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Chen C, Yang M, Wang Y, Jiang D, Du Y, Cao K, Zhang X, Wu X, Chen M, You Y, Zhou W, Qi J, Yan R, Zhu C, Yang S. Intensity and drivers of subtypes interference between seasonal influenza viruses in mainland China: A modeling study. iScience 2024; 27:109323. [PMID: 38487011 PMCID: PMC10937832 DOI: 10.1016/j.isci.2024.109323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
Subtype interference has a significant impact on the epidemiological patterns of seasonal influenza viruses (SIVs). We used attributable risk percent [the absolute value of the ratio of the effective reproduction number (Rₑ) of different subtypes minus one] to quantify interference intensity between A/H1N1 and A/H3N2, as well as B/Victoria and B/Yamagata. The interference intensity between A/H1N1 and A/H3N2 was higher in southern China 0.26 (IQR: 0.11-0.46) than in northern China 0.17 (IQR: 0.07-0.24). Similarly, interference intensity between B/Victoria and B/Yamagata was also higher in southern China 0.14 (IQR: 0.07-0.24) than in norther China 0.10 (IQR: 0.04-0.18). High relative humidity significantly increased subtype interference, with the highest relative risk reaching 20.59 (95% CI: 6.12-69.33) in southern China. Southern China exhibited higher levels of subtype interference, particularly between A/H1N1 and A/H3N2. Higher relative humidity has a more pronounced promoting effect on subtype interference.
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Affiliation(s)
- Can Chen
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengya Yang
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Wang
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Daixi Jiang
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yuxia Du
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Kexin Cao
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaobao Zhang
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaoyue Wu
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengsha Chen
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yue You
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wenkai Zhou
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jiaxing Qi
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Rui Yan
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Changtai Zhu
- Department of Transfusion Medicine, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Shigui Yang
- Department of Emergency Medicine, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
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Fan R, Geritz SAH. Evolution of pathogens with cross-immunity in response to healthcare interventions. J Theor Biol 2023; 572:111575. [PMID: 37423484 DOI: 10.1016/j.jtbi.2023.111575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Cross-immunity, as an evolutionary driver, can contribute to pathogen evolution, particularly pathogen diversity. Healthcare interventions aimed at reducing disease severity or transmission are commonly used to control diseases and can also induce pathogen evolution. Understanding pathogen evolution in the context of cross-immunity and healthcare interventions is crucial for infection control. This study starts by modelling cross-immunity, the extent of which is determined by strain traits and host characteristics. Given that all hosts have the same characteristics, full cross-immunity between residents and mutants occurs when mutation step sizes are small enough. Cross-immunity can be partial when the step size is large. The presence of partial cross-immunity reduces pathogen load and shortens the infectious period inside hosts, reducing transmission between hosts and improving host population survival and recovery. This study focuses on how pathogens evolve through small and large mutational steps and how healthcare interventions affect pathogen evolution. Using the theory of adaptive dynamics, we found that when mutational steps are small (only full cross-immunity is present), pathogen diversity cannot occur because it maximises the basic reproduction number. This results in intermediate values for both pathogen growth and clearance rates. However, when large mutational steps are allowed (with full and partial cross-immunity present), pathogens can evolve into multiple strains and induce pathogen diversity. The study also shows that different healthcare interventions can have varying effects on pathogen evolution. Generally, low levels of intervention are more likely to induce strain diversity, while high levels are more likely to result in strain reduction.
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Affiliation(s)
- Ruili Fan
- Department of Mathematics and Statistics, University of Helsinki, FIN-00014, Finland.
| | - Stefan A H Geritz
- Department of Mathematics and Statistics, University of Helsinki, FIN-00014, Finland
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Sachak-Patwa R, Lafferty EI, Schmit CJ, Thompson RN, Byrne HM. A target-cell limited model can reproduce influenza infection dynamics in hosts with differing immune responses. J Theor Biol 2023; 567:111491. [PMID: 37044357 DOI: 10.1016/j.jtbi.2023.111491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
We consider a hierarchy of ordinary differential equation models that describe the within-host viral kinetics of influenza infections: the IR model explicitly accounts for an immune response to the virus, while the simpler, target-cell limited TEIV and TV models do not. We show that when the IR model is fitted to pooled experimental murine data of the viral load, fraction of dead cells, and immune response levels, its parameters values can be determined. However, if, as is common, only viral load data are available, we can estimate parameters of the TEIV and TV models but not the IR model. These results are substantiated by a structural and practical identifiability analysis. We then use the IR model to generate synthetic data representing infections in hosts whose immune responses differ. We fit the TV model to these synthetic datasets and show that it can reproduce the characteristic exponential increase and decay of viral load generated by the IR model. Furthermore, the values of the fitted parameters of the TV model can be mapped from the immune response parameters in the IR model. We conclude that, if only viral load data are available, a simple target-cell limited model can reproduce influenza infection dynamics and distinguish between hosts with differing immune responses.
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Affiliation(s)
- Rahil Sachak-Patwa
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK.
| | - Erin I Lafferty
- Biosensors Beyond Borders Limited, 9 Bedford Square, London, WC1B 3RE, UK
| | - Claude J Schmit
- Biosensors Beyond Borders Limited, 9 Bedford Square, London, WC1B 3RE, UK
| | - Robin N Thompson
- Mathematics Institute, University of Warwick, Zeeman Building, Coventry, CV4 7AL, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4 7AL, UK
| | - Helen M Byrne
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
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Sachak-Patwa R, Byrne HM, Dyson L, Thompson RN. The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions. COMMUNICATIONS MEDICINE 2021; 1:39. [PMID: 35602220 PMCID: PMC9053223 DOI: 10.1038/s43856-021-00038-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022] Open
Abstract
Background Countries around the world have introduced travel restrictions to reduce SARS-CoV-2 transmission. As vaccines are gradually rolled out, attention has turned to when travel restrictions and other non-pharmaceutical interventions (NPIs) can be relaxed. Methods Using SARS-CoV-2 as a case study, we develop a mathematical branching process model to assess the risk that, following the removal of NPIs, cases arriving in low prevalence settings initiate a local outbreak. Our model accounts for changes in background population immunity due to vaccination. We consider two locations with low prevalence in which the vaccine rollout has progressed quickly – specifically, the Isle of Man (a British crown dependency in the Irish Sea) and the country of Israel. Results We show that the outbreak risk is unlikely to be eliminated completely when travel restrictions and other NPIs are removed. This general result is the most important finding of this study, rather than exact quantitative outbreak risk estimates in different locations. It holds even once vaccine programmes are completed. Key factors underlying this result are the potential for transmission even following vaccination, incomplete vaccine uptake, and the recent emergence of SARS-CoV-2 variants with increased transmissibility. Conclusions Combined, the factors described above suggest that, when travel restrictions are relaxed, it may still be necessary to implement surveillance of incoming passengers to identify infected individuals quickly. This measure, as well as tracing and testing (and/or isolating) contacts of detected infected passengers, remains useful to suppress potential outbreaks while global case numbers are high. The effectiveness of public health measures against COVID-19 has varied between countries, with some experiencing many infections and others containing transmission successfully. As vaccines are deployed, an important challenge is deciding when to relax measures. Here, we consider locations with few cases, and investigate whether vaccination can ever eliminate the risk of COVID-19 outbreaks completely, allowing measures to be removed risk-free. Using a mathematical model, we demonstrate that there is still a risk that imported cases initiate outbreaks when measures are removed, even if most of the population is fully vaccinated. This highlights the need for continued vigilance in low prevalence settings to prevent imported cases leading to local transmission. Until case numbers are reduced globally, so that SARS-CoV-2 spread between countries is less likely, the risk of outbreaks in low prevalence settings will remain. Sachak-Patwa et al. estimate the risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions and other non-pharmaceutical interventions, with the Isle of Man and Israel as case studies. Using a branching process mathematical model, the authors show that even after a large proportion of the population is vaccinated, there remains a risk of local outbreaks from imported cases.
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