in Lineage Diversity. Viruses 2024; 16:132. [PMID: 38257832 PMCID: PMC10821529 DOI: 10.3390/v16010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Sever Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still a threat to human health globally despite the World Health Organization (WHO) announcing the end of the COVID-19 pandemic. Continued surveillance of SARS-CoV-2 at national borders would be helpful in understanding the epidemics of novel imported variants and updating local strategies for disease prevention and treatment. This study focuses on the surveillance of imported SARS-CoV-2 variants among travelers entering Xiamen International Airport and the Port of Xiamen from February to August 2023. A total of 97 imported SARS-CoV-2 sequences among travelers from 223 cases collected from 12 different countries and regions were identified by real-time RT-PCR. Next-generation sequencing was used to generate high-quality complete sequences for phylogenetic and population dynamic analysis. The study revealed a dominant shift in variant distribution, in which the XBB subvariant (XBB.1.5, XBB.1.16, XBB.1.9, XBB.2.3, and EG.5.1) accounted for approximately 88.8% of the sequenced samples. In detail, clades 23D and 23E accounted for 26.2% and 21.4% of the sequenced samples, respectively, while clades 23B (13.6%) and 23F (10.7%) took the third and fourth spots in the order of imported sequences, respectively. Additionally, the XBB.2.3 variants were first identified in imported cases from the mainland of Xiamen, China on 27 February 2023. The spatiotemporal analyses of recent viral genome sequences from a limited number of travelers into Xiamen provide valuable insights into the situation surrounding SARS-CoV-2 and highlight the importance of sentinel surveillance of SARS-CoV-2 variants in the national border screening of incoming travelers, which serves as an early warning system for the presence of highly transmissible circulating SARS-CoV-2 lineages.
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Affiliation(s)
- Ruiluan You
- Xiamen International Travel Healthcare Center, Xiamen Entry-Exit Inspection and Quarantine Bureau, Xiamen 361001, China;
| | - Ruotong Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
| | - Xijing Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
| | - Rao Fu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
| | - Yixin Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
| | - Kunyu Yang
- Xiamen International Travel Healthcare Center, Xiamen Entry-Exit Inspection and Quarantine Bureau, Xiamen 361001, China;
| | - Junyu Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
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Wee LE, Tang N, Pang D, Chiew C, Yung CF, Chong CY, Lee V, Ong B, Lye DC, Tan KB. Effectiveness of Monovalent mRNA Vaccines Against Omicron XBB Infection in Singaporean Children Younger Than 5 Years. JAMA Pediatr 2023; 177:1324-1331. [PMID: 37843856 PMCID: PMC10580153 DOI: 10.1001/jamapediatrics.2023.4505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/22/2023] [Indexed: 10/17/2023]
Abstract
Importance Literature on vaccine effectiveness of SARS-CoV-2 messenger RNA (mRNA) vaccines for children younger than 5 years is limited. Objective To report the effectiveness of monovalent mRNA vaccines against SARS-CoV-2 infection among Singaporean children aged 1 through 4 years during a COVID-19 pandemic wave of the Omicron XBB variant. Design, Setting, and Participants This was a population-based cohort study, conducted over a 6-month study period from October 1, 2022, through March 31, 2023, after the implementation of community vaccination among all Singaporean children aged 1 through 4 years. The study period was dominated by the Omicron XBB subvariant. Exposure Receipt of SARS-CoV-2 mRNA vaccines. Main Outcome Measure Vaccine effectiveness against confirmed SARS-CoV-2 infection. The adjusted incidence rate ratio for confirmed infections using Poisson regression was reported, with the reference group being those who were unvaccinated. Analyses were stratified by prior documented SARS-CoV-2 infection. Results A total of 121 628 children (median [IQR] age, 3.1 [2.2-3.9] years; 61 925 male [50.9%]) were included in the study, contributing 21 015 956 person-days of observation. The majority of children (11 294 of 11 705 [96.5%]) received the mRNA-1273 COVID-19 vaccine (Moderna). Vaccine effectiveness against confirmed infection was 45.2% (95% CI, 24.7%-60.2%) in partially vaccinated, infection-naive children and 63.3% (95% CI, 40.6%-77.3%) in fully vaccinated, infection-naive children compared with the unvaccinated group. Among previously infected children, vaccine effectiveness against reinfections in those with at least 1 vaccine dose was estimated at 74.6% (95% CI, 38.7%-89.5%). Conclusions and Relevance Study results suggest that completion of a primary mRNA vaccine series provided protection against SARS-CoV-2 infection in children aged 1 through 4 years. Although incidence of hospitalization and severe illness is low in this age group, there is potential benefit of vaccination in preventing infection and potential sequelae.
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Affiliation(s)
- Liang En Wee
- National Centre for Infectious Diseases, Singapore
- Duke-NUS Graduate Medical School, National University of Singapore, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | | | | | - Calvin Chiew
- National Centre for Infectious Diseases, Singapore
- Ministry of Health, Singapore
| | - Chee-Fu Yung
- Duke-NUS Graduate Medical School, National University of Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Infectious Disease Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Chia Yin Chong
- Duke-NUS Graduate Medical School, National University of Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Infectious Disease Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vernon Lee
- National Centre for Infectious Diseases, Singapore
- Ministry of Health, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Benjamin Ong
- Ministry of Health, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Kelvin Bryan Tan
- Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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Goh O, Pang D, Tan J, Lye D, Chong CY, Ong B, Tan KB, Yung CF. mRNA SARS-CoV-2 Vaccination Before vs During Pregnancy and Omicron Infection Among Infants. JAMA Netw Open 2023; 6:e2342475. [PMID: 37948079 PMCID: PMC10638647 DOI: 10.1001/jamanetworkopen.2023.42475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023] Open
Abstract
Importance Infants younger than 6 months are at risk of severe SARS-CoV-2 infection. Data are lacking on the optimum timing for maternal vaccination and estimated effectiveness against Omicron variants, including XBB, for infants. Objective To investigate maternal vaccination against Omicron variants, including XBB, and the association of vaccination timing during pregnancy vs prior to pregnancy and risks of SARS-CoV-2 infection among infants aged 6 months or younger. Design, Setting, and Participants This population-based cohort study was conducted between January 1, 2022, and March 31, 2023. Singapore's national dataset was used to study infants born at greater than 32 weeks' gestation between January 1, 2022, and September 30, 2022. The study included infants whose parents had a confirmed SARS-CoV-2 infection from the date of birth up to 6 months of age. Of 21 609 infants born during this period, 7292 (33.7%) had at least 1 parent infected with SARS-CoV-2 before the age of 7 months. Statistical analysis was performed from April to July 2023. Exposure Infants' mothers were unvaccinated, vaccinated prior to pregnancy, or vaccinated with a messenger RNA (mRNA) SARS-CoV-2 vaccine during pregnancy. Main Outcome and Measure Infants were considered infected if they had a positive polymerase chain reaction test. Results Among 7292 infants included in this study, 4522 (62.0%) had mothers who were Chinese, 527 (7.2%) had mothers who were Indian, 2007 (27.5%) had mothers who were Malay, and 236 (3.2%) had mothers who were other ethnicity; 6809 infants (93.4%) were born at full term, and 1272 infants (17.4%) were infected during the study period. There were 7120 infants (97.6%) born to mothers who had been fully vaccinated or boosted as of 14 days prior to delivery. The crude incidence rate was 174.3 per 100 000 person-days among infants born to mothers who were unvaccinated, 122.2 per 100 000 person-days among infants born to mothers who were vaccinated before pregnancy, and 128.5 per 100 000 person-days among infants born to mothers who were vaccinated during pregnancy. The estimated vaccine effectiveness (VE) was 41.5% (95% CI, 22.8% to 55.7%) among infants born to mothers vaccinated during pregnancy. Infants of mothers who received vaccination prior to pregnancy did not have a lower risk for infection (estimated VE, 15.4% [95% CI, -17.6% to 39.1%]). A lower risk for Omicron XBB infection was only observed among mothers vaccinated with the third (booster) dose antenatally (estimated VE, 76.7% [95% CI, 12.8% to 93.8%]). Conclusions and Relevance In this population-based cohort study, maternal mRNA vaccination was associated with a lower risk of Omicron SARS-CoV-2 infection among infants up to 6 months of age only if the vaccine was given during the antenatal period. These findings suggest that mRNA vaccination during pregnancy may be needed for lower risk of SARS-CoV-2 infection among newborns.
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Affiliation(s)
- Orlanda Goh
- Department of Internal Medicine, Singapore General Hospital, Singapore
- SingHealth Duke-NUS Medicine Academic Clinical Programme, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | | | | | - David Lye
- Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National Centre for Infectious Disease, Singapore
| | - Chia Yin Chong
- Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Infectious Disease Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Paediatrics Academic Clinical Programme, Singapore
- Duke-NUS Medical School, Singapore
| | - Benjamin Ong
- Ministry of Health, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kelvin Bryan Tan
- Ministry of Health, Singapore
- Duke-NUS Medical School, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chee Fu Yung
- Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore
- Infectious Disease Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Paediatrics Academic Clinical Programme, Singapore
- Duke-NUS Medical School, Singapore
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Wee LE, Pang D, Chiew C, Tan J, Lee V, Ong B, Lye DC, Tan KB. Long-term Real-world Protection Afforded by Third mRNA Doses Against Symptomatic Severe Acute Respiratory Syndrome Coronavirus 2 Infections, Coronavirus Disease 19-related Emergency Attendances and Hospitalizations Amongst Older Singaporeans During an Omicron XBB Wave. Clin Infect Dis 2023; 77:1111-1119. [PMID: 37280047 DOI: 10.1093/cid/ciad345] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/23/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Literature on long-term real-world vaccine effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) booster vaccines (up to and beyond 360 days) is scarce. We report estimates of protection against symptomatic infection, emergency department (ED) attendances and hospitalizations up to and beyond 360 days post-receipt of booster messenger RNA (mRNA) vaccines among Singaporeans aged ≥60 years during an Omicron XBB wave. METHODS We conducted a population-based cohort study including all Singaporeans aged ≥60 years with no documented prior SARS-CoV-2 infection who had previously received ≥3 doses of mRNA vaccines (BNT162b2/mRNA-1273), over a 4-month period during transmission of Omicron XBB. We reported the adjusted incidence-rate-ratio (IRR) for symptomatic infections, ED attendances and hospitalizations at different time-intervals from both first and second boosters, using Poisson regression; with the reference group being those who received their first booster 90 to 179 days prior. RESULTS In total, 506 856 boosted adults were included, contributing 55 846 165 person-days of observation. Protection against symptomatic infections among those who received a third vaccine dose (first booster) waned after 180 days with increasing adjusted IRRs; however, protection against ED attendances and hospitalizations held up, with comparable adjusted IRRs with increasing time from third vaccine doses (≥360 days from third dose: adjusted IRR [ED attendances] = 0.73, 95% confidence interval [CI] = .62-.85; adjusted IRR [hospitalization] = 0.58, 95% CI = .49-.70). CONCLUSIONS Our results highlight the benefit of a booster dose in reducing ED attendances and hospitalizations amongst older adults aged ≥60 years with no documented prior SARS-CoV-2 infection, during an Omicron XBB wave; up to and beyond 360 days post-booster. A second booster provided further reduction.
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Affiliation(s)
- Liang En Wee
- National Centre for Infectious Diseases, Singapore, Singapore
- Duke-NUS Graduate Medical School, National University of Singapore, Singapore, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | | | - Calvin Chiew
- National Centre for Infectious Diseases, Singapore, Singapore
- Ministry of Health, Singapore, Singapore
| | - Janice Tan
- Ministry of Health, Singapore, Singapore
| | - Vernon Lee
- Ministry of Health, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Benjamin Ong
- Ministry of Health, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kelvin Bryan Tan
- Ministry of Health, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
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Wee LE, Kee T, Thangaraju S, Liew IT, Ho QY, Yong JH, Xia H, Qian YKN, Ng GTE, Abdul Rahman MB, Kay XLJ, Chung SMJ, Wijaya L, Ko KKK, Tan WJM, Tan CS, Tan BH, Tan TT. Clinical Outcomes Among Kidney Transplant Recipients During Omicron XBB Contrasted Against Preceding BA.1, BA.2, and BA.4/5 Pandemic Waves. Transplantation 2023; 107:e277-e278. [PMID: 37389648 DOI: 10.1097/tp.0000000000004716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Affiliation(s)
- Liang En Wee
- Department of Infectious Diseases, Singapore General Hospital, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Terence Kee
- Department of Renal Medicine, Singapore General Hospital, Singapore
- Singhealth Duke-NUS Transplant Centre, Singapore
| | - Sobhana Thangaraju
- Department of Renal Medicine, Singapore General Hospital, Singapore
- Singhealth Duke-NUS Transplant Centre, Singapore
| | - Ian Tatt Liew
- Department of Renal Medicine, Singapore General Hospital, Singapore
- Singhealth Duke-NUS Transplant Centre, Singapore
| | - Quan Yao Ho
- Department of Renal Medicine, Singapore General Hospital, Singapore
- Singhealth Duke-NUS Transplant Centre, Singapore
| | - Jin Hua Yong
- Singhealth Duke-NUS Transplant Centre, Singapore
| | - He Xia
- Singhealth Duke-NUS Transplant Centre, Singapore
| | | | | | | | | | - Shi-Min Jasmine Chung
- Department of Infectious Diseases, Singapore General Hospital, Singapore
- Singhealth Duke-NUS Transplant Centre, Singapore
| | - Limin Wijaya
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Kwan Ki Karrie Ko
- Department of Molecular Pathology, Singapore General Hospital, Singapore
- Department of Microbiology, Singapore General Hospital, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Woei-Jen Michelle Tan
- Department of Family Medicine and Continuing Care, Singapore General Hospital, Singapore
| | - Chieh Suai Tan
- Department of Renal Medicine, Singapore General Hospital, Singapore
| | - Ban Hock Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore
- Singhealth Duke-NUS Transplant Centre, Singapore
| | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore
- Singhealth Duke-NUS Transplant Centre, Singapore
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8
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Affiliation(s)
- Kayoko Shioda
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
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9
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Carr EJ, Wu MY, Gahir J, Harvey R, Townsley H, Bailey C, Fowler AS, Dowgier G, Hobbs A, Herman L, Ragno M, Miah M, Bawumia P, Smith C, Miranda M, Mears HV, Adams L, Haptipoglu E, O'Reilly N, Warchal S, Sawyer C, Ambrose K, Kelly G, Beale R, Papineni P, Corrah T, Gilson R, Gamblin S, Kassiotis G, Libri V, Williams B, Swanton C, Gandhi S, Lv Bauer D, Wall EC. Neutralising immunity to omicron sublineages BQ.1.1, XBB, and XBB.1.5 in healthy adults is boosted by bivalent BA.1-containing mRNA vaccination and previous Omicron infection. Lancet Infect Dis 2023:S1473-3099(23)00289-X. [PMID: 37290472 DOI: 10.1016/s1473-3099(23)00289-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Edward J Carr
- The Francis Crick Institute, London, UK; University College London, London, UK
| | - Mary Y Wu
- COVID Surveillance Unit, London, UK; The Francis Crick Institute, London, UK
| | - Joshua Gahir
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | - Hermaleigh Townsley
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Chris Bailey
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Emine Haptipoglu
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | | | | | | | | | - Rupert Beale
- The Francis Crick Institute, London, UK; University College London, London, UK
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, UK
| | - Richard Gilson
- Central and North West London NHS Foundation Trust, London, UK
| | | | - George Kassiotis
- The Francis Crick Institute, London, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | - Vincenzo Libri
- University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Bryan Williams
- University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London, UK; University College London, London, UK
| | | | - Emma C Wall
- The Francis Crick Institute, London, UK; University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK.
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10
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Karyakarte RP, Das R, Rajmane MV, Dudhate S, Agarasen J, Pillai P, Chandankhede PM, Labhshetwar RS, Gadiyal Y, Kulkarni PP, Nizarudeen S, Joshi S, Karmodiya K, Potdar V. Chasing SARS-CoV-2 XBB.1.16 Recombinant Lineage in India and the Clinical Profile of XBB.1.16 Cases in Maharashtra, India. Cureus 2023; 15:e39816. [PMID: 37397651 PMCID: PMC10314318 DOI: 10.7759/cureus.39816] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
Background SARS-CoV-2 has evolved rapidly, resulting in the emergence of lineages with a competitive advantage over one another. Co-infections with different SARS-CoV-2 lineages can give rise to recombinant lineages. To date, the XBB lineage is the most widespread recombinant lineage worldwide, with the recently named XBB.1.16 lineage causing a surge in the number of COVID-19 cases in India. Methodology The present study involved retrieval of SARS-CoV-2 genome sequences from India (between December 1, 2022 and April 8, 2023) through GISAID; sequences were curated, followed by lineage and phylogenetic analysis. Demographic and clinical data from Maharashtra, India were collected telephonically, recorded in Microsoft® Excel, and analyzed using IBM® SPSS statistics, version 29.0.0.0 (241). Results A total of 2,944 sequences were downloaded from the GISAID database, of which 2,856 were included in the study following data curation. The sequences from India were dominated by the XBB.1.16* lineage (36.17%) followed by XBB.2.3* (12.11%) and XBB.1.5* (10.36%). Of the 2,856 cases, 693 were from Maharashtra; 386 of these were included in the clinical study. The clinical features of COVID-19 cases with XBB.1.16* infection (XBB.1.16* cases, 276 in number) showed that 92% of those had a symptomatic disease, with fever (67%), cough (42%), rhinorrhea (33.7%), body ache (14.5%) and fatigue (14.1%) being the most common symptoms. The presence of comorbidity was found in 17.7% of the XBB.1.16* cases. Among the XBB.1.16* cases, 91.7% were vaccinated with at least one dose of vaccine against COVID-19. While 74.3% of XBB.1.16* cases were home-isolated; 25.7% needed hospitalization/institutional quarantine, of these, 33.8% needed oxygen therapy. Out of 276 XBB.1.16* cases, seven (2.5%) cases succumbed to the disease. The majority of XBB.1.16* cases who died belonged to an elderly age group (60 years and above), had underlying comorbid condition/s, and needed supplemental oxygen therapy. The clinical features of COVID-19 cases infected with other co-circulating Omicron variants were similar to XBB.1.16* cases. Conclusion The study reveals that XBB.1.16* lineage has become the most predominant SARS-CoV-2 lineage in India. The study also shows that the clinical features and outcome of XBB.1.16* cases were similar to those of other co-circulating Omicron lineage infected cases in Maharashtra, India.
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Affiliation(s)
- Rajesh P Karyakarte
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Rashmita Das
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Mansi V Rajmane
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Sonali Dudhate
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Jeanne Agarasen
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Praveena Pillai
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Priyanka M Chandankhede
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Rutika S Labhshetwar
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Yogita Gadiyal
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Preeti P Kulkarni
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Safanah Nizarudeen
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Suvarna Joshi
- Microbiology, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
| | | | - Varsha Potdar
- Infectious Disease, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, IND
- Pediatrics, Byramjee Jeejeebhoy Government Medical College & Sassoon General Hospitals, Pune, IND
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