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Leung K, Lau EHY, Wong CKH, Leung GM, Wu JT. Estimating the transmission dynamics of SARS-CoV-2 Omicron BF.7 in Beijing after adjustment of the zero-COVID policy in November-December 2022. Nat Med 2023; 29:579-582. [PMID: 36638825 DOI: 10.1038/s41591-023-02212-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
We tracked the effective reproduction number (Rt) of the predominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron BF.7 in Beijing in November-December 2022 by fitting a transmission dynamic model parameterized with real-time mobility data to (i) the daily number of new symptomatic cases on 1-11 November (when China's zero-COVID interventions were still strictly enforced) and (ii) the proportion of individuals who participated in online polls on 10-22 December and self-reported to have been test-positive since 1 November. After China's announcement of 20 measures to transition from zero-COVID, we estimated that Rt increased to 3.44 (95% credible interval (CrI): 2.82-4.14) on 18 November and the infection incidence peaked on 11 December. We estimated that the cumulative infection attack rate (IAR; that is, proportion of the population infected since 1 November) in Beijing was 75.7% (95% CrI: 60.7-84.4) on 22 December 2022 and 92.3% (95% CrI: 91.4-93.1) on 31 January 2023. Surveillance programs should be rapidly set up to monitor the evolving epidemiology and evolution of SARS-CoV-2 across China.
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Affiliation(s)
- Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China.
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Carlos K H Wong
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Family Medicine and Primary Care, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
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2
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Axfors C, Pezzullo AM, Contopoulos-Ioannidis DG, Apostolatos A, Ioannidis JPA. Differential COVID-19 infection rates in children, adults, and elderly: Systematic review and meta-analysis of 38 pre-vaccination national seroprevalence studies. J Glob Health 2023; 13:06004. [PMID: 36655924 PMCID: PMC9850866 DOI: 10.7189/jogh.13.06004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background Debate exists about whether extra protection of elderly and other vulnerable individuals is feasible in COVID-19. We aimed to assess the relative infection rates in the elderly vs the non-elderly and, secondarily, in children vs adults. Methods We performed a systematic review and meta-analysis of seroprevalence studies conducted in the pre-vaccination era. We identified representative national studies without high risk of bias through SeroTracker and PubMed searches (last updated May 17, 2022). We noted seroprevalence estimates for children, non-elderly adults, and elderly adults, using cut-offs of 20 and 60 years (or as close to these ages, if they were unavailable) and compared them between different age groups. Results We included 38 national seroprevalence studies from 36 different countries comprising 826 963 participants. Twenty-six of these studies also included pediatric populations and twenty-five were from high-income countries. The median ratio of seroprevalence in elderly vs non-elderly adults (or non-elderly in general, if pediatric and adult population data were not offered separately) was 0.90-0.95 in different analyses, with large variability across studies. In five studies (all in high-income countries), we observed significant protection of the elderly with a ratio of <0.40, with a median of 0.83 in high-income countries and 1.02 elsewhere. The median ratio of seroprevalence in children vs adults was 0.89 and only one study showed a significant ratio of <0.40. The main limitation of our study is the inaccuracies and biases in seroprevalence studies. Conclusions Precision shielding of elderly community-dwelling populations before the availability of vaccines was indicated in some high-income countries, but most countries failed to achieve any substantial focused protection. Registration Open Science Framework (available at: https://osf.io/xvupr).
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Affiliation(s)
- Cathrine Axfors
- Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, USA,Department for Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Angelo Maria Pezzullo
- Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, USA,Section of Hygiene, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Despina G Contopoulos-Ioannidis
- Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, USA,Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Alexandre Apostolatos
- Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, USA,Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - John PA Ioannidis
- Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, USA,Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, Stanford University, Stanford, California, USA
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3
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Tran TNA, Wikle NB, Yang F, Inam H, Leighow S, Gentilesco B, Chan P, Albert E, Strong ER, Pritchard JR, Hanage WP, Hanks EM, Crawford FW, Boni MF. SARS-CoV-2 Attack Rate and Population Immunity in Southern New England, March 2020 to May 2021. JAMA Netw Open 2022; 5:e2214171. [PMID: 35616938 PMCID: PMC9136627 DOI: 10.1001/jamanetworkopen.2022.14171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Importance In emergency epidemic and pandemic settings, public health agencies need to be able to measure the population-level attack rate, defined as the total percentage of the population infected thus far. During vaccination campaigns in such settings, public health agencies need to be able to assess how much the vaccination campaign is contributing to population immunity; specifically, the proportion of vaccines being administered to individuals who are already seropositive must be estimated. Objective To estimate population-level immunity to SARS-CoV-2 through May 31, 2021, in Rhode Island, Massachusetts, and Connecticut. Design, Setting, and Participants This observational case series assessed cases, hospitalizations, intensive care unit occupancy, ventilator occupancy, and deaths from March 1, 2020, to May 31, 2021, in Rhode Island, Massachusetts, and Connecticut. Data were analyzed from July 2021 to November 2021. Exposures COVID-19-positive test result reported to state department of health. Main Outcomes and Measures The main outcomes were statistical estimates, from a bayesian inference framework, of the percentage of individuals as of May 31, 2021, who were (1) previously infected and vaccinated, (2) previously uninfected and vaccinated, and (3) previously infected but not vaccinated. Results At the state level, there were a total of 1 160 435 confirmed COVID-19 cases in Rhode Island, Massachusetts, and Connecticut. The median age among individuals with confirmed COVID-19 was 38 years. In autumn 2020, SARS-CoV-2 population immunity (equal to the attack rate at that point) in these states was less than 15%, setting the stage for a large epidemic wave during winter 2020 to 2021. Population immunity estimates for May 31, 2021, were 73.4% (95% credible interval [CrI], 72.9%-74.1%) for Rhode Island, 64.1% (95% CrI, 64.0%-64.4%) for Connecticut, and 66.3% (95% CrI, 65.9%-66.9%) for Massachusetts, indicating that more than 33% of residents in these states were fully susceptible to infection when the Delta variant began spreading in July 2021. Despite high vaccine coverage in these states, population immunity in summer 2021 was lower than planned owing to an estimated 34.1% (95% CrI, 32.9%-35.2%) of vaccines in Rhode Island, 24.6% (95% CrI, 24.3%-25.1%) of vaccines in Connecticut, and 27.6% (95% CrI, 26.8%-28.6%) of vaccines in Massachusetts being distributed to individuals who were already seropositive. Conclusions and Relevance These findings suggest that future emergency-setting vaccination planning may have to prioritize high vaccine coverage over optimized vaccine distribution to ensure that sufficient levels of population immunity are reached during the course of an ongoing epidemic or pandemic.
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Affiliation(s)
- Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park
| | - Nathan B. Wikle
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park
| | - Fuhan Yang
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park
| | - Haider Inam
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park
| | - Scott Leighow
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park
| | | | - Philip Chan
- Department of Medicine, Brown University, Providence, Rhode Island
| | - Emmy Albert
- Department of Physics, Pennsylvania State University, University Park
| | - Emily R. Strong
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park
| | - Justin R. Pritchard
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ephraim M. Hanks
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park
| | - Forrest W. Crawford
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
- Department of Statistics and Data Science, Yale University, New Haven, Connecticut
| | - Maciej F. Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park
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4
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Qiu Z, Cao Z, Zou M, Tang K, Zhang C, Tang J, Zeng J, Wang Y, Sun Q, Wang D, Du X. The effectiveness of governmental nonpharmaceutical interventions against COVID-19 at controlling seasonal influenza transmission: an ecological study. BMC Infect Dis 2022; 22:331. [PMID: 35379168 PMCID: PMC8977560 DOI: 10.1186/s12879-022-07317-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/28/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND A range of strict nonpharmaceutical interventions (NPIs) were implemented in many countries to combat the coronavirus 2019 (COVID-19) pandemic. These NPIs may also be effective at controlling seasonal influenza virus infections, as influenza viruses have the same transmission path as severe acute respiratory syndrome coronavirus 2. The aim of this study was to evaluate the effects of different NPIs on the control of seasonal influenza. METHODS Data for 14 NPIs implemented in 33 countries and the corresponding influenza virological surveillance data were collected. The influenza suppression index was calculated as the difference between the influenza positivity rate during its period of decline from 2019 to 2020 and during the influenza epidemic seasons in the previous 9 years. A machine learning model was developed using an extreme gradient boosting tree regressor to fit the NPI and influenza suppression index data. The SHapley Additive exPlanations tool was used to characterize the NPIs that suppressed the transmission of influenza. RESULTS Of all NPIs tested, gathering limitations had the greatest contribution (37.60%) to suppressing influenza transmission during the 2019-2020 influenza season. The three most effective NPIs were gathering limitations, international travel restrictions, and school closures. For these three NPIs, their intensity threshold required to generate an effect were restrictions on the size of gatherings less than 1000 people, ban of travel to all regions or total border closures, and closing only some categories of schools, respectively. There was a strong positive interaction effect between mask-wearing requirements and gathering limitations, whereas merely implementing a mask-wearing requirement, and not other NPIs, diluted the effectiveness of mask-wearing requirements at suppressing influenza transmission. CONCLUSIONS Gathering limitations, ban of travel to all regions or total border closures, and closing some levels of schools were found to be the most effective NPIs at suppressing influenza transmission. It is recommended that the mask-wearing requirement be combined with gathering limitations and other NPIs. Our findings could facilitate the precise control of future influenza epidemics and other potential pandemics.
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Affiliation(s)
- Zekai Qiu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zicheng Cao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Zou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Kang Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chi Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jing Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yaqi Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qianru Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Daoze Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China. .,School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510030, People's Republic of China.
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5
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Reconstructing antibody dynamics to estimate the risk of influenza virus infection. Nat Commun 2022; 13:1557. [PMID: 35322048 PMCID: PMC8943152 DOI: 10.1038/s41467-022-29310-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
For >70 years, a 4-fold or greater rise in antibody titer has been used to confirm influenza virus infections in paired sera, despite recognition that this heuristic can lack sensitivity. Here we analyze with a novel Bayesian model a large cohort of 2353 individuals followed for up to 5 years in Hong Kong to characterize influenza antibody dynamics and develop an algorithm to improve the identification of influenza virus infections. After infection, we estimate that hemagglutination-inhibiting (HAI) titers were boosted by 16-fold on average and subsequently decrease by 14% per year. In six epidemics, the infection risks for adults were 3%-19% while the infection risks for children were 1.6-4.4 times higher than that of younger adults. Every two-fold increase in pre-epidemic HAI titer was associated with 19%-58% protection against infection. Our inferential framework clarifies the contributions of age and pre-epidemic HAI titers to characterize individual infection risk.
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6
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Wikle NB, Tran TNA, Gentilesco B, Leighow SM, Albert E, Strong ER, Brinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks EM, Boni MF. SARS-CoV-2 epidemic after social and economic reopening in three U.S. states reveals shifts in age structure and clinical characteristics. SCIENCE ADVANCES 2022; 8:eabf9868. [PMID: 35080987 PMCID: PMC8791616 DOI: 10.1126/sciadv.abf9868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/03/2021] [Indexed: 05/03/2023]
Abstract
State-level reopenings in late spring 2020 facilitated the resurgence of severe acute respiratory syndrome coronavirus 2 transmission. Here, we analyze age-structured case, hospitalization, and death time series from three states-Rhode Island, Massachusetts, and Pennsylvania-that had successful reopenings in May 2020 without summer waves of infection. Using 11 daily data streams, we show that from spring to summer, the epidemic shifted from an older to a younger age profile and that elderly individuals were less able to reduce contacts during the lockdown period when compared to younger individuals. Clinical case management improved from spring to summer, resulting in fewer critical care admissions and lower infection fatality rate. Attack rate estimates through 31 August 2020 are 6.2% [95% credible interval (CI), 5.7 to 6.8%] of the total population infected for Rhode Island, 6.7% (95% CI, 5.4 to 7.6%) in Massachusetts, and 2.7% (95% CI, 2.5 to 3.1%) in Pennsylvania.
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Affiliation(s)
- Nathan B. Wikle
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA, USA
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | - Scott M. Leighow
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA, USA
| | - Emmy Albert
- Department of Physics, Pennsylvania State University, University Park, PA, USA
| | - Emily R. Strong
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA, USA
| | - Karel Brinda
- Center for Communicable Disease Dynamic, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Haider Inam
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA, USA
| | - Fuhan Yang
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Sajid Hossain
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Philip Chan
- Department of Medicine, Brown University, Providence, RI, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamic, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Maria Messick
- Rhode Island Office of the Governor and Rhode Island Department of Health, Providence, RI, USA
| | - Justin R. Pritchard
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA, USA
| | - Ephraim M. Hanks
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA, USA
| | - Maciej F. Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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7
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Wu JT, Mei S, Luo S, Leung K, Liu D, Lv Q, Liu J, Li Y, Prem K, Jit M, Weng J, Feng T, Zheng X, Leung GM. A global assessment of the impact of school closure in reducing COVID-19 spread. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20210124. [PMID: 34802277 PMCID: PMC8607143 DOI: 10.1098/rsta.2021.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Prolonged school closure has been adopted worldwide to control COVID-19. Indeed, UN Educational, Scientific and Cultural Organization figures show that two-thirds of an academic year was lost on average worldwide due to COVID-19 school closures. Such pre-emptive implementation was predicated on the premise that school children are a core group for COVID-19 transmission. Using surveillance data from the Chinese cities of Shenzhen and Anqing together, we inferred that compared with the elderly aged 60 and over, children aged 18 and under and adults aged 19-59 were 75% and 32% less susceptible to infection, respectively. Using transmission models parametrized with synthetic contact matrices for 177 jurisdictions around the world, we showed that the lower susceptibility of school children substantially limited the effectiveness of school closure in reducing COVID-19 transmissibility. Our results, together with recent findings that clinical severity of COVID-19 in children is lower, suggest that school closure may not be ideal as a sustained, primary intervention for controlling COVID-19. This article is part of the theme issue 'Data science approach to infectious disease surveillance'.
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Affiliation(s)
- Joseph T. Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
- Laboratory of Data Discovery for Health (D4H), Hong Kong Science Park, New Territories, Hong Kong
| | - Shujiang Mei
- Department of Communicable Diseases Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, People's Republic of China
| | - Sihui Luo
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, People's Republic of China
- Clinical Research Hospital (Hefei) of Chinese Academy of Science, Hefei, People's Republic of China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
- Laboratory of Data Discovery for Health (D4H), Hong Kong Science Park, New Territories, Hong Kong
| | - Di Liu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
- Laboratory of Data Discovery for Health (D4H), Hong Kong Science Park, New Territories, Hong Kong
| | - Qiuying Lv
- Department of Communicable Diseases Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, People's Republic of China
| | - Jian Liu
- Anqing Hospital Affiliated to Anhui Medical University (Anqing Municipal Hospital), Anqing, People's Republic of China
| | - Yuan Li
- Department of Communicable Diseases Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, People's Republic of China
| | - Kiesha Prem
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Jit
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
- Laboratory of Data Discovery for Health (D4H), Hong Kong Science Park, New Territories, Hong Kong
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Jianping Weng
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, People's Republic of China
- Clinical Research Hospital (Hefei) of Chinese Academy of Science, Hefei, People's Republic of China
| | - Tiejian Feng
- Department of Communicable Diseases Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, People's Republic of China
| | - Xueying Zheng
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, People's Republic of China
- Clinical Research Hospital (Hefei) of Chinese Academy of Science, Hefei, People's Republic of China
| | - Gabriel M. Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
- Laboratory of Data Discovery for Health (D4H), Hong Kong Science Park, New Territories, Hong Kong
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8
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Tran TNA, Wikle NB, Yang F, Inam H, Leighow S, Gentilesco B, Chan P, Albert E, Strong ER, Pritchard JR, Hanage WP, Hanks EM, Crawford FW, Boni MF. SARS-CoV-2 attack rate and population immunity in southern New England, March 2020 - May 2021. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.12.06.21267375. [PMID: 34909789 PMCID: PMC8669856 DOI: 10.1101/2021.12.06.21267375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Estimating an infectious disease attack rate requires inference on the number of reported symptomatic cases of a disease, the number of unreported symptomatic cases, and the number of asymptomatic infections. Population-level immunity can then be estimated as the attack rate plus the number of vaccine recipients who had not been previously infected; this requires an estimate of the fraction of vaccines that were distributed to seropositive individuals. To estimate attack rates and population immunity in southern New England, we fit a validated dynamic epidemiological model to case, clinical, and death data streams reported by Rhode Island, Massachusetts, and Connecticut for the first 15 months of the COVID-19 pandemic, from March 1 2020 to May 31 2021. This period includes the initial spring 2020 wave, the major winter wave of 2020-2021, and the lagging wave of lineage B.1.1.7(Alpha) infections during March-April 2021. In autumn 2020, SARS-CoV-2 population immunity (equal to the attack rate at that point) in southern New England was still below 15%, setting the stage for a large winter wave. After the roll-out of vaccines in early 2021, population immunity in many states was expected to approach 70% by spring 2021, with more than half of this immune population coming from vaccinations. Our population immunity estimates for May 31 2021 are 73.4% (95% CrI: 72.9% - 74.1%) for Rhode Island, 64.1% (95% CrI: 64.0% - 64.4%) for Connecticut, and 66.3% (95% CrI: 65.9% - 66.9%) for Massachusetts, indicating that >33% of southern Englanders were still susceptible to infection when the Delta variant began spreading in July 2021. Despite high vaccine coverage in these states, population immunity in summer 2021 was lower than planned due to 34% (Rhode Island), 25% (Connecticut), and 28% (Massachusetts) of vaccine distribution going to seropositive individuals. Future emergency-setting vaccination planning will likely have to consider over-vaccination as a strategy to ensure that high levels of population immunity are reached during the course of an ongoing epidemic.
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Affiliation(s)
- Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA
| | - Nathan B Wikle
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA
| | - Fuhan Yang
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA
| | - Haider Inam
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA
| | - Scott Leighow
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA
| | | | - Philip Chan
- Department of Medicine, Brown University, Providence, RI
| | - Emmy Albert
- Department of Physics, Pennsylvania State University, University Park, PA
| | - Emily R Strong
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA
| | - Justin R Pritchard
- Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Ephraim M Hanks
- Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA
| | - Forrest W Crawford
- Department of Biostatistics, Yale Schools of Public Health, Yale University, New Haven, CT
- Department of Biostatistics, Yale Schools of Public Health, Yale University, New Haven, CT
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA
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9
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Lei H, Wu X, Wang X, Xu M, Xie Y, Du X, Cowling BJ, Li Y, Shu Y. Different transmission dynamics of COVID-19 and influenza suggest the relative efficiency of isolation/quarantine and social distancing against COVID-19 in China. Clin Infect Dis 2020; 73:e4305-e4311. [PMID: 33080000 PMCID: PMC7665384 DOI: 10.1093/cid/ciaa1584] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Indexed: 01/12/2023] Open
Abstract
Background Non-pharmaceutical interventions (NPIs) against Coronavirus Disease 2019 (COVID-19) are vital to reducing the transmission risks. However, the relative efficiency of social distancing against COVID-19 remains controversial, since social distancing and isolation/quarantine were implemented almost at the same time in China. Methods In this study, surveillance data of COVID-19 and seasonal influenza in the year 2018-2020 were used to quantify the relative efficiency of NPIs against COVID-19 in China, since isolation/quarantine was not used for the influenza epidemics. Given that the relative age-dependent susceptibility to influenza and COVID-19 may vary, an age-structured Susceptible-Infected-Recovered model was built to explore the efficiency of social distancing against COVID-19 under different population susceptibility scenarios. Results The mean effective reproductive number, Rt, of COVID-19 before NPIs was 2.12 (95% confidential interval (CI): 2.02-2.21). By March 11, 2020, the overall reduction in Rt of COVID-19 was 66.1% (95% CI: 60.1%-71.2%). In the epidemiological year 2019/20, influenza transmissibility reduced by 34.6% (95% CI: 31.3%-38.2%) compared with that in the epidemiological year 2018/19. Under the observed contact patterns changes in China, social distancing had similar efficiency against COVID-19 in three different scenarios. By assuming same efficiency of social distancing against seasonal influenza and COVID-19 transmission, isolation/quarantine and social distancing could lead to a 48.1% (95% CI: 35.4%-58.1%) and 34.6% (95% CI: 31.3%-38.2%) reduction of the transmissibility of COVID-19. Conclusions Though isolation/quarantine is more effective than social distancing, given that typical basic reproductive number of COVID-19 is 2-3, isolation/quarantine alone could not contain the COVID-19 pandemic effectively in China.
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Affiliation(s)
- Hao Lei
- Department of Big Data in Health Science, School of Public Health, Zhejiang University, Hangzhou, P.R. China
| | - Xifeng Wu
- Department of Big Data in Health Science, School of Public Health, Zhejiang University, Hangzhou, P.R. China.,Center for Biostatistics, Bioinformatics, and Big Data, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P.R. China
| | - Xiao Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, P.R. China
| | - Modi Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, P.R. China
| | - Yu Xie
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, P.R. China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, P.R. China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, P.R. China
| | - Yuguo Li
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, P.R. China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, P.R. China
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10
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Yang W, Lau EHY, Cowling BJ. Dynamic interactions of influenza viruses in Hong Kong during 1998-2018. PLoS Comput Biol 2020; 16:e1007989. [PMID: 32542015 PMCID: PMC7316359 DOI: 10.1371/journal.pcbi.1007989] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 06/25/2020] [Accepted: 05/27/2020] [Indexed: 11/19/2022] Open
Abstract
Influenza epidemics cause substantial morbidity and mortality every year worldwide. Currently, two influenza A subtypes, A(H1N1) and A(H3N2), and type B viruses co-circulate in humans and infection with one type/subtype could provide cross-protection against the others. However, it remains unclear how such ecologic competition via cross-immunity and antigenic mutations that allow immune escape impact influenza epidemic dynamics at the population level. Here we develop a comprehensive model-inference system and apply it to study the evolutionary and epidemiological dynamics of the three influenza types/subtypes in Hong Kong, a city of global public health significance for influenza epidemic and pandemic control. Utilizing long-term influenza surveillance data since 1998, we are able to estimate the strength of cross-immunity between each virus-pairs, the timing and frequency of punctuated changes in population immunity in response to antigenic mutations in influenza viruses, and key epidemiological parameters over the last 20 years including the 2009 pandemic. We find evidence of cross-immunity in all types/subtypes, with strongest cross-immunity from A(H1N1) against A(H3N2). Our results also suggest that A(H3N2) may undergo antigenic mutations in both summers and winters and thus monitoring the virus in both seasons may be important for vaccine development. Overall, our study reveals intricate epidemiological interactions and underscores the importance of simultaneous monitoring of population immunity, incidence rates, and viral genetic and antigenic changes.
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Affiliation(s)
- Wan Yang
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Eric H. Y. Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong Special Administrative Region, China
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11
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Zhang Y, Leung K, Perera RAPM, Lee CK, Peiris JSM, Wu JT. Harnessing the potential of blood donation archives for influenza surveillance and control. PLoS One 2020; 15:e0233605. [PMID: 32470010 PMCID: PMC7259782 DOI: 10.1371/journal.pone.0233605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/10/2020] [Indexed: 02/04/2023] Open
Abstract
Many blood donation services around the globe maintain large archives of serum and/or plasma specimens of blood donations which could potentially be used for serologic surveillance and risk assessment of influenza. Harnessing this potential requires robust evidence that the outcomes of influenza serology in plasma, which is rarely used, is consistent with that in serum, which is the conventional choice of specimens for influenza serology. We harvested EDTA-plasma specimens from the blood donation archives of Hong Kong Red Cross Transfusion Services, where EDTA is the type of anticoagulant used for plasma collection, compared their antibody titers and responses to that in serum. Influenza A/H1N1/California/7/2009 and A/H3N2/Victoria/208/2009 were the test strains. Our results showed that antibody titers in 609 matched serum/EDTA-plasma specimens (i.e. obtained from the same donor at the same time) had good agreement inferred by Intraclass Correlation Coefficient, the value of which was 0.82 (95% CI: 0.77-0.86) for hemagglutination inhibition assay and 0.95 (95% CI: 0.93-0.96) for microneutralization assay; seroconversion rates (based on hemagglutination inhibition titers) during the 2010 and 2011 influenza seasons in Hong Kong inferred from paired EDTA-plasma were similar to that inferred from paired sera. Our study provided the proof-of-concept that blood donation archives could be leveraged as a valuable source of longitudinal blood specimens for the surveillance, control and risk assessment of both pandemic and seasonal influenza.
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Affiliation(s)
- Yanyu Zhang
- School of Public Health, WHO Collaborating Center for Infectious Disease Epidemiology and Control, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kathy Leung
- School of Public Health, WHO Collaborating Center for Infectious Disease Epidemiology and Control, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ranawaka A. P. M. Perera
- Center of Influenza Research and School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Cheuk-Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong Special Administrative Region, China
| | - J. S. Malik Peiris
- Center of Influenza Research and School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Joseph T. Wu
- School of Public Health, WHO Collaborating Center for Infectious Disease Epidemiology and Control, The University of Hong Kong, Hong Kong Special Administrative Region, China
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12
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Hay JA, Minter A, Ainslie KEC, Lessler J, Yang B, Cummings DAT, Kucharski AJ, Riley S. An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver. PLoS Comput Biol 2020; 16:e1007840. [PMID: 32365062 PMCID: PMC7241836 DOI: 10.1371/journal.pcbi.1007840] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/21/2020] [Accepted: 04/01/2020] [Indexed: 11/19/2022] Open
Abstract
We present a flexible, open source R package designed to obtain biological and epidemiological insights from serological datasets. Characterising past exposures for multi-strain pathogens poses a specific statistical challenge: observed antibody responses measured in serological assays depend on multiple unobserved prior infections that produce cross-reactive antibody responses. We provide a general modelling framework to jointly infer infection histories and describe immune responses generated by these infections using antibody titres against current and historical strains. We do this by linking latent infection dynamics with a mechanistic model of antibody kinetics that generates expected antibody titres over time. Our aim is to provide a flexible package to identify infection histories that can be applied to a range of pathogens. We present two case studies to illustrate how our model can infer key immunological parameters, such as antibody titre boosting, waning and cross-reaction, as well as latent epidemiological processes such as attack rates and age-stratified infection risk.
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Affiliation(s)
- James A. Hay
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Amanda Minter
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kylie E. C. Ainslie
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Bingyi Yang
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Derek A. T. Cummings
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Adam J. Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
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13
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Cowling BJ, Ali ST, Ng TWY, Tsang TK, Li JCM, Fong MW, Liao Q, Kwan MY, Lee SL, Chiu SS, Wu JT, Wu P, Leung GM. Impact assessment of non-pharmaceutical interventions against coronavirus disease 2019 and influenza in Hong Kong: an observational study. Lancet Public Health 2020; 5:e279-e288. [PMID: 32311320 DOI: 10.1101/2020.03.12.20034660] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND A range of public health measures have been implemented to suppress local transmission of coronavirus disease 2019 (COVID-19) in Hong Kong. We examined the effect of these interventions and behavioural changes of the public on the incidence of COVID-19, as well as on influenza virus infections, which might share some aspects of transmission dynamics with COVID-19. METHODS We analysed data on laboratory-confirmed COVID-19 cases, influenza surveillance data in outpatients of all ages, and influenza hospitalisations in children. We estimated the daily effective reproduction number (Rt) for COVID-19 and influenza A H1N1 to estimate changes in transmissibility over time. Attitudes towards COVID-19 and changes in population behaviours were reviewed through three telephone surveys done on Jan 20-23, Feb 11-14, and March 10-13, 2020. FINDINGS COVID-19 transmissibility measured by Rt has remained at approximately 1 for 8 weeks in Hong Kong. Influenza transmission declined substantially after the implementation of social distancing measures and changes in population behaviours in late January, with a 44% (95% CI 34-53%) reduction in transmissibility in the community, from an estimated Rt of 1·28 (95% CI 1·26-1·30) before the start of the school closures to 0·72 (0·70-0·74) during the closure weeks. Similarly, a 33% (24-43%) reduction in transmissibility was seen based on paediatric hospitalisation rates, from an Rt of 1·10 (1·06-1·12) before the start of the school closures to 0·73 (0·68-0·77) after school closures. Among respondents to the surveys, 74·5%, 97·5%, and 98·8% reported wearing masks when going out, and 61·3%, 90·2%, and 85·1% reported avoiding crowded places in surveys 1 (n=1008), 2 (n=1000), and 3 (n=1005), respectively. INTERPRETATION Our study shows that non-pharmaceutical interventions (including border restrictions, quarantine and isolation, distancing, and changes in population behaviour) were associated with reduced transmission of COVID-19 in Hong Kong, and are also likely to have substantially reduced influenza transmission in early February, 2020. FUNDING Health and Medical Research Fund, Hong Kong.
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Affiliation(s)
- Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheikh Taslim Ali
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tiffany W Y Ng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Julian C M Li
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Min Whui Fong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Qiuyan Liao
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Mike Yw Kwan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - So Lun Lee
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital and Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Susan S Chiu
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital and Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
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14
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Cowling BJ, Ali ST, Ng TWY, Tsang TK, Li JCM, Fong MW, Liao Q, Kwan MY, Lee SL, Chiu SS, Wu JT, Wu P, Leung GM. Impact assessment of non-pharmaceutical interventions against coronavirus disease 2019 and influenza in Hong Kong: an observational study. LANCET PUBLIC HEALTH 2020; 5:e279-e288. [PMID: 32311320 PMCID: PMC7164922 DOI: 10.1016/s2468-2667(20)30090-6] [Citation(s) in RCA: 743] [Impact Index Per Article: 185.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 02/03/2023]
Abstract
Background A range of public health measures have been implemented to suppress local transmission of coronavirus disease 2019 (COVID-19) in Hong Kong. We examined the effect of these interventions and behavioural changes of the public on the incidence of COVID-19, as well as on influenza virus infections, which might share some aspects of transmission dynamics with COVID-19. Methods We analysed data on laboratory-confirmed COVID-19 cases, influenza surveillance data in outpatients of all ages, and influenza hospitalisations in children. We estimated the daily effective reproduction number (Rt) for COVID-19 and influenza A H1N1 to estimate changes in transmissibility over time. Attitudes towards COVID-19 and changes in population behaviours were reviewed through three telephone surveys done on Jan 20–23, Feb 11–14, and March 10–13, 2020. Findings COVID-19 transmissibility measured by Rt has remained at approximately 1 for 8 weeks in Hong Kong. Influenza transmission declined substantially after the implementation of social distancing measures and changes in population behaviours in late January, with a 44% (95% CI 34–53%) reduction in transmissibility in the community, from an estimated Rt of 1·28 (95% CI 1·26–1·30) before the start of the school closures to 0·72 (0·70–0·74) during the closure weeks. Similarly, a 33% (24–43%) reduction in transmissibility was seen based on paediatric hospitalisation rates, from an Rt of 1·10 (1·06–1·12) before the start of the school closures to 0·73 (0·68–0·77) after school closures. Among respondents to the surveys, 74·5%, 97·5%, and 98·8% reported wearing masks when going out, and 61·3%, 90·2%, and 85·1% reported avoiding crowded places in surveys 1 (n=1008), 2 (n=1000), and 3 (n=1005), respectively. Interpretation Our study shows that non-pharmaceutical interventions (including border restrictions, quarantine and isolation, distancing, and changes in population behaviour) were associated with reduced transmission of COVID-19 in Hong Kong, and are also likely to have substantially reduced influenza transmission in early February, 2020. Funding Health and Medical Research Fund, Hong Kong.
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Affiliation(s)
- Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheikh Taslim Ali
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tiffany W Y Ng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Julian C M Li
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Min Whui Fong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Qiuyan Liao
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Mike Yw Kwan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - So Lun Lee
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital and Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Susan S Chiu
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital and Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
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15
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Kim S, Kim YJ, Peck KR, Jung E. School Opening Delay Effect on Transmission Dynamics of Coronavirus Disease 2019 in Korea: Based on Mathematical Modeling and Simulation Study. J Korean Med Sci 2020; 35:e143. [PMID: 32242349 PMCID: PMC7131906 DOI: 10.3346/jkms.2020.35.e143] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 03/30/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Nonpharmaceutical intervention strategy is significantly important to mitigate the coronavirus disease 2019 (COVID-19) spread. One of the interventions implemented by the government is a school closure. The Ministry of Education decided to postpone the school opening from March 2 to April 6 to minimize epidemic size. We aimed to quantify the school closure effect on the COVID-19 epidemic. METHODS The potential effects of school opening were measured using a mathematical model considering two age groups: children (aged 19 years and younger) and adults (aged over 19). Based on susceptible-exposed-infectious-recovered model, isolation and behavior-changed susceptible individuals are additionally considered. The transmission parameters were estimated from the laboratory confirmed data reported by the Korea Centers for Disease Control and Prevention from February 16 to March 22. The model was extended with estimated parameters and estimated the expected number of confirmed cases as the transmission rate increased after school opening. RESULTS Assuming the transmission rate between children group would be increasing 10 fold after the schools open, approximately additional 60 cases are expected to occur from March 2 to March 9, and approximately additional 100 children cases are expected from March 9 to March 23. After March 23, the number of expected cases for children is 28.4 for 7 days and 33.6 for 14 days. CONCLUSION The simulation results show that the government could reduce at least 200 cases, with two announcements by the Ministry of education. After March 23, although the possibility of massive transmission in the children's age group is lower, group transmission is possible to occur.
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Affiliation(s)
- Soyoung Kim
- Department of Mathematics, Konkuk University, Seoul, Korea
| | - Yae Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eunok Jung
- Department of Mathematics, Konkuk University, Seoul, Korea.
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16
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Perera RA, Mok CK, Tsang OT, Lv H, Ko RL, Wu NC, Yuan M, Leung WS, Chan JM, Chik TS, Choi CY, Leung K, Chan KH, Chan KC, Li KC, Wu JT, Wilson IA, Monto AS, Poon LL, Peiris M. Serological assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), March 2020. Euro Surveill 2020; 25:2000421. [PMID: 32347204 PMCID: PMC7189648 DOI: 10.2807/1560-7917.es.2020.25.16.2000421] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/14/2020] [Indexed: 12/29/2022] Open
Abstract
BackgroundThe ongoing coronavirus disease (COVID-19) pandemic has major impacts on health systems, the economy and society. Assessing infection attack rates in the population is critical for estimating disease severity and herd immunity which is needed to calibrate public health interventions. We have previously shown that it is possible to achieve this in real time to impact public health decision making.AimOur objective was to develop and evaluate serological assays applicable in large-scale sero-epidemiological studies.MethodsWe developed an ELISA to detect IgG and IgM antibodies to the receptor-binding domain (RBD) of the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluated its sensitivity and specificity in combination with confirmatory microneutralisation (MN) and 90% plaque reduction neutralisation tests (PRNT90) in 51 sera from 24 patients with virologically confirmed COVID-19 and in age-stratified sera from 200 healthy controls.ResultsIgG and IgM RBD ELISA, MN and PRNT90 were reliably positive after 29 days from illness onset with no detectable cross-reactivity in age-stratified controls. We found that PRNT90 tests were more sensitive in detecting antibody than MN tests carried out with the conventional 100 tissue culture infectious dose challenge. Heparinised plasma appeared to reduce the infectivity of the virus challenge dose and may confound interpretation of neutralisation test.ConclusionUsing IgG ELISA based on the RBD of the spike protein to screen sera for SARS-CoV-2 antibody, followed by confirmation using PRNT90, is a valid approach for large-scale sero-epidemiology studies.
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Affiliation(s)
- Ranawaka Apm Perera
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Contributed equally to the research
| | - Chris Kp Mok
- Contributed equally to the research
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Owen Ty Tsang
- Contributed equally to the research
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Huibin Lv
- Contributed equally to the research
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ronald Lw Ko
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States
| | - Wai Shing Leung
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Jacky Mc Chan
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Thomas Sh Chik
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Chris Yc Choi
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Kathy Leung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kin Ho Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Karl Ck Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ka-Chi Li
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Joseph T Wu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States
| | - Leo Lm Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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17
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Brugger J, Althaus CL. Transmission of and susceptibility to seasonal influenza in Switzerland from 2003 to 2015. Epidemics 2019; 30:100373. [PMID: 31635972 DOI: 10.1016/j.epidem.2019.100373] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the seasonal patterns of influenza transmission is critical to help plan public health measures for the management and control of epidemics. Mathematical models of infectious disease transmission have been widely used to quantify the transmissibility of and susceptibility to past influenza seasons in many countries. The objective of this study was to obtain a detailed picture of the transmission dynamics of seasonal influenza in Switzerland from 2003 to 2015. To this end, we developed a compartmental influenza transmission model taking into account social mixing between different age groups and seasonal forcing. We applied a Bayesian approach using Markov chain Monte Carlo (MCMC) methods to fit the model to the reported incidence of influenza-like-illness (ILI) and virological data from Sentinella, the Swiss Sentinel Surveillance Network. The maximal basic reproduction number, R0, ranged from 1.46 to 1.81 (median). Median estimates of susceptibility to influenza ranged from 29% to 98% for different age groups, and typically decreased with age. We also found a decline in ascertainability of influenza cases with age. Our study illustrates how influenza surveillance data from Switzerland can be integrated into a Bayesian modeling framework in order to assess age-specific transmission of and susceptibility to influenza.
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Affiliation(s)
- Jon Brugger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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18
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Babu TM, Perera RAPM, Wu JT, Fitzgerald T, Nolan C, Cowling BJ, Krauss S, Treanor JJ, Peiris M. Population Serologic Immunity to Human and Avian H2N2 Viruses in the United States and Hong Kong for Pandemic Risk Assessment. J Infect Dis 2019; 218:1054-1060. [PMID: 29762672 PMCID: PMC6107991 DOI: 10.1093/infdis/jiy291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/11/2018] [Indexed: 01/19/2023] Open
Abstract
Background Influenza A pandemics cause significant mortality and morbidity. H2N2 viruses have caused a prior pandemic, and are circulating in avian reservoirs. The age-related frequency of current population immunity to H2 viruses was evaluated. Methods Hemagglutinin inhibition (HAI) assays against historical human and recent avian influenza A(H2N2) viruses were performed across age groups in Rochester, New York, and Hong Kong, China. The impact of existing cross-reactive HAI immunity on the effective reproduction number was modeled. Results One hundred fifty individual sera from Rochester and 295 from Hong Kong were included. Eighty-five percent of patients born in Rochester and Hong Kong before 1968 had HAI titers ≥1:40 against A/Singapore/1/57, and >50% had titers ≥1:40 against A/Berkeley/1/68. The frequency of titers ≥1:40 to avian H2N2 A/mallard/England/727/06 and A/mallard/Netherlands/14/07 in subjects born before 1957 was 62% and 24%, respectively. There were no H2 HAI titers >1:40 in individuals born after 1968. These levels of seroprevalence reduce the initial reproduction number of A/Singapore/1/1957 or A/Berkeley/1/68 by 15%-20%. A basic reproduction number (R0) of the emerging transmissible virus <1.2 predicts a preventable pandemic. Conclusions Population immunity to H2 viruses is insufficient to block epidemic spread of H2 virus. An H2N2 pandemic would have lower impact in those born before 1968.
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Affiliation(s)
- Tara M Babu
- Department of Infectious Diseases, University of Rochester Medical Center, New York
| | | | - Joseph T Wu
- School of Public Health, The University of Hong Kong
| | - Theresa Fitzgerald
- Department of Infectious Diseases, University of Rochester Medical Center, New York
| | - Carolyn Nolan
- Department of Infectious Diseases, University of Rochester Medical Center, New York
| | | | - Scott Krauss
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | - John J Treanor
- Department of Infectious Diseases, University of Rochester Medical Center, New York
| | - Malik Peiris
- School of Public Health, The University of Hong Kong
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19
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Yang B, Lau EHY, Cowling BJ. Estimating the Severity Profile of Enterovirus A71 Infections in Children: A Bayesian Synthesis Framework. Am J Epidemiol 2019; 188:475-483. [PMID: 30358846 DOI: 10.1093/aje/kwy238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/11/2018] [Indexed: 11/14/2022] Open
Abstract
Enterovirus A71 (EV-A71) is responsible for the majority of severe cases of hand, foot, and mouth disease, but little evidence is available on the severity profile of EV-A71 infections. We formulated a hierarchical Bayesian model that synthesized data on diseases/events associated with EV-A71 and EV-A71 antibody responses to infection among unvaccinated children from large clinical trials of EV-A71 vaccination, which were conducted in Jiangsu and Beijing during 2012 and 2013, to reconstruct the severity profile in a unified framework. On average, 15.1% of the children aged 6-35 months were infected by EV-A71 during 1-year follow-up in a mild epidemic season. We estimated that 9.7%, 2.2%, and 0.6% of children infected with EV-A71 were diagnosed with EV-A71-associated diseases, were hospitalized, and showed severe complications, respectively. We estimated on average 1 death per 10,000 EV-A71 infections for children aged 6-35 months. Approximately 70% of children had ≥4-fold rises in antibody titers after infection. Most EV-A71 infections in young children are mild, and overall 2.2% of the infected patients were hospitalized in the 2 trials. There remain several uncertainties about the immune response after infection and the duration of immunity against EV-A71 reinfection.
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Affiliation(s)
- Bingyi Yang
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
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20
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Cope RC, Ross JV, Chilver M, Stocks NP, Mitchell L. Characterising seasonal influenza epidemiology using primary care surveillance data. PLoS Comput Biol 2018; 14:e1006377. [PMID: 30114215 PMCID: PMC6112683 DOI: 10.1371/journal.pcbi.1006377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 08/28/2018] [Accepted: 07/18/2018] [Indexed: 11/19/2022] Open
Abstract
Understanding the epidemiology of seasonal influenza is critical for healthcare resource allocation and early detection of anomalous seasons. It can be challenging to obtain high-quality data of influenza cases specifically, as clinical presentations with influenza-like symptoms may instead be cases of one of a number of alternate respiratory viruses. We use a new dataset of confirmed influenza virological data from 2011-2016, along with high-quality denominators informing a hierarchical observation process, to model seasonal influenza dynamics in New South Wales, Australia. We use approximate Bayesian computation to estimate parameters in a climate-driven stochastic epidemic model, including the basic reproduction number R0, the proportion of the population susceptible to the circulating strain at the beginning of the season, and the probability an infected individual seeks treatment. We conclude that R0 and initial population susceptibility were strongly related, emphasising the challenges of identifying these parameters. Relatively high R0 values alongside low initial population susceptibility were among the results most consistent with these data. Our results reinforce the importance of distinguishing between R0 and the effective reproduction number (Re) in modelling studies. When patients present to their doctor with influenza-like symptoms, they may have influenza, or some other respiratory virus. The only way to discriminate between these viruses is with an expensive test, which is not performed in many cases. Additionally, results other than influenza may not be reported. This means that it can be difficult to determine how much influenza is circulating in the population each season. We used a unique dataset of confirmed influenza with denominators to fit models for seasonal influenza in New South Wales, Australia. Knowing the denominators allowed us to estimate population level trends. We found that the relationship between influenza transmission rates and immunity due to previous infections was critical, with relatively high transmission corresponding to substantial preexisting immunity likely. This existing immunity is critical to understanding and effectively modeling influenza dynamics.
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Affiliation(s)
- Robert C. Cope
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Joshua V. Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Monique Chilver
- Discipline of General Practice, The University of Adelaide, Adelaide, South Australia, Australia
| | - Nigel P. Stocks
- Discipline of General Practice, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lewis Mitchell
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Stream Lead, Data to Decisions CRC, Adelaide, South Australia, Australia
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21
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Sologuren I, Martínez-Saavedra MT, Solé-Violán J, de Borges de Oliveira E, Betancor E, Casas I, Oleaga-Quintas C, Martínez-Gallo M, Zhang SY, Pestano J, Colobran R, Herrera-Ramos E, Pérez C, López-Rodríguez M, Ruiz-Hernández JJ, Franco N, Ferrer JM, Bilbao C, Andújar-Sánchez M, Álvarez Fernández M, Ciancanelli MJ, Rodríguez de Castro F, Casanova JL, Bustamante J, Rodríguez-Gallego C. Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. J Clin Immunol 2018; 38:513-526. [PMID: 29882021 PMCID: PMC6429553 DOI: 10.1007/s10875-018-0512-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/28/2018] [Indexed: 11/18/2022]
Abstract
The pathogenesis of life-threatening influenza A virus (IAV) disease remains elusive, as infection is benign in most individuals. We studied two relatives who died from influenza. We Sanger sequenced GATA2 and evaluated the mutation by gene transfer, measured serum cytokine levels, and analyzed circulating T- and B-cells. Both patients (father and son, P1 and P2) died in 2011 of H1N1pdm IAV infection at the ages of 54 and 31 years, respectively. They had not suffered from severe or moderately severe infections in the last 17 (P1) and 15 years (P2). A daughter of P1 had died at 20 years from infectious complications. Low B-cell, NK- cell, and monocyte numbers and myelodysplastic syndrome led to sequence GATA2. Patients were heterozygous for a novel, hypomorphic, R396L mutation leading to haplo-insufficiency. B- and T-cell rearrangement in peripheral blood from P1 during the influenza episode showed expansion of one major clone. No T-cell receptor excision circles were detected in P1 and P3 since they were 35 and 18 years, respectively. Both patients presented an exuberant, interferon (IFN)-γ-mediated hypercytokinemia during H1N1pdm infection. No data about patients with viremia was available. Two previously reported adult GATA2-deficient patients died from severe H1N1 IAV infection; GATA2 deficiency may predispose to life-threatening influenza in adulthood. However, a role of other genetic variants involved in immune responses cannot be ruled out. Patients with GATA2 deficiency can reach young adulthood without severe infections, including influenza, despite long-lasting complete B-cell and natural killer (NK) cell deficiency, as well as profoundly diminished T-cell thymic output.
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Affiliation(s)
- Ithaisa Sologuren
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | | | - Jordi Solé-Violán
- Intensive Care Unit, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Edgar de Borges de Oliveira
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
| | - Eva Betancor
- Department of Biochemistry, Molecular Biology, Physiology, Genetics and Immunology, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Inmaculada Casas
- National Influenza Center-Madrid, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
| | | | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
| | - Jose Pestano
- Department of Biochemistry, Molecular Biology, Physiology, Genetics and Immunology, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Roger Colobran
- Department of Immunology, Vall d'Hebrón University Hospital, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Estefanía Herrera-Ramos
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Carmen Pérez
- Department of Microbiology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Marta López-Rodríguez
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - José Juan Ruiz-Hernández
- Department of Internal Medicine, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Nieves Franco
- Intensive Care Unit, Mostoles University Hospital, Madrid, Spain
| | - José María Ferrer
- Intensive Care Unit, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Bilbao
- Department of Hematology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Miguel Andújar-Sánchez
- Department of Pathology, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de Gran Canaria, Spain
| | | | - Michael J Ciancanelli
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
| | - Felipe Rodríguez de Castro
- Department of Respiratory Diseases, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
- Department of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Calle Barranco de la Ballena s/n, 35019, Las Palmas de Gran Canaria, Spain
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain.
- Department of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Calle Barranco de la Ballena s/n, 35019, Las Palmas de Gran Canaria, Spain.
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22
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Tönsing C, Timmer J, Kreutz C. Profile likelihood-based analyses of infectious disease models. Stat Methods Med Res 2018; 27:1979-1998. [PMID: 29512437 DOI: 10.1177/0962280217746444] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ordinary differential equation models are frequently applied to describe the temporal evolution of epidemics. However, ordinary differential equation models are also utilized in other scientific fields. We summarize and transfer state-of-the art approaches from other fields like Systems Biology to infectious disease models. For this purpose, we use a simple SIR model with data from an influenza outbreak at an English boarding school in 1978 and a more complex model of a vector-borne disease with data from the Zika virus outbreak in Colombia in 2015-2016. Besides parameter estimation using a deterministic multistart optimization approach, a multitude of analyses based on the profile likelihood are presented comprising identifiability analysis and model reduction. The analyses were performed using the freely available modeling framework Data2Dynamics (data2dynamics.org) which has been awarded as best performing within the DREAM6 parameter estimation challenge and in the DREAM7 network reconstruction challenge.
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Affiliation(s)
- Christian Tönsing
- 1 Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jens Timmer
- 1 Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany.,2 Center for Biosystems Analysis (ZBSA), University of Freiburg, Freiburg im Breisgau, Germany.,3 BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Clemens Kreutz
- 1 Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany.,2 Center for Biosystems Analysis (ZBSA), University of Freiburg, Freiburg im Breisgau, Germany
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23
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Sahu M, Singh N, Shukla MK, Potdar VA, Sharma RK, Sahare LK, Ukey MJ, Barde PV. Molecular and epidemiological analysis of pandemic and post-pandemic influenza A(H1N1)pdm09 virus from central India. J Med Virol 2017; 90:447-455. [PMID: 29073730 DOI: 10.1002/jmv.24982] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/24/2017] [Indexed: 02/05/2023]
Abstract
Influenza A(H1N1)pdm09 virus pandemic struck India in 2009 and continues to cause outbreaks in its post-pandemic phase. Diminutive information is available about influenza A(H1N1)pdm09 from central India. This observational study presents epidemiological and molecular findings for the period of 6 years. Throat swab samples referred from districts of Madhya Pradesh were subjected to diagnosis of influenza A(H1N1)pdm09 following WHO guidelines. Clinical and epidemiological data were recorded and analyzed. Hemagglutinin (HA) gene sequencing and phylogenetic analysis were performed. The H275Y mutation responsible for antiviral resistance was tested using allelic real-time RT-PCR. Out of 7365 tested samples, 2406 (32.7%) were positive for influenza A(H1N1)pdm09, of which 363 (15.08%) succumbed to infection. Significant trends were observed in positivity (χ2 = 50.8; P < 0.001) and mortality (χ2 = 24.4; P < 0.001) with increasing age. Mutations having clinical and epidemiological importance were detected. Phylogenetic analysis of HA gene sequences revealed that clade 7, 6A, and 6B viruses were in circulation. Oseltamivir resistance was detected in three fatal cases. Influenza A(H1N1)pdm09 viruses having genetic diversity were detected from central India and continues to be a concern for public health. This study highlights the need of year-round monitoring by establishment of strong molecular and clinical surveillance program.
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Affiliation(s)
- Mahima Sahu
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Neeru Singh
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Mohan K Shukla
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | | | - Ravendra K Sharma
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Lalit Kumar Sahare
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Mahendra J Ukey
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Pradip V Barde
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
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24
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Leung K, Jit M, Lau EHY, Wu JT. Social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Sci Rep 2017. [PMID: 28801623 DOI: 10.5281/zenodo.3874808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The spread of many respiratory infections is determined by contact patterns between infectious and susceptible individuals in the population. There are no published data for quantifying social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong which is a hotspot for emerging infectious diseases due to its high population density and connectivity in the air transportation network. We adopted a commonly used diary-based design to conduct a social contact survey in Hong Kong in 2015/16 using both paper and online questionnaires. Participants using paper questionnaires reported more contacts and longer contact duration than those using online questionnaires. Participants reported 13 person-hours of contact and 8 contacts per day on average, which decreased over age but increased with household size, years of education and income level. Prolonged and frequent contacts, and contacts at home, school and work were more likely to involve physical contacts. Strong age-assortativity was observed in all age groups. We evaluated the characteristics of social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Our findings could help to improve the design of future social contact surveys, parameterize transmission models of respiratory infectious diseases, and inform intervention strategies based on model outputs.
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Affiliation(s)
- Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Mark Jit
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Modelling and Economics Unit, Public Health England, London, United Kingdom
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China.
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25
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Social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Sci Rep 2017; 7:7974. [PMID: 28801623 PMCID: PMC5554254 DOI: 10.1038/s41598-017-08241-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/10/2017] [Indexed: 11/08/2022] Open
Abstract
The spread of many respiratory infections is determined by contact patterns between infectious and susceptible individuals in the population. There are no published data for quantifying social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong which is a hotspot for emerging infectious diseases due to its high population density and connectivity in the air transportation network. We adopted a commonly used diary-based design to conduct a social contact survey in Hong Kong in 2015/16 using both paper and online questionnaires. Participants using paper questionnaires reported more contacts and longer contact duration than those using online questionnaires. Participants reported 13 person-hours of contact and 8 contacts per day on average, which decreased over age but increased with household size, years of education and income level. Prolonged and frequent contacts, and contacts at home, school and work were more likely to involve physical contacts. Strong age-assortativity was observed in all age groups. We evaluated the characteristics of social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Our findings could help to improve the design of future social contact surveys, parameterize transmission models of respiratory infectious diseases, and inform intervention strategies based on model outputs.
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26
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Structure of general-population antibody titer distributions to influenza A virus. Sci Rep 2017; 7:6060. [PMID: 28729702 PMCID: PMC5519701 DOI: 10.1038/s41598-017-06177-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/09/2017] [Indexed: 12/24/2022] Open
Abstract
Seroepidemiological studies aim to understand population-level exposure and immunity to infectious diseases. Their results are normally presented as binary outcomes describing the presence or absence of pathogen-specific antibody, despite the fact that many assays measure continuous quantities. A population's natural distribution of antibody titers to an endemic infectious disease may include information on multiple serological states - naiveté, recent infection, non-recent infection, childhood infection - depending on the disease in question and the acquisition and waning patterns of immunity. In this study, we investigate 20,152 general-population serum samples from southern Vietnam collected between 2009 and 2013 from which we report antibody titers to the influenza virus HA1 protein using a continuous titer measurement from a protein microarray assay. We describe the distributions of antibody titers to subtypes 2009 H1N1 and H3N2. Using a model selection approach to fit mixture distributions, we show that 2009 H1N1 antibody titers fall into four titer subgroups and that H3N2 titers fall into three subgroups. For H1N1, our interpretation is that the two highest-titer subgroups correspond to recent and historical infection, which is consistent with 2009 pandemic attack rates. Similar interpretations are available for H3N2, but right-censoring of titers makes these interpretations difficult to validate.
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27
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Zhao X, Siegel K, Chen MIC, Cook AR. Rethinking thresholds for serological evidence of influenza virus infection. Influenza Other Respir Viruses 2017; 11:202-210. [PMID: 28294578 PMCID: PMC5410725 DOI: 10.1111/irv.12452] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2017] [Indexed: 11/29/2022] Open
Abstract
Introduction For pathogens such as influenza that cause many subclinical cases, serologic data can be used to estimate attack rates and the severity of an epidemic in near real time. Current methods for analysing serologic data tend to rely on use of a simple threshold or comparison of titres between pre‐ and post‐epidemic, which may not accurately reflect actual infection rates. Methods We propose a method for quantifying infection rates using paired sera and bivariate probit models to evaluate the accuracy of thresholds currently used for influenza epidemics with low and high existing herd immunity levels, and a subsequent non‐influenza period. Pre‐ and post‐epidemic sera were taken from a cohort of adults in Singapore (n=838). Bivariate probit models with latent titre levels were fit to the joint distribution of haemagglutination‐inhibition assay‐determined antibody titres using Markov chain Monte Carlo simulation. Results Estimated attack rates were 15% (95% credible interval: 12%‐19%) for the first H1N1 pandemic wave. For a large outbreak due to a new strain, a threshold of 1:20 and a twofold rise (if pared sera is available) would result in a more accurate estimate of incidence. Conclusion The approach presented here offers the basis for a reconsideration of methods used to assess diagnostic tests by both reconsidering the thresholds used and by analysing serological data with a novel statistical model.
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Affiliation(s)
- Xiahong Zhao
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Karen Siegel
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Mark I-Cheng Chen
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore.,Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
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Yuan HY, Baguelin M, Kwok KO, Arinaminpathy N, van Leeuwen E, Riley S. The impact of stratified immunity on the transmission dynamics of influenza. Epidemics 2017; 20:84-93. [PMID: 28395850 PMCID: PMC5628170 DOI: 10.1016/j.epidem.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 12/09/2022] Open
Abstract
The disease model with stratified immunity improves the accuracy on influenza epidemic reconstruction. Antibody boosting in children is greater than adults during influenza outbreak. Age-specific mixing pattern and the relative infectivity of children to adults are the key drivers of infection heterogeneity.
Although empirical studies show that protection against influenza infection in humans is closely related to antibody titres, influenza epidemics are often described under the assumption that individuals are either susceptible or not. Here we develop a model in which antibody titre classes are enumerated explicitly and mapped onto a variable scale of susceptibility in different age groups. Fitting only with pre- and post-wave serological data during 2009 pandemic in Hong Kong, we demonstrate that with stratified immunity, the timing and the magnitude of the epidemic dynamics can be reconstructed more accurately than is possible with binary seropositivity data. We also show that increased infectiousness of children relative to adults and age-specific mixing are required to reproduce age-specific seroprevalence observed in Hong Kong, while pre-existing immunity in the elderly is not. Overall, our results suggest that stratified immunity in an aged-structured heterogeneous population plays a significant role in determining the shape of influenza epidemics.
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Affiliation(s)
- Hsiang-Yu Yuan
- MRC Centre for Outbreak Analysis and Disease Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Marc Baguelin
- Respiratory Diseases Department, Public Health England, London, United Kingdom; Centre for the Mathematical Modelling of Infectious Disease, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom.
| | - Kin O Kwok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Nimalan Arinaminpathy
- MRC Centre for Outbreak Analysis and Disease Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Edwin van Leeuwen
- MRC Centre for Outbreak Analysis and Disease Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom; Respiratory Diseases Department, Public Health England, London, United Kingdom
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Disease Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.
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Pepin KM, Kay SL, Golas BD, Shriner SS, Gilbert AT, Miller RS, Graham AL, Riley S, Cross PC, Samuel MD, Hooten MB, Hoeting JA, Lloyd‐Smith JO, Webb CT, Buhnerkempe MG. Inferring infection hazard in wildlife populations by linking data across individual and population scales. Ecol Lett 2017; 20:275-292. [PMID: 28090753 PMCID: PMC7163542 DOI: 10.1111/ele.12732] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/28/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022]
Abstract
Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed. Specifically, within-host antibody kinetics in wildlife hosts can be short-lived and produce patterns that are repeatable across individuals, suggesting individual-level antibody concentrations could be used to infer time since infection and hence FOI. Using simulations and case studies (influenza A in lesser snow geese and Yersinia pestis in coyotes), we argue that with careful experimental and surveillance design, the population-level FOI signal can be recovered from individual-level antibody kinetics, despite substantial individual-level variation. In addition to improving inference, the cross-scale quantitative antibody approach we describe can reveal insights into drivers of individual-based variation in disease response, and the role of poorly understood processes such as secondary infections, in population-level dynamics of disease.
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Affiliation(s)
- Kim M. Pepin
- National Wildlife Research CenterUnited States Department of Agriculture4101 Laporte Ave.Fort CollinsCO80521USA
| | - Shannon L. Kay
- National Wildlife Research CenterUnited States Department of Agriculture4101 Laporte Ave.Fort CollinsCO80521USA
| | - Ben D. Golas
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Susan S. Shriner
- National Wildlife Research CenterUnited States Department of Agriculture4101 Laporte Ave.Fort CollinsCO80521USA
| | - Amy T. Gilbert
- National Wildlife Research CenterUnited States Department of Agriculture4101 Laporte Ave.Fort CollinsCO80521USA
| | - Ryan S. Miller
- Animal and Plant Health Inspection ServiceUnited States Department of AgricultureVeterinary Services2155 Center DriveBuilding BFort CollinsCO80523USA
| | - Andrea L. Graham
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJ08544USA
| | - Steven Riley
- MRC Centre for Outbreak Analysis and ModellingImperial CollegeLondonUK
| | - Paul C. Cross
- U.S. Geological SurveyNorthern Rocky Mountain Science Center2327 University WayBozemanMT59715USA
| | - Michael D. Samuel
- U. S. Geological SurveyWisconsin Cooperative Wildlife Research Unit1630 Linden DroveUniversity of WisconsinMadisonWI53706USA
| | - Mevin B. Hooten
- U.S. Geological SurveyColorado Cooperative Fish and Wildlife Research Unit; Departments of FishWildlife& Conservation Biology and StatisticsColorado State University1484 Campus DeliveryFort CollinsCO80523USA
| | | | | | - Colleen T. Webb
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
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Horby PW, Laurie KL, Cowling BJ, Engelhardt OG, Sturm‐Ramirez K, Sanchez JL, Katz JM, Uyeki TM, Wood J, Van Kerkhove MD. CONSISE statement on the reporting of Seroepidemiologic Studies for influenza (ROSES-I statement): an extension of the STROBE statement. Influenza Other Respir Viruses 2017; 11:2-14. [PMID: 27417916 PMCID: PMC5155648 DOI: 10.1111/irv.12411] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Population-based serologic studies are a vital tool for understanding the epidemiology of influenza and other respiratory viruses, including the early assessment of the transmissibility and severity of the 2009 influenza pandemic, and Middle East respiratory syndrome coronavirus. However, interpretation of the results of serologic studies has been hampered by the diversity of approaches and the lack of standardized methods and reporting. OBJECTIVE The objective of the CONSISE ROSES-I statement was to improve the quality and transparency of reporting of influenza seroepidemiologic studies and facilitate the assessment of the validity and generalizability of published results. METHODS The ROSES-I statement was developed as an expert consensus of the CONSISE epidemiology and laboratory working groups. The recommendations are presented in the familiar format of a reporting guideline. Because seroepidemiologic studies are a specific type of observational epidemiology study, the ROSES-I statement is built upon the STROBE guidelines. As such, the ROSES-I statement should be seen as an extension of the STROBE guidelines. RESULTS The ROSES-I statement presents 42 items that can be used as a checklist of the information that should be included in the results of published seroepidemiologic studies, and which can also serve as a guide to the items that need to be considered during study design and implementation. CONCLUSIONS We hope that the ROSES-I statement will contribute to improving the quality of reporting of seroepidemiologic studies.
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Affiliation(s)
- Peter W. Horby
- Nuffield Department of MedicineCentre for Tropical Medicine and Global HealthUniversity of OxfordOxfordUK
| | - Karen L. Laurie
- WHO Collaborating Centre for Reference and Research on Influenzaat the Peter Doherty Institute for Infectious DiseasesMelbourneAustralia
| | - Benjamin J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and ControlSchool of Public HealthLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong Special Administrative RegionChina
| | - Othmar G. Engelhardt
- National Institute for Biological Standards and ControlMedicines and Healthcare products Regulatory AgencyPotters BarUK
| | - Katharine Sturm‐Ramirez
- Influenza Division, National Center for Immunization and Respiratory DiseasesCenters for Disease Control and PreventionAtlantaGAUSA
| | - Jose L. Sanchez
- Armed Forces Health Surveillance Center (AFHSC) and Cherokee Nation Technology Solutions, IncSilver SpringMDUSA
| | - Jacqueline M. Katz
- Influenza Division, National Center for Immunization and Respiratory DiseasesCenters for Disease Control and PreventionAtlantaGAUSA
| | - Timothy M. Uyeki
- Influenza Division, National Center for Immunization and Respiratory DiseasesCenters for Disease Control and PreventionAtlantaGAUSA
| | - John Wood
- National Institute for Biological Standards and ControlMedicines and Healthcare products Regulatory AgencyPotters BarUK
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Leung K, Lipsitch M, Yuen KY, Wu JT. Monitoring the fitness of antiviral-resistant influenza strains during an epidemic: a mathematical modelling study. THE LANCET. INFECTIOUS DISEASES 2016; 17:339-347. [PMID: 27914853 DOI: 10.1016/s1473-3099(16)30465-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Antivirals (eg, oseltamivir) are important for mitigating influenza epidemics. In 2007, an oseltamivir-resistant influenza seasonal A H1N1 strain emerged and spread to global fixation within 1 year. This event showed that antiviral-resistant (AVR) strains can be intrinsically more transmissible than their contemporaneous antiviral-sensitive (AVS) counterpart. Surveillance of AVR fitness is therefore essential. Our objective was to develop a simple method for estimating AVR fitness from surveillance data. METHODS We defined the fitness of AVR strains as their reproductive number relative to their co-circulating AVS counterparts. We developed a simple method for real-time estimation of AVR fitness from surveillance data. This method requires only information on generation time without other specific details regarding transmission dynamics. We first used simulations to validate this method by showing that it yields unbiased and robust fitness estimates in most epidemic scenarios. We then applied this method to two retrospective case studies and one hypothetical case study. FINDINGS We estimated that the oseltamivir-resistant A H1N1 strain that emerged in 2007 was 4% (95% credible interval [CrI] 3-5) more transmissible than its oseltamivir-sensitive predecessor and the oseltamivir-resistant pandemic A H1N1 strain that emerged and circulated in Japan during 2013-14 was 24% (95% CrI 17-30) less transmissible than its oseltamivir-sensitive counterpart. We show that in the event of large-scale antiviral interventions during a pandemic with co-circulation of AVS and AVR strains, our method can be used to inform optimal use of antivirals by monitoring intrinsic AVR fitness and drug pressure on the AVS strain. INTERPRETATION We developed a simple method that can be easily integrated into contemporary influenza surveillance systems to provide reliable estimates of AVR fitness in real time. FUNDING Research Fund for the Control of Infectious Disease (09080792) and a commissioned grant from the Health and Medical Research Fund from the Government of the Hong Kong Special Administrative Region, Harvard Center for Communicable Disease Dynamics from the National Institute of General Medical Sciences (grant number U54 GM088558), Area of Excellence Scheme of the Hong Kong University Grants Committee (grant number AoE/M-12/06).
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Affiliation(s)
- Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Marc Lipsitch
- Department of Epidemiology, Centre for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Kwok Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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32
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Li HJ, Cheng Q, Wang L. Understanding spatial spread of emerging infectious diseases in contemporary populations: Comment on "Pattern transitions in spatial epidemics: Mechanisms and emergent properties" by Gui-Quan Sun et al. Phys Life Rev 2016; 19:95-97. [PMID: 27818036 DOI: 10.1016/j.plrev.2016.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/21/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Hui-Jia Li
- School of Management Science and Engineering, Central University of Finance and Economics, Beijing 100080, China
| | - Qing Cheng
- Science and Technology on Information Systems Engineering Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Lin Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Abstract
BACKGROUND In influenza epidemiology, analysis of paired sera collected from people before and after influenza seasons has been used for decades to study the cumulative incidence of influenza virus infections in populations. However, interpretation becomes challenging when sera are collected after the start or before the end of an epidemic, and do not neatly bracket the epidemic. METHODS Serum samples were collected longitudinally in a community-based study. Most participants provided their first serum after the start of circulation of influenza A(H1N1)pdm09 virus in 2009. We developed a Bayesian hierarchical model to correct for nonbracketing sera and estimate the cumulative incidence of infection from the serological data and surveillance data in Hong Kong. RESULTS We analyzed 4,843 sera from 2,097 unvaccinated participants in the study, collected from April 2009 to December 2010. After accounting for nonbracketing, we estimated that the cumulative incidence of H1N1pdm09 virus infection was 45% (95% credible interval [CI] = 40%, 49%), 17% (95% CI = 13%, 20%), and 11% (95% CI = 6%, 18%) for children ages 0-18 years, adults 19-50 years, and older adults >50 years, respectively. Including all available data substantially increased precision compared with a simpler analysis based only on sera collected at 6-month intervals in a subset of participants. CONCLUSIONS We developed a framework for the analysis of antibody titers that accounted for the timing of sera collection with respect to influenza activity and permitted robust estimation of the cumulative incidence of infection during an epidemic.
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Quantifying homologous and heterologous antibody titre rises after influenza virus infection. Epidemiol Infect 2016; 144:2306-16. [PMID: 27018720 DOI: 10.1017/s0950268816000583] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most influenza virus infections are associated with mild disease. One approach to estimate the occurrence of influenza virus infections in individuals is via repeated measurement of humoral antibody titres. We used baseline and convalescent antibody titres measured by haemagglutination inhibition (HI) and viral neutralization (VN) assays against influenza A(H1N1), A(H3N2) and B viruses to investigate the characteristics of antibody rises following virologically confirmed influenza virus infections in participants in a community-based study. Multivariate models were fitted in a Bayesian framework to characterize the distribution of changes in antibody titres following influenza A virus infections. In 122 participants with PCR-confirmed influenza A virus infection, homologous antibody titres rose by geometric means of 1·2- to 10·2-fold after infection with A(H1N1), A(H3N2) and A(H1N1)pdm09. Significant cross-reactions were observed between A(H1N1)pdm09 and seasonal A(H1N1). Antibody titre rises for some subtypes and assays varied by age, receipt of oseltamivir treatment, and recent receipt of influenza vaccination. In conclusion, we provided a quantitative description of the mean and variation in rises in influenza virus antibody titres following influenza virus infection. The multivariate patterns in boosting of antibody titres following influenza virus infection could be taken into account to improve estimates of cumulative incidence of infection in seroepidemiological studies.
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Peiris JSM, Cowling BJ, Wu JT, Feng L, Guan Y, Yu H, Leung GM. Interventions to reduce zoonotic and pandemic risks from avian influenza in Asia. THE LANCET. INFECTIOUS DISEASES 2016; 16:252-8. [PMID: 26654122 PMCID: PMC5479702 DOI: 10.1016/s1473-3099(15)00502-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/15/2015] [Accepted: 04/23/2015] [Indexed: 01/29/2023]
Abstract
Novel influenza viruses continue to emerge, posing zoonotic and potentially pandemic threats, such as with avian influenza A H7N9. Although closure of live poultry markets (LPMs) in mainland China stopped H7N9 outbreaks temporarily, closures are difficult to sustain, in view of poultry production and marketing systems in China. In this Personal View, we summarise interventions taken in mainland China, and provide evidence for other more sustainable but effective interventions in the live poultry market systems that reduce risk of zoonotic influenza including rest days, and banning live poultry in markets overnight. Separation of live ducks and geese from land-based (ie, non-aquatic) poultry in LPM systems can reduce the risk of emergence of zoonotic and epizootic viruses at source. In view of evidence that H7N9 is now endemic in over half of the provinces in mainland China and will continue to cause recurrent zoonotic disease in the winter months, such interventions should receive high priority in China and other Asian countries at risk of H7N9 through cross-border poultry movements. Such generic measures are likely to reduce known and future threats of zoonotic influenza.
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Affiliation(s)
- J S Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Luzhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Guan
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hongjie Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Affiliation(s)
- Baijayantimala Mishra
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
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37
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Vinh DN, Boni MF. Statistical identifiability and sample size calculations for serial seroepidemiology. Epidemics 2015; 12:30-9. [PMID: 26342240 PMCID: PMC4558460 DOI: 10.1016/j.epidem.2015.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 02/12/2015] [Accepted: 02/24/2015] [Indexed: 11/30/2022] Open
Abstract
We investigate whether disease dynamics can be inferred by repeated serum collections. Measuring antibody waning is critical for inference in serological time series. Collecting 200 samples every 2 months allows for inference of transmission parameters. Low-level seasonality is difficult to detect statistically.
Inference on disease dynamics is typically performed using case reporting time series of symptomatic disease. The inferred dynamics will vary depending on the reporting patterns and surveillance system for the disease in question, and the inference will miss mild or underreported epidemics. To eliminate the variation introduced by differing reporting patterns and to capture asymptomatic or subclinical infection, inferential methods can be applied to serological data sets instead of case reporting data. To reconstruct complete disease dynamics, one would need to collect a serological time series. In the statistical analysis presented here, we consider a particular kind of serological time series with repeated, periodic collections of population-representative serum. We refer to this study design as a serial seroepidemiology (SSE) design, and we base the analysis on our epidemiological knowledge of influenza. We consider a study duration of three to four years, during which a single antigenic type of influenza would be circulating, and we evaluate our ability to reconstruct disease dynamics based on serological data alone. We show that the processes of reinfection, antibody generation, and antibody waning confound each other and are not always statistically identifiable, especially when dynamics resemble a non-oscillating endemic equilibrium behavior. We introduce some constraints to partially resolve this confounding, and we show that transmission rates and basic reproduction numbers can be accurately estimated in SSE study designs. Seasonal forcing is more difficult to identify as serology-based studies only detect oscillations in antibody titers of recovered individuals, and these oscillations are typically weaker than those observed for infected individuals. To accurately estimate the magnitude and timing of seasonal forcing, serum samples should be collected every two months and 200 or more samples should be included in each collection; this sample size estimate is sensitive to the antibody waning rate and the assumed level of seasonal forcing.
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Affiliation(s)
- Dao Nguyen Vinh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Viet Nam
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
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Donis RO. Antigenic analyses of highly pathogenic avian influenza a viruses. Curr Top Microbiol Immunol 2014; 385:403-40. [PMID: 25190014 DOI: 10.1007/82_2014_422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
In response to the ongoing threat to animal and human health posed by HPAI endemic in poultry, Asia (H5N1) and North America (H7N3) have revived efforts to reduce pandemic risk by disease control at the source and improved pandemic vaccines. Discovery of conserved neutralization epitopes in the HA, which mediate broad protection within and across HA subtypes have changed the paradigm of "broadly reactive" or "universal" vaccine design. Development of such vaccines would benefit from comparative antigenic analysis of viruses with increasing divergence within (and between) HA subtypes. A review of recent work to define the antigenic properties of HPAI viruses revealed data generated through an array of experimental approaches. This information has supported diagnostics and vaccine development for animal and human health. Further harmonization of analytical methods is needed to determine the antigenic relationships among multiple lineages of rapidly evolving HPAI viruses.
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Affiliation(s)
- Ruben O Donis
- Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road NE Mailstop A20, Atlanta, GA, 30333, USA,
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