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Townsend JP, Hassler HB, Lamb AD, Sah P, Alvarez Nishio A, Nguyen C, Tew AD, Galvani AP, Dornburg A. Seasonality of endemic COVID-19. mBio 2023; 14:e0142623. [PMID: 37937979 PMCID: PMC10746271 DOI: 10.1128/mbio.01426-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE The seasonality of COVID-19 is important for effective healthcare and public health decision-making. Previous waves of SARS-CoV-2 infections have indicated that the virus will likely persist as an endemic pathogen with distinct surges. However, the timing and patterns of potentially seasonal surges remain uncertain, rendering effective public health policies uninformed and in danger of poorly anticipating opportunities for intervention, such as well-timed booster vaccination drives. Applying an evolutionary approach to long-term data on closely related circulating coronaviruses, our research provides projections of seasonal surges that should be expected at major temperate population centers. These projections enable local public health efforts that are tailored to expected surges at specific locales or regions. This knowledge is crucial for enhancing medical preparedness and facilitating the implementation of targeted public health interventions.
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Affiliation(s)
- Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Program in Microbiology, Yale University, New Haven, USA
| | - Hayley B. Hassler
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
| | - April D. Lamb
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Pratha Sah
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | | | - Cameron Nguyen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alexandra D. Tew
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alison P. Galvani
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
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2
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Scabbia G, Sanfilippo A, Mazzoni A, Bachour D, Perez-Astudillo D, Bermudez V, Wey E, Marchand-Lasserre M, Saboret L. Does climate help modeling COVID-19 risk and to what extent? PLoS One 2022; 17:e0273078. [PMID: 36070304 PMCID: PMC9451080 DOI: 10.1371/journal.pone.0273078] [Citation(s) in RCA: 4] [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: 01/22/2022] [Accepted: 08/01/2022] [Indexed: 11/25/2022] Open
Abstract
A growing number of studies suggest that climate may impact the spread of COVID-19. This hypothesis is supported by data from similar viral contagions, such as SARS and the 1918 Flu Pandemic, and corroborated by US influenza data. However, the extent to which climate may affect COVID-19 transmission rates and help modeling COVID-19 risk is still not well understood. This study demonstrates that such an understanding is attainable through the development of regression models that verify how climate contributes to modeling COVID-19 transmission, and the use of feature importance techniques that assess the relative weight of meteorological variables compared to epidemiological, socioeconomic, environmental, and global health factors. The ensuing results show that meteorological factors play a key role in regression models of COVID-19 risk, with ultraviolet radiation (UV) as the main driver. These results are corroborated by statistical correlation analyses and a panel data fixed-effect model confirming that UV radiation coefficients are significantly negatively correlated with COVID-19 transmission rates.
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Affiliation(s)
- Giovanni Scabbia
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University – Qatar Foundation, Doha, Qatar
| | - Antonio Sanfilippo
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University – Qatar Foundation, Doha, Qatar
| | - Annamaria Mazzoni
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University – Qatar Foundation, Doha, Qatar
| | - Dunia Bachour
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University – Qatar Foundation, Doha, Qatar
| | - Daniel Perez-Astudillo
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University – Qatar Foundation, Doha, Qatar
| | - Veronica Bermudez
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University – Qatar Foundation, Doha, Qatar
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3
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Chirumbolo S, Pandolfi S, Valdenassi L. Seasonality of COVID-19 deaths. Did social restrictions and vaccination actually impact the official reported dynamic of COVID-19 pandemic in Italy? ENVIRONMENTAL RESEARCH 2022; 212:113229. [PMID: 35405125 PMCID: PMC8989664 DOI: 10.1016/j.envres.2022.113229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/22/2022] [Accepted: 03/30/2022] [Indexed: 05/30/2023]
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Zhu M, Zeng Q, Saputro BIL, Chew SP, Chew I, Frendy H, Tan JW, Li L. Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data. Virol J 2022; 19:103. [PMID: 35710544 PMCID: PMC9202327 DOI: 10.1186/s12985-022-01830-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. METHODS For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID's EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. RESULTS As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia's daily infections during the period of March-May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. CONCLUSIONS SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential.
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Affiliation(s)
- Mingjian Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianli Zeng
- Shanghai Institute of Biological Products, Shanghai, China
| | | | - Sien Ping Chew
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ian Chew
- Zhejiang University School of Medicine, Hangzhou, China
| | - Holie Frendy
- Faculty of Medicine and Health Sciences, Krida Wacana Christian University, Jakarta, Indonesia
| | - Joanna Weihui Tan
- Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Inaida S, Paul RE, Matsuno S. Viral transmissibility of SARS-CoV-2 accelerates in the winter, similarly to influenza epidemics. Am J Infect Control 2022; 50:1070-1076. [PMID: 35605752 PMCID: PMC9121648 DOI: 10.1016/j.ajic.2022.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023]
Abstract
The transmissibility of SARS-CoV-2 is anticipated to increase in the winter because of increased viral survival in cold damp air and thus would exacerbate viral spread in community. Analysis to capture the seasonal trend is needed to be prepared for future epidemics. We compared regression models for the 5-week case prior to each epidemic peak week for both the COVID-19 and influenza epidemics in winter and summer. The weekly case increase ratio was compared, using non-paired t tests between seasons. In order to test the robustness of seasonal transmission patterns, the normalized weekly case numbers of COVID-19 and influenza case rates of all seasons were assessed in a combined quadratic regression analysis. In winter, the weekly case increase ratio accelerated before epidemic peaks, similarly, for both COVID-19 and influenza. The quadratic regression models of weekly cases were observed to be convex curves in the winter and concave curves in the spring/summer for both COVID-19 and influenza. A significant increase of case increase ratio (3.19 [95%CI:0.01-6.37, P = .049]) of the COVID-19 and influenza epidemics was observed in winter as compared to spring/summer before the epidemic peak. The epidemic of COVID-19 was found to mirror that of influenza, suggesting a strong underlying seasonal transmissibility. Influenza epidemics can potentially be a useful reference for the COVID-19 epidemics.
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Coccia M. COVID-19 pandemic over 2020 (withlockdowns) and 2021 (with vaccinations): similar effects for seasonality and environmental factors. ENVIRONMENTAL RESEARCH 2022; 208:112711. [PMID: 35033552 PMCID: PMC8757643 DOI: 10.1016/j.envres.2022.112711] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 05/19/2023]
Abstract
How is the dynamics of Coronavirus Disease 2019 (COVID-19) in 2020 with an health policy of full lockdowns and in 2021 with a vast campaign of vaccinations? The present study confronts this question here by developing a comparative analysis of the effects of COVID-19 pandemic between April-September 2020 (based upon strong control measures) and April-September 2021 (focused on health policy of vaccinations) in Italy, which was one of the first European countries to experience in 2020 high numbers of COVID-19 related infected individuals and deaths and in 2021 Italy has a high share of people fully vaccinated against COVID-19 (>89% of population aged over 12 years in January 2022). Results suggest that over the period under study, the arithmetic mean of confirmed cases, hospitalizations of people and admissions to Intensive Care Units (ICUs) in 2020 and 2021 is significantly equal (p-value<0.01), except fatality rate. Results suggest in December 2021 lower hospitalizations, admissions to ICUs, and fatality rate of COVID-19 than December 2020, though confirmed cases and mortality rates are in 2021 higher than 2020, and likely converging trends in the first quarter of 2022. These findings reveal that COVID-19 pandemic is driven by seasonality and environmental factors that reduce the negative effects in summer period, regardless control measures and/or vaccination campaigns. These findings here can be of benefit to design health policy responses of crisis management considering the growth of COVID-19 pandemic in winter months having reduced temperatures and low solar radiations ( COVID-19 has a behaviour of influenza-like illness). Hence, findings here suggest that strategies of prevention and control of infectious diseases similar to COVID-19 should be set up in summer months and fully implemented during low-solar-irradiation periods (autumn and winter period).
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Affiliation(s)
- Mario Coccia
- CNR, National Research Council of Italy - Via Real Collegio, n. 30 (Collegio Carlo Alberto), 10024, Moncalieri (TO), Italy.
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Albergamo A, Apprato G, Silvagno F. The Role of Vitamin D in Supporting Health in the COVID-19 Era. Int J Mol Sci 2022; 23:3621. [PMID: 35408981 PMCID: PMC8998275 DOI: 10.3390/ijms23073621] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
The genomic activity of vitamin D is associated with metabolic effects, and the hormone has a strong impact on several physiological functions and, therefore, on health. Among its renowned functions, vitamin D is an immunomodulator and a molecule with an anti-inflammatory effect, and, recently, it has been much studied in relation to its response against viral infections, especially against COVID-19. This review aims to take stock of the correlation studies between vitamin D deficiency and increased risks of severe COVID-19 disease and, similarly, between vitamin D deficiency and acute respiratory distress syndrome. Based on this evidence, supplementation with vitamin D has been tested in clinical trials, and the results are discussed. Finally, this study includes a biochemical analysis on the effects of vitamin D in the body's defense mechanisms against viral infection. In particular, the antioxidant and anti-inflammatory functions are considered in relation to energy metabolism, and the potential, beneficial effect of vitamin D in COVID-19 is described, with discussion of its influence on different biochemical pathways. The proposed, broader view of vitamin D activity could support a better-integrated approach in supplementation strategies against severe COVID-19, which could be valuable in a near future of living with an infection becoming endemic.
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Affiliation(s)
- Alice Albergamo
- Department of Oncology, University of Torino, 10126 Torino, Italy
| | - Giulia Apprato
- Department of Oncology, University of Torino, 10126 Torino, Italy
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Sun W, Hu X, Hu Y, Zhang G, Guo Z, Lin J, Huang J, Cai X, Dai J, Wang X, Zhang X, Bi X, Zhong N. 大气环境对SARS-CoV-2传播的影响研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2021-1228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mukherjee SB, Gorohovski A, Merzon E, Levy E, Mukherjee S, Frenkel‐Morgenstern M. Seasonal UV exposure and vitamin D: association with the dynamics of COVID-19 transmission in Europe. FEBS Open Bio 2022; 12:106-117. [PMID: 34608759 PMCID: PMC8653358 DOI: 10.1002/2211-5463.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/12/2021] [Accepted: 10/04/2021] [Indexed: 12/23/2022] Open
Abstract
Several recent studies have demonstrated that low plasma 25(OH) vitamin D levels are associated with the risk of COVID-19 infection. The primary source of vitamin D production in humans is environmental UV radiation. In many viral respiratory diseases, peak infection rates are observed during winter due to reduced UV exposure and low temperatures. In Europe, the second wave of COVID-19 began early in the winter of 2020. Investigating the impact of seasonal temperature and UV exposure on COVID-19 transmission could thus aid in prevention and intervention. As such, we first performed a comprehensive meta-analysis of all related published literature based on the association between vitamin D and COVID-19, which supported the hypothesis that the low vitamin D level is a critical risk factor for COVID-19 infection. Next, to understand the potential impact of seasonal UV and temperature levels on COVID-19 cases, we analyzed meteorological data and daily COVID-19 cases per million in the populations of 26 European countries. We observed that low temperature, UV index, and cloud-free vitamin D UV dose (UVDVF) levels are negatively correlated with COVID-19 prevalence in Europe. Furthermore, a distributed lag nonlinear model was used to assess the nonlinear delayed effects of individual seasonal factors on COVID-19 cases. Such analysis highlighted the significantly delayed impact of UVDVF on the cumulative relative risk of COVID-19 infection. The findings of this study suggest that low UV exposure can affect the required production of vitamin D in the body, which substantially influences the dynamics of COVID-19 transmission and severity.
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Affiliation(s)
- Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases LabAzrieli Faculty of MedicineBar‐Ilan UniversitySafedIsrael
| | - Alessandro Gorohovski
- Cancer Genomics and BioComputing of Complex Diseases LabAzrieli Faculty of MedicineBar‐Ilan UniversitySafedIsrael
| | - Eugene Merzon
- Leumit Health ServicesTel AvivIsrael
- Department of Family MedicineSackler School of MedicineTel Aviv UniversityIsrael
| | - Eliad Levy
- Cancer Genomics and BioComputing of Complex Diseases LabAzrieli Faculty of MedicineBar‐Ilan UniversitySafedIsrael
| | - Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases LabAzrieli Faculty of MedicineBar‐Ilan UniversitySafedIsrael
| | - Milana Frenkel‐Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases LabAzrieli Faculty of MedicineBar‐Ilan UniversitySafedIsrael
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Caetano-Anollés K, Hernandez N, Mughal F, Tomaszewski T, Caetano-Anollés G. The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike. METHODS IN MICROBIOLOGY 2021; 50:27-81. [PMID: 38620818 PMCID: PMC8590929 DOI: 10.1016/bs.mim.2021.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.
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Affiliation(s)
| | - Nicolas Hernandez
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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