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Liu S, Anzai A, Nishiura H. Assessing exit screening of SARS-CoV-2 in Japan: an analysis of the airport screening data of passengers from the United Kingdom, 2020-2022. BMC Infect Dis 2024; 24:962. [PMID: 39267012 PMCID: PMC11395470 DOI: 10.1186/s12879-024-09894-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: 12/05/2023] [Accepted: 09/06/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Japan implemented strict border control measures and all incoming passengers were subject to entry screening with reverse transcription-polymerase chain reaction or antigen testing. From late 2020, exit screening within 72 h of departure to Japan also became mandatory. In this study, we evaluated the effectiveness of the exit screening policy in Japan by analyzing airport screening data from October 2020 to April 2022. METHODS In addition to assessing entry screening data over time of passengers from the United Kingdom, we examined the prevalence of coronavirus disease 2019 (COVID-19) in the United Kingdom based on the Office of National Statistics infection survey. We constructed a statistical model that described entry screening positivity over time using Office of National Statistics prevalence data as the explanatory variable. Ideally, the time-dependent patterns of entry screening and Office of National Statistics prevalence data should resemble each other; however, we found that, sometimes, they were different and regarded the difference to statistically partly reflect the effectiveness of exit screening. RESULTS The average proportion positive in one month before mandatory exit screening was implemented among Japanese passengers was 0.67% (95% confidence interval [CI]: 0.45, 0.98), whereas the proportion positive decreased to 0.49% (95% CI: 0.21, 1.15) in the first month of exit screening. Adjusting for time-dependent prevalence at the origin, we concluded that exit screening contributed to reducing passenger positivity by 59.3% (95% CI: 19.6, 81.3). The overall positivity values among passengers during the Delta and Omicron variant periods were 3.46 times and 1.46 times that during the pre-Delta variant period, respectively. CONCLUSIONS We used a simplistic statistical model and empirical data from passengers arriving in Japan from the United Kingdom to support that exit screening helped to reduce the proportion positive by 59%. Although the proportion positive later increased considerably and precluded preventing the introduction of imported cases, submitting a certificate for a negative test result contributed to reducing the positivity among travelers.
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Affiliation(s)
- Shiqi Liu
- Kyoto University School of Public Health, Yoshidakonoecho, Sakyo-ku, Kyoto, Japan
| | - Asami Anzai
- Kyoto University School of Public Health, Yoshidakonoecho, Sakyo-ku, Kyoto, Japan
| | - Hiroshi Nishiura
- Kyoto University School of Public Health, Yoshidakonoecho, Sakyo-ku, Kyoto, Japan.
- Center for Health Security, Kyoto University Graduate School of Medicine, Yoshidakonoecho, Sakyo-ku, Kyoto, Japan.
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Wagner C, Kistler KE, Perchetti GA, Baker N, Frisbie LA, Torres LM, Aragona F, Yun C, Figgins M, Greninger AL, Cox A, Oltean HN, Roychoudhury P, Bedford T. Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution. Nat Commun 2024; 15:3207. [PMID: 38615031 PMCID: PMC11016114 DOI: 10.1038/s41467-024-47599-5] [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: 09/27/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024] Open
Abstract
Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones. Indeed, ORF8 is truncated more frequently and knockouts circulate for longer than for any other gene. Using a global phylogeny, we find evidence of positive selection to explain this phenomenon: nonsense mutations resulting in shortened protein products occur more frequently and are associated with faster clade growth rates than synonymous mutations in ORF8. Loss of ORF8 is also associated with reduced clinical severity, highlighting the diverse clinical impacts of SARS-CoV-2 evolution.
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Affiliation(s)
- Cassia Wagner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Kathryn E Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Noah Baker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Frank Aragona
- Washington State Department of Health, Shoreline, WA, USA
| | - Cory Yun
- Washington State Department of Health, Shoreline, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alex Cox
- Washington State Department of Health, Shoreline, WA, USA
| | - Hanna N Oltean
- Washington State Department of Health, Shoreline, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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3
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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] [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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Kawamura H, Arimura S, Saida R, Murata N, Shigemi A, Kodama Y, Nakamura M, Obama Y, Fukuyama R, Hamada Y, Shinkawa N, Sunagawa T, Kamiya H, Nishi J. Enhanced measures, including PCR-based screening and syndromic surveillance for nosocomial outbreaks of the COVID-19 Omicron variant, using descriptive epidemiology and whole-genome sequencing in a Japanese tertiary care hospital. J Infect Chemother 2024; 30:104-110. [PMID: 37717606 DOI: 10.1016/j.jiac.2023.09.015] [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: 06/22/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
INTRODUCTION In this study, we aimed to analyze the effectiveness of enhanced preventive measures against nosocomial COVID-19 Omicron outbreaks based on those encountered. METHODS We introduced PCR-based screening and syndromic surveillance, in addition to standard and transmission-based precautions, during a COVID-19 outbreak in three wards of Kagoshima University Hospital, a Japanese tertiary care hospital, in February 2022, amid the Omicron variant endemic. Furthermore, we analyzed the descriptive epidemiology and whole-genome sequencing (WGS) of positive SARS-CoV-2 PCR samples from this outbreak. RESULTS PCR-based screening tests were conducted following the identification of three cases through syndromic surveillance. As a result, 30 individuals tested positive for SARS-CoV-2, including 13 inpatients, five attendant family members, and 12 healthcare workers across the three wards. Notably, no new infections were observed within eight days following the implementation of preventive measures. Among the SARS-CoV-2 genomes analyzed (n = 16; 53.3%), all strains were identified as belonged to BA.1.1 variant. Detailed analysis of descriptive and molecular epidemiology, incorporating single-nucleotide polymorphism analysis of WGS and clarification of transmission links, considering two potential entry routes to the hospital. CONCLUSIONS Introduction of additional preventive measures, including PCR-based screening and syndromic surveillance, in addition to WGS and descriptive epidemiology, is useful for the early intervention of nosocomial outbreaks and for revealing the transmission route of the COVID-19 Omicron variant.
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Affiliation(s)
- Hideki Kawamura
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan.
| | - Shoko Arimura
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Ryuichi Saida
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Nao Murata
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Akari Shigemi
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Yuichi Kodama
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Masatoshi Nakamura
- Clinical Laboratory, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Yuki Obama
- Clinical Laboratory, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Ryuko Fukuyama
- Clinical Laboratory, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Yuka Hamada
- Kagoshima Prefectural Institute for Environmental Research and Public Health, 11-40 Kinko-cho, Kagoshima, 892-0835, Japan
| | - Naomi Shinkawa
- Kagoshima Prefectural Institute for Environmental Research and Public Health, 11-40 Kinko-cho, Kagoshima, 892-0835, Japan
| | - Tomimasa Sunagawa
- Center for Field Epidemiology Intelligence, Research, and Professional Development, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Hajime Kamiya
- Center for Surveillance, Immunization and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Junichiro Nishi
- Department of Infection Control and Prevention, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
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5
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Taboada BI, Zárate S, García-López R, Muñoz-Medina JE, Gómez-Gil B, Herrera-Estrella A, Sanchez-Flores A, Salas-Lais AG, Roche B, Martínez-Morales G, Domínguez Zárate H, Duque Molina C, Avilés Hernández R, López S, Arias CF. SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico. Microb Genom 2023; 9:001120. [PMID: 38112714 PMCID: PMC10763511 DOI: 10.1099/mgen.0.001120] [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: 10/09/2023] [Indexed: 12/21/2023] Open
Abstract
In Mexico, the BA.4 and BA.5 Omicron variants dominated the fifth epidemic wave (summer 2022), superseding BA.2, which had circulated during the inter-wave period. The present study uses genome sequencing and statistical and phylogenetic analyses to examine these variants' abundance, distribution, and genetic diversity in Mexico from April to August 2022. Over 35 % of the sequenced genomes in this period corresponded to the BA.2 variant, 8 % to the BA.4 and 56 % to the BA.5 variant. Multiple subvariants were identified, but the most abundant, BA.2.9, BA.2.12.1, BA.5.1, BA.5.2, BA.5.2.1 and BA.4.1, circulated across the entire country, not forming geographical clusters. Contrastingly, other subvariants exhibited a geographically restricted distribution, most notably in the Southeast region, which showed a distinct subvariant dynamic. This study supports previous results showing that this region may be a significant entry point and contributed to introducing and evolving novel variants in Mexico. Furthermore, a differential distribution was observed for certain subvariants among specific States through time, which may have contributed to the overall increased diversity observed during this wave compared to the previous ones. This study highlights the importance of sustaining genomic surveillance to identify novel variants that may impact public health.
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Affiliation(s)
- Blanca Itzelt Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlan 82100, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato 36824, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
| | - Benjamin Roche
- Infectious Diseases: Vector, Control, Genetic, Ecology and Evolution (MIVEGEC) Université de Montpellier, IRD, CNRS, 34090 Montpellier, France
| | - Gabriela Martínez-Morales
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
| | - Hermilo Domínguez Zárate
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Célida Duque Molina
- Dirección de Prestaciones Médicas, Instituto Mexicano del Seguro Social, Ciudad de México 06700, Mexico
| | - Ricardo Avilés Hernández
- Unidad de Planeación e Innovación en Salud, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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Chapman LAC, Aubry M, Maset N, Russell TW, Knock ES, Lees JA, Mallet HP, Cao-Lormeau VM, Kucharski AJ. Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia. Nat Commun 2023; 14:7330. [PMID: 37957160 PMCID: PMC10643399 DOI: 10.1038/s41467-023-43002-x] [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: 03/29/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Estimating the impact of vaccination and non-pharmaceutical interventions on COVID-19 incidence is complicated by several factors, including successive emergence of SARS-CoV-2 variants of concern and changing population immunity from vaccination and infection. We develop an age-structured multi-strain COVID-19 transmission model and inference framework to estimate vaccination and non-pharmaceutical intervention impact accounting for these factors. We apply this framework to COVID-19 waves in French Polynesia and estimate that the vaccination programme averted 34.8% (95% credible interval: 34.5-35.2%) of 223,000 symptomatic cases, 49.6% (48.7-50.5%) of 5830 hospitalisations and 64.2% (63.1-65.3%) of 1540 hospital deaths that would have occurred in a scenario without vaccination up to May 2022. We estimate the booster campaign contributed 4.5%, 1.9%, and 0.4% to overall reductions in cases, hospitalisations, and deaths. Our results suggest that removing lockdowns during the first two waves would have had non-linear effects on incidence by altering accumulation of population immunity. Our estimates of vaccination and booster impact differ from those for other countries due to differences in age structure, previous exposure levels and timing of variant introduction relative to vaccination, emphasising the importance of detailed analysis that accounts for these factors.
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Affiliation(s)
- Lloyd A C Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK.
| | - Maite Aubry
- Laboratoire de recherche sur les infections virales émergentes, Institut Louis Malardé, Tahiti, French Polynesia
| | - Noémie Maset
- Cellule Epi-surveillance Plateforme COVID-19, Tahiti, French Polynesia
| | - Timothy W Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Edward S Knock
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Cambridgeshire, UK
| | | | - Van-Mai Cao-Lormeau
- Laboratoire de recherche sur les infections virales émergentes, Institut Louis Malardé, Tahiti, French Polynesia
| | - Adam J Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Laboratoire de recherche sur les infections virales émergentes, Institut Louis Malardé, Tahiti, French Polynesia
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7
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Shikha S, Jogi MK, Jha R, Kumar RA, Sah T, Singh P, Sagar R, Kumar A, Marwal R, Ponnusamy K, Agarwal SM, Kumar RS, Arif N, Bharadwaj M, Singh S, Kumar P. Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein. Front Immunol 2023; 14:1209513. [PMID: 37849762 PMCID: PMC10577267 DOI: 10.3389/fimmu.2023.1209513] [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: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike's mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.
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Affiliation(s)
- Sristy Shikha
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mukesh Kumar Jogi
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Ruchika Jha
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh, Jharkhand, India
| | - Rana Amit Kumar
- Department of Biotechnology, Anugrah Narayan College, Patna, Bihar, India
| | - Tathagat Sah
- Department of Chemical Engineering and Biotechnology, Beant College of Engineering and Technology, Gurdaspur, Punjab, India
| | - Pushpendra Singh
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Ritu Sagar
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Anuj Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control, Delhi, India
| | | | - Subhash Mohan Agarwal
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - R. Suresh Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Nazneen Arif
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mausumi Bharadwaj
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Shalini Singh
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Pramod Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
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8
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Xu X, Wu Y, Kummer AG, Zhao Y, Hu Z, Wang Y, Liu H, Ajelli M, Yu H. Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis. BMC Med 2023; 21:374. [PMID: 37775772 PMCID: PMC10541713 DOI: 10.1186/s12916-023-03070-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND After the first COVID-19 wave caused by the ancestral lineage, the pandemic has been fueled from the continuous emergence of new SARS-CoV-2 variants. Understanding key time-to-event periods for each emerging variant of concern is critical as it can provide insights into the future trajectory of the virus and help inform outbreak preparedness and response planning. Here, we aim to examine how the incubation period, serial interval, and generation time have changed from the ancestral SARS-CoV-2 lineage to different variants of concern. METHODS We conducted a systematic review and meta-analysis that synthesized the estimates of incubation period, serial interval, and generation time (both realized and intrinsic) for the ancestral lineage, Alpha, Beta, and Omicron variants of SARS-CoV-2. RESULTS Our study included 280 records obtained from 147 household studies, contact tracing studies, or studies where epidemiological links were known. With each emerging variant, we found a progressive shortening of each of the analyzed key time-to-event periods, although we did not find statistically significant differences between the Omicron subvariants. We found that Omicron BA.1 had the shortest pooled estimates for the incubation period (3.49 days, 95% CI: 3.13-4.86 days), Omicron BA.5 for the serial interval (2.37 days, 95% CI: 1.71-3.04 days), and Omicron BA.1 for the realized generation time (2.99 days, 95% CI: 2.48-3.49 days). Only one estimate for the intrinsic generation time was available for Omicron subvariants: 6.84 days (95% CrI: 5.72-8.60 days) for Omicron BA.1. The ancestral lineage had the highest pooled estimates for each investigated key time-to-event period. We also observed shorter pooled estimates for the serial interval compared to the incubation period across the virus lineages. When pooling the estimates across different virus lineages, we found considerable heterogeneities (I2 > 80%; I2 refers to the percentage of total variation across studies that is due to heterogeneity rather than chance), possibly resulting from heterogeneities between the different study populations (e.g., deployed interventions, social behavior, demographic characteristics). CONCLUSIONS Our study supports the importance of conducting contact tracing and epidemiological investigations to monitor changes in SARS-CoV-2 transmission patterns. Our findings highlight a progressive shortening of the incubation period, serial interval, and generation time, which can lead to epidemics that spread faster, with larger peak incidence, and harder to control. We also consistently found a shorter serial interval than incubation period, suggesting that a key feature of SARS-CoV-2 is the potential for pre-symptomatic transmission. These observations are instrumental to plan for future COVID-19 waves.
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Affiliation(s)
- Xiangyanyu Xu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yanpeng Wu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Allisandra G Kummer
- Laboratory of Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Yuchen Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zexin Hu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hengcong Liu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Marco Ajelli
- Laboratory of Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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9
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Wang Z, Wu P, Wang L, Li B, Liu Y, Ge Y, Wang R, Wang L, Tan H, Wu CH, Laine M, Salje H, Song H. Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study. PLoS Comput Biol 2023; 19:e1011492. [PMID: 37721947 PMCID: PMC10538769 DOI: 10.1371/journal.pcbi.1011492] [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: 05/23/2023] [Revised: 09/28/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact tracing and isolation, based on 419 million travel movements among 366 Chinese cities. The study period for this model began from September 2022. The COVID-19 disease burden was evaluated, considering 8 types of underlying health conditions in the Chinese population. We identified the marginal effects between the testing speed and reduction in the epidemic duration. The findings suggest that assuming a vaccine coverage of 89%, the Omicron-like wave could be suppressed by 3-day interval population-level testing (PLT), while it would become endemic with 4-day interval PLT, and without testing, it would result in an epidemic. PLT conducted every 3 days would not only eliminate infections but also keep hospital bed occupancy at less than 29.46% (95% CI, 22.73-38.68%) of capacity for respiratory illness and ICU bed occupancy at less than 58.94% (95% CI, 45.70-76.90%) during an outbreak. Furthermore, the underlying health conditions would lead to an extra 2.35 (95% CI, 1.89-2.92) million hospital admissions and 0.16 (95% CI, 0.13-0.2) million ICU admissions. Our study provides insights into health preparedness to balance the disease burden and sustainability for a country with a population of billions.
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Affiliation(s)
- Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Peiyi Wu
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Lin Wang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yonghong Liu
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yuxi Ge
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Ruixue Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Ligui Wang
- Center of Disease Control and Prevention, PLA, Beijing, China
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Marko Laine
- Finnish Meteorological Institute, Meteorological Research Unit, Helsinki, Finland
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Hongbin Song
- Center of Disease Control and Prevention, PLA, Beijing, China
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10
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Bhatia S, Wardle J, Nash RK, Nouvellet P, Cori A. Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study. Epidemics 2023; 44:100692. [PMID: 37399634 PMCID: PMC10284428 DOI: 10.1016/j.epidem.2023.100692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/20/2023] [Accepted: 05/29/2023] [Indexed: 07/05/2023] Open
Abstract
The evolution of SARS-CoV-2 has demonstrated that emerging variants can set back the global COVID-19 response. The ability to rapidly assess the threat of new variants is critical for timely optimisation of control strategies. We present a novel method to estimate the effective transmission advantage of a new variant compared to a reference variant combining information across multiple locations and over time. Through an extensive simulation study designed to mimic real-time epidemic contexts, we show that our method performs well across a range of scenarios and provide guidance on its optimal use and interpretation of results. We also provide an open-source software implementation of our method. The computational speed of our tool enables users to rapidly explore spatial and temporal variations in the estimated transmission advantage. We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44-1.47) and 1.29 (95% CrI 1.29-1.30) times more transmissible than the wild type, using data from England and France respectively. We further estimate that Delta is 1.77 (95% CrI 1.69-1.85) times more transmissible than Alpha (England data). Our approach can be used as an important first step towards quantifying the threat of emerging or co-circulating variants of infectious pathogens in real-time.
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Affiliation(s)
- Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK; NIHR Health Protection Research Unit in Modelling and Health Economics, Modelling & Economics Unit, UK Health Security Agency, London, UK
| | - Jack Wardle
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Rebecca K Nash
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK; School of Life Sciences, University of Sussex, Brighton, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK.
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11
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Arantes I, Bello G, Nascimento V, Souza V, da Silva A, Silva D, Nascimento F, Mejía M, Brandão MJ, Gonçalves L, Silva G, da Costa CF, Abdalla L, Santos JH, Ramos TCA, Piantham C, Ito K, Siqueira MM, Resende PC, Wallau GL, Delatorre E, Gräf T, Naveca FG. Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas. Nat Commun 2023; 14:2048. [PMID: 37041143 PMCID: PMC10089528 DOI: 10.1038/s41467-023-37541-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 04/13/2023] Open
Abstract
The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil's most heavily affected regions. We sequenced the virus genome from 4128 patients collected in Amazonas between July 1st, 2021, and January 31st, 2022, and investigated the viral dynamics using a phylodynamic approach. The VOCs Delta and Omicron BA.1 displayed similar patterns of phylogeographic spread but different epidemic dynamics. The replacement of Gamma by Delta was gradual and occurred without an upsurge of COVID-19 cases, while the rise of Omicron BA.1 was extremely fast and fueled a sharp increase in cases. Thus, the dissemination dynamics and population-level impact of new SARS-CoV-2 variants introduced in the Amazonian population after mid-2021, a setting with high levels of acquired immunity, greatly vary according to their viral phenotype.
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Affiliation(s)
- Ighor Arantes
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Victor Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Arlesson da Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Dejanane Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Matilde Mejía
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Maria Júlia Brandão
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Luciana Gonçalves
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto, Manaus, Brazil
| | - George Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Fundação Centro de Controle de Oncologia do Estado do Amazonas, Manaus, Brazil
| | - Cristiano Fernandes da Costa
- Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto, Manaus, Brazil
- Conselho de Secretários Municipais de Saúde do Amazonas COSEMS - AM, Manaus, Brazil
| | | | | | | | - Chayada Piantham
- Graduate School of Infectious Diseases, Hokkaido University, Hokkaido, Japan
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - 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
| | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil.
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
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12
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Sangsanont J, Rattanakul S, Makkaew P, Precha N, Rukthanapitak P, Sresung M, Siri Y, Kitajima M, Takeda T, Haramoto E, Puenpa J, Wanlapakorn N, Poovorawan Y, Mongkolsuk S, Sirikanchana K. Wastewater monitoring in tourist cities as potential sentinel sites for near real-time dynamics of imported SARS-CoV-2 variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160317. [PMID: 36436629 PMCID: PMC9691270 DOI: 10.1016/j.scitotenv.2022.160317] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) complements the clinical surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants' distribution in populations. Many developed nations have established national and regional WBE systems; however, governance and budget constraints could be obstacles for low- and middle-income countries. An urgent need thus exists to identify hotspots to serve as sentinel sites for WBE. We hypothesized that representative wastewater treatment plants (WWTPs) in two international gateway cities, Bangkok and Phuket, Thailand, could be sentineled for SARS-CoV-2 and its variants to reflect the clinical distribution patterns at city level and serve as early indicators of new variants entering the country. Municipal wastewater samples (n = 132) were collected from eight representative municipal WWTPs in Bangkok and Phuket during 19 sampling events from October 2021 to March 2022, which were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using the US CDC N1 and N2 multiplex and variant (Alpha, Delta, and Omicron BA.1 and BA.2) singleplex assays. The variant detection ratios from Bangkok and Phuket followed similar trends to the national clinical testing data, and each variant's viral loads agreed with the daily new cases (3-d moving average). Omicron BA.1 was detected in Phuket wastewater prior to Bangkok, possibly due to Phuket's WWTPs serving tourist communities. We found that the Omicron BA.1 and BA.2 viral loads predominantly drove the SARS-CoV-2 resurgence. We also noted a shifting pattern in the Bangkok WBE from a 22-d early warning in early 2021 to a near real-time pattern in late 2021. The potential application of tourist hotspots for WBE to indicate the arrival of new variants and re-emerging or unprecedented infectious agents could support tourism-dependent economies by complementing the reduced clinical regulations while maintaining public health protection via wastewater surveillance.
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Affiliation(s)
- Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Pratchaya Rukthanapitak
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, 113-0033, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand.
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13
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Zárate S, Taboada B, Rosales-Rivera M, García-López R, Muñoz-Medina JE, Sanchez-Flores A, Herrera-Estrella A, Gómez-Gil B, Selem Mojica N, Salas-Lais AG, Vazquez-Perez JA, Cabrera-Gaytán DA, Fernandes-Matano L, Uribe-Noguez LA, Chale-Dzul JB, Maldonado Meza BI, Mejía-Nepomuceno F, Pérez-Padilla R, Gutiérrez-Ríos RM, Loza A, Roche B, López S, Arias CF. Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants. Viruses 2023; 15:243. [PMID: 36680283 PMCID: PMC9863047 DOI: 10.3390/v15010243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
PURPOSE The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. METHODS The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread. RESULTS BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed. CONCLUSIONS Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Mauricio Rosales-Rivera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato 36821, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlan 82100, Mexico
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia 58089, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Joel Armando Vazquez-Perez
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - David Alejandro Cabrera-Gaytán
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Larissa Fernandes-Matano
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Luis Antonio Uribe-Noguez
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City, 02990, Mexico
| | - Juan Bautista Chale-Dzul
- Unidad de Investigación Médica Yucatán, Instituto Mexicano del Seguro Social, Merida 97150, Mexico
| | | | - Fidencio Mejía-Nepomuceno
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - Rogelio Pérez-Padilla
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Benjamin Roche
- Infectious Diseases: Vector, Control, Genetic, Ecology and Evolution (MIVEGEC) Université de Montpellier, IRD, CNRS, 34090 Montpellier, France
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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14
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Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol 2023; 95:e28138. [PMID: 36097349 PMCID: PMC9538491 DOI: 10.1002/jmv.28138] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID-19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild-type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.
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Affiliation(s)
- Yongbing Zhou
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huilin Zhi
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Teng
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Mimura W, Ishiguro C, Maeda M, Murata F, Fukuda H. Effectiveness of a Third Dose of COVID-19 mRNA Vaccine During the Omicron BA.1- and BA.2-Predominant Periods in Japan: The VENUS Study. Open Forum Infect Dis 2022; 9:ofac636. [PMID: 36589480 PMCID: PMC9792082 DOI: 10.1093/ofid/ofac636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Vaccine effectiveness against the severe acute respiratory syndrome coronavirus 2 Omicron BA.2 sublineage in Japan is unknown. We assessed the effectiveness of a third dose of COVID-19 mRNA vaccine compared with that of 2 doses. Methods We performed a population-based cohort study using a municipality database located in the Chubu region of Japan during the Omicron BA.1- and BA.2-predominant periods (January 1-March 31, 2022 and April 1-27, 2022, respectively). We included residents aged ≥16 years who received a second vaccine dose at ≥14 days before the start of each period, regardless of the third dose. We compared the data at 14 days after the second and third dose and at 2-week intervals from 14 days to 10 weeks after the third dose using a Cox regression model. Vaccine effectiveness was defined as (1 - hazard ratio) × 100 (%). Results In total, 295 705 and 288 184 individuals were included in the BA.1- and BA.2-predominant periods, respectively. The effectiveness of a third dose against infection was 62.4% and 48.1% in the BA.1- and BA.2-predominant periods, respectively. Vaccine effectiveness at 2-3 weeks and ≥10 weeks after the third dose decreased from 63.6% (95% confidence interval [CI], 56.4-69.5%) to 52.9% (95% CI, 41.1-62.3%) and from 54.5% (95% CI, 3.0-78.7%) to 40.1% (95% CI, 15.1-57.7%) in the BA.1- and BA.2-predominant periods, respectively. Conclusions A third dose was moderately effective against BA.1 and BA.2 sublineages, but its effectiveness decreased by approximately 10% age points from 2-3 weeks to ≥10 weeks after the third vaccination.
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Affiliation(s)
- Wataru Mimura
- Section of Clinical Epidemiology, Department of Data Science, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Chieko Ishiguro
- Correspondence: Chieko Ishiguro, MPH, PhD, Section of Clinical Epidemiology, Department of Data Science, Center for Clinical Sciences, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan ()
| | - Megumi Maeda
- Department of Health Care Administration and Management, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Fumiko Murata
- Department of Health Care Administration and Management, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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Piantham C, Ito K. Predicting the Trajectory of Replacements of SARS-CoV-2 Variants Using Relative Reproduction Numbers. Viruses 2022; 14:v14112556. [PMID: 36423165 PMCID: PMC9697243 DOI: 10.3390/v14112556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
New variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high effective reproduction numbers are continuously being selected by natural selection. To establish effective control measures for new variants, it is crucial to know their transmissibility and replacement trajectory in advance. In this paper, we conduct retrospective prediction tests for the variant replacement from Alpha to Delta in England, using the relative reproduction numbers of Delta with respect to Alpha estimated from partial observations. We found that once Delta's relative frequency reached 0.15, the date when the relative frequency of Delta would reach 0.90 was predicted with maximum absolute prediction errors of three days. This means that the time course of the variant replacement could be accurately predicted from early observations. Together with the estimated relative reproduction number of a new variant with respect to old variants, the predicted replacement timing will be crucial information for planning control strategies against the new variant.
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Affiliation(s)
- Chayada Piantham
- Graduate School of Infectious Diseases, Hokkaido University, Hokkaido 060-0818, Japan
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido 001-0020, Japan
- Correspondence:
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Jarnig G, Kerbl R, van Poppel MNM. Effects of Wearing FFP2 Masks on SARS-CoV-2 Infection Rates in Classrooms. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13511. [PMID: 36294092 PMCID: PMC9603337 DOI: 10.3390/ijerph192013511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
In this retrospective cohort study involving 614 secondary school students, the likelihood of becoming infected with SARS-CoV-2 in schools with different focus (sports focus vs. general branch; the only difference in the sports focus school was that PE was allowed at all times without restrictions) and different prevailing restrictions were compared. A significantly higher likelihood of infection with SARS-CoV-2 was found in sports classes during the period with a strict FFP-2 mask requirement compared to general branch classes (for Delta from November 2021 to December 2021, and for Omicron from January 2022 to February 2022). The higher likelihood of infection was observed both during the Delta and the Omicron wave. After the relaxation of the mitigation measures, however, students in general branch classes showed a clear "catch-up" of infections, leading to a higher incidence of infections during this phase. By the end of the observation period (30 April 2022), only a small difference in cumulative SARS-CoV-2 infection rates (p = 0.037, φ = 0.09) was detected between classes with a sports focus and those without a sports focus. The results suggest that SARS-CoV-2 transmission can be reduced in school classes by mandatory FFP-2 mask use. In many cases, however, infection appears to be postponed rather than avoided.
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Affiliation(s)
- Gerald Jarnig
- Institute of Human Movement Science, Sport and Health, University of Graz, 8010 Graz, Austria
| | - Reinhold Kerbl
- Department of Pediatrics and Adolescent Medicine, LKH Hochsteiermark, 8700 Leoben, Austria
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Chen SLS, Jen GHH, Hsu CY, Yen AMF, Lai CC, Yeh YP, Chen THH. A new approach to modeling pre-symptomatic incidence and transmission time of imported COVID-19 cases evolving with SARS-CoV-2 variants. STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT : RESEARCH JOURNAL 2022; 37:441-452. [PMID: 36120386 PMCID: PMC9464357 DOI: 10.1007/s00477-022-02305-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
There is paucity of the statistical model that is specified for data on imported COVID-19 cases with the unique global information on infectious properties of SARS-CoV-2 variant different from local outbreak data used for estimating transmission and infectiousness parameters via the established epidemic models. To this end, a new approach with a four-state stochastic model was proposed to formulate these well-established infectious parameters with three new parameters, including the pre-symptomatic incidence rate, the median of pre-symptomatic transmission time (MPTT) to symptomatic state, and the incidence (proportion) of asymptomatic cases using imported COVID-19 data. We fitted the proposed stochastic model to empirical data on imported COVID-19 cases from D614G to Omicron with the corresponding calendar periods according to the classification GISAID information on the evolution of SARS-CoV-2 variant between March 2020 and Jan 2022 in Taiwan. The pre-symptomatic incidence rate was the highest for Omicron followed by Alpha, Delta, and D614G. The MPTT (in days) increased from 3.45 (first period) ~ 4.02 (second period) of D614G until 3.94-4.65 of VOC Alpha but dropped to 3.93-3.49 of Delta and 2 days (only first period) of Omicron. The proportion of asymptomatic cases increased from 29% of D-614G period to 59.2% of Omicron. Modeling data on imported cases across strains of SARS-CoV-2 not only bridges the link between the underlying natural infectious properties elucidated in the previous epidemic models and different disease phenotypes of COVID-19 but also provides precision quarantine and isolation policy for border control in the face of various emerging SRAS-CoV-2 variants globally.
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Affiliation(s)
- Sam Li-Sheng Chen
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Grace Hsiao-Hsuan Jen
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chen-Yang Hsu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Room 533, No. 17, Hsuchow Road, Taipei, 100 Taiwan
| | - Amy Ming-Fang Yen
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chao-Chih Lai
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Room 533, No. 17, Hsuchow Road, Taipei, 100 Taiwan
- Emergency Department of Taipei City Hospital, Ren-Ai Branch, Taipei, Taiwan
| | - Yen-Po Yeh
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Room 533, No. 17, Hsuchow Road, Taipei, 100 Taiwan
- Changhua County Public Health Bureau, Changhua, Taiwan
| | - Tony Hsiu-Hsi Chen
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Room 533, No. 17, Hsuchow Road, Taipei, 100 Taiwan
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