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Special Issue "Infectious Disease Epidemiology and Transmission Dynamics"

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 9803

Special Issue Editors

Dr. Lin Wang
E-Mail Website
Guest Editor
Department of Genetics, University of Cambridge, Cambridge, UK
Interests: infectious disease dynamics; epidemiology; Bayesian modeling; machine learning; immunology; pathogen evolution
Dr. Zhanwei Du
E-Mail Website
Guest Editor
School of Public Health, University of Hong Kong, Hong Kong Special Administrative Region, China
Interests: computational epidemiology; viral epidemiology; infectious diseases
Dr. Wei Luo
E-Mail Website
Guest Editor
Department of Geography, National University of Singapore, Singapore
Interests: computational epidemiology; agent-based epidemic modeling; infectious diseases surveillance, transmission, and control
Dr. Rachel Sippy
E-Mail Website
Guest Editor
Department of Genetics, University of Cambridge, Cambridge, UK
Interests: epidemiology; infectious diseases; machine learning; statistics; mathematical modeling; phylogenetics

Special Issue Information

Dear Colleagues,

To understand the epidemiology and transmission dynamics of infectious diseases (e.g., COVID-19, influenza, arboviruses, human papillomavirus (HPV), and human immunodeficiency virus (HIV)), epidemiologists and mathematical modelers are continuously developing new methods to characterize transmission patterns and transmission mechanisms, estimate infection and disease burdens, reconstruct transmission history, forecast disease trends and healthcare demands, and evaluate the effectiveness or cost-effectiveness of intervention policies (e.g., mass testing, vaccination champions, stockpiling of antivirals). This Special Issue of Viruses welcomes submissions of epidemiological and infectious disease modeling studies. In particular, research that is relevant to the evaluation of the epidemiological and/or economic impacts of ramping up treatments by mass testing, existing or next generation antivirals, and vaccinations is welcome.

This Special Issue aims to explore different research areas and to collect articles that focus on infectious disease epidemiology and transmission dynamics. Furthermore, we expect to gain more insight into the applications of such approaches in various areas such as public health, health economics, health informatics, evolution, immunity, and medical affairs.

We encourage the submission of high-quality original research, review, protocol, and perspective articles to this Special Issue. Areas of interest include but are not limited to the following topics:

  1. Infectious disease epidemiology and transmission dynamics;
  2. Spatial and temporal transmission patterns of infectious diseases;
  3. Effects of pharmaceutical interventions such as mass testing, vaccines, or antivirals;
  4. Inference of key epidemiological parameters;
  5. Phylogenetics and phylodynamics;
  6. Seroepidemiology.

Dr. Lin Wang
Dr. Zhanwei Du
Dr. Wei Luo
Dr. Rachel Sippy
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • infectious disease epidemiology
  • mathematical modeling
  • computational epidemiology
  • pharmaceutical interventions (e.g., mass testing, vaccination, antiviral)
  • infection and fatality burden
  • serology
  • phylogenetics and phylodynamics

Published Papers (9 papers)

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Research

Article
The Preventive Role of mRNA Vaccines in Reducing Death among Moderate Omicron-Infected Patients: A Follow-Up Study
Viruses 2022, 14(12), 2622; https://doi.org/10.3390/v14122622 - 24 Nov 2022
Viewed by 237
Abstract
Very few studies have been conducted to assess the potential preventive role of vaccines, particularly mRNA vaccines, in the improvement of survival among moderate and severe hospitalized patients with COVID-19. After community-acquired outbreaks of the Omicron variant from 18 March until 31 May [...] Read more.
Very few studies have been conducted to assess the potential preventive role of vaccines, particularly mRNA vaccines, in the improvement of survival among moderate and severe hospitalized patients with COVID-19. After community-acquired outbreaks of the Omicron variant from 18 March until 31 May 2022, occurred in Taiwan, this retrospective cohort of 4090 moderate and 1378 severe patients admitted to hospital was classified according to whether they were administered an mRNA-based vaccine, and followed up to ascertain rates of death in both the vaccinated (≥2 doses) and unvaccinated (no or 1 dose) groups. The age-adjusted hazard ratio (aHR) of less than 1 was used to assess the preventive role of mRNA vaccines in reducing deaths among moderate and severe Omicron-infected patients. Survival was statistically significantly better for the ≥2 dose jab group (aHR, 0.75, 95% confidence interval [CI], 0.60 to 0.94) and even higher among those who had received a booster jab (aHR, 0.71; 95% CI, 0.55 to 0.91) compared with the unvaccinated group among moderate patients, but not among severe patients. In conclusion, unveiling the role of mRNA vaccines in preventing moderate but not severe COVID-19 patients from death provides new insights into how mRNA vaccines play a role in the pathway leading to a severe outcome due to Omicron COVID-19. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Article
Estimation of R0 for the Spread of the First ASF Epidemic in Italy from Fresh Carcasses
Viruses 2022, 14(10), 2240; https://doi.org/10.3390/v14102240 - 12 Oct 2022
Viewed by 688
Abstract
After fifty years of spread in the European continent, the African swine fever (ASF) virus was detected for the first time in the north of Italy (Piedmont) in a wild boar carcass in December, 2021. During the first six months of the epidemic, [...] Read more.
After fifty years of spread in the European continent, the African swine fever (ASF) virus was detected for the first time in the north of Italy (Piedmont) in a wild boar carcass in December, 2021. During the first six months of the epidemic, the central role of wild boars in disease transmission was confirmed by more than 200 outbreaks, which occurred in two different areas declared as infected. The virus entered a domestic pig farm in the second temporal cluster identified in the center of the country (Lazio). Understanding ASF dynamics in wild boars is a prerequisite for preventing the spread, and for designing and applying effective surveillance and control plans. The aim of this work was to describe and evaluate the data collected during the first six months of the ASF epidemic in Italy, and to estimate the basic reproduction number (R0) in order to quantify the extent of disease spread. The R0 estimates were significantly different for the two spatio-temporal clusters of ASF in Italy, and they identified the two infected areas based on the time necessary for the number of cases to double (td) and on an exponential decay model. These results (R0 = 1.41 in Piedmont and 1.66 in Lazio) provide quantitative knowledge on the epidemiology of ASF in Italy. These parameters could represent a fundamental tool for modeling country-specific ASF transmission and for monitoring both the spread and sampling effort needed to detect the disease early. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Article
Finding Asymptomatic Spreaders in a COVID-19 Transmission Network by Graph Attention Networks
Viruses 2022, 14(8), 1659; https://doi.org/10.3390/v14081659 - 28 Jul 2022
Cited by 1 | Viewed by 714
Abstract
In the COVID-19 epidemic the mildly symptomatic and asymptomatic infections generate a substantial portion of virus spread; these undetected individuals make it difficult to assess the effectiveness of preventive measures as most epidemic prevention strategies are based on the detected data. Effectively identifying [...] Read more.
In the COVID-19 epidemic the mildly symptomatic and asymptomatic infections generate a substantial portion of virus spread; these undetected individuals make it difficult to assess the effectiveness of preventive measures as most epidemic prevention strategies are based on the detected data. Effectively identifying the undetected infections in local transmission will be of great help in COVID-19 control. In this work, we propose an RNA virus transmission network representation model based on graph attention networks (RVTR); this model is constructed using the principle of natural language processing to learn the information of gene sequence and using a graph attention network to catch the topological character of COVID-19 transmission networks. Since SARS-CoV-2 will mutate when it spreads, our approach makes use of graph context loss function, which can reflect that the genetic sequence of infections with close spreading relation will be more similar than those with a long distance, to train our model. Our approach shows its ability to find asymptomatic spreaders both on simulated and real COVID-19 datasets and performs better when compared with other network representation and feature extraction methods. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Article
EpiRegress: A Method to Estimate and Predict the Time-Varying Effective Reproduction Number
Viruses 2022, 14(7), 1576; https://doi.org/10.3390/v14071576 - 20 Jul 2022
Cited by 1 | Viewed by 658
Abstract
The time-varying reproduction (Rt) provides a real-time estimate of pathogen transmissibility and may be influenced by exogenous factors such as mobility and mitigation measures which are not directly related to epidemiology parameters and observations. Meanwhile, evaluating the impacts of these [...] Read more.
The time-varying reproduction (Rt) provides a real-time estimate of pathogen transmissibility and may be influenced by exogenous factors such as mobility and mitigation measures which are not directly related to epidemiology parameters and observations. Meanwhile, evaluating the impacts of these factors is vital for policy makers to propose and adjust containment strategies. Here, we developed a Bayesian regression framework, EpiRegress, to provide Rt estimates and assess impacts of diverse factors on virus transmission, utilising daily case counts, mobility, and policy data. To demonstrate the method’s utility, we used simulations as well as data in four regions from the Western Pacific with periods of low COVID-19 incidence, namely: New South Wales, Australia; New Zealand; Singapore; and Taiwan, China. We found that imported cases had a limited contribution on the overall epidemic dynamics but may degrade the quality of the Rt estimate if not explicitly accounted for. We additionally demonstrated EpiRegress’s capability in nowcasting disease transmissibility before contemporaneous cases diagnosis. The approach was proved flexible enough to respond to periods of atypical local transmission during epidemic lulls and to periods of mass community transmission. Furthermore, in epidemics where travel restrictions are present, it is able to distinguish the influence of imported cases. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Article
Modeling the Impact of Vaccination on COVID-19 and Its Delta and Omicron Variants
Viruses 2022, 14(7), 1482; https://doi.org/10.3390/v14071482 - 06 Jul 2022
Cited by 3 | Viewed by 969
Abstract
Vaccination is an important means to fight against the spread of the SARS-CoV-2 virus and its variants. In this work, we propose a general susceptible-vaccinated-exposed-infected-hospitalized-removed (SVEIHR) model and derive its basic and effective reproduction numbers. We set Hong Kong as an example and [...] Read more.
Vaccination is an important means to fight against the spread of the SARS-CoV-2 virus and its variants. In this work, we propose a general susceptible-vaccinated-exposed-infected-hospitalized-removed (SVEIHR) model and derive its basic and effective reproduction numbers. We set Hong Kong as an example and calculate conditions of herd immunity for multiple vaccines and disease variants. The model shows how the number of confirmed COVID-19 cases in Hong Kong during the second and third waves of the COVID-19 pandemic would have been reduced if vaccination were available then. We then investigate the relationships between various model parameters and the cumulative number of hospitalized COVID-19 cases in Hong Kong for the ancestral, Delta, and Omicron strains. Numerical results demonstrate that the static herd immunity threshold corresponds to one percent of the population requiring hospitalization or isolation at some point in time. We also demonstrate that when the vaccination rate is high, the initial proportion of vaccinated individuals can be lowered while still maintaining the same proportion of cumulative hospitalized/isolated individuals. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Article
Strategies to Mitigate Establishment under the Wolbachia Incompatible Insect Technique
Viruses 2022, 14(6), 1132; https://doi.org/10.3390/v14061132 - 24 May 2022
Viewed by 1008
Abstract
The Incompatible Insect Technique (IIT) strategy involves the release of male mosquitoes infected with the bacterium Wolbachia. Regular releases of male Wolbachia-infected mosquitoes can lead to the suppression of mosquito populations, thereby reducing the risk of transmission of vector-borne diseases such [...] Read more.
The Incompatible Insect Technique (IIT) strategy involves the release of male mosquitoes infected with the bacterium Wolbachia. Regular releases of male Wolbachia-infected mosquitoes can lead to the suppression of mosquito populations, thereby reducing the risk of transmission of vector-borne diseases such as dengue. However, due to imperfect sex-sorting under IIT, fertile Wolbachia-infected female mosquitoes may potentially be unintentionally released into the environment, which may result in replacement and failure to suppress the mosquito populations. As such, mitigating Wolbachia establishment requires a combination of IIT with other strategies. We introduced a simple compartmental model to simulate ex-ante mosquito population dynamics subjected to a Wolbachia-IIT programme. In silico, we explored the risk of replacement, and strategies that could mitigate the establishment of the released Wolbachia strain in the mosquito population. Our results suggest that mitigation may be achieved through the application of a sterile insect technique. Our simulations indicate that these interventions do not override the intended wild type suppression of the IIT approach. These findings will inform policy makers of possible ways to mitigate the potential establishment of Wolbachia using the IIT population control strategy. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Article
Modelling the Impact of Mass Testing to Transition from Pandemic Mitigation to Endemic COVID-19
Viruses 2022, 14(5), 967; https://doi.org/10.3390/v14050967 - 05 May 2022
Cited by 1 | Viewed by 945
Abstract
As countries transition from pandemic mitigation to endemic COVID-19, mass testing may blunt the impact on the healthcare system of the liminal wave. We used GeoDEMOS-R, an agent-based model of Singapore’s population with demographic distributions and vaccination status. A 250-day COVID-19 Delta variant [...] Read more.
As countries transition from pandemic mitigation to endemic COVID-19, mass testing may blunt the impact on the healthcare system of the liminal wave. We used GeoDEMOS-R, an agent-based model of Singapore’s population with demographic distributions and vaccination status. A 250-day COVID-19 Delta variant model was run at varying maximal rapid antigen test sensitivities and frequencies. Without testing, the number of infections reached 1,021,000 (899,400–1,147,000) at 250 days. When conducting fortnightly and weekly mass routine rapid antigen testing 30 days into the outbreak at a maximal test sensitivity of 0.6, this was reduced by 12.8% (11.3–14.5%) and 25.2% (22.5–28.5%). An increase in maximal test sensitivity of 0.2 results a corresponding reduction of 17.5% (15.5–20.2%) and 34.4% (30.5–39.1%). Within the maximal test sensitivity range of 0.6–0.8, test frequency has a greater impact than maximal test sensitivity with an average reduction of 2.2% in infections for each day removed between tests in comparison to a 0.43% average reduction per 1% increase in test frequency. Our findings highlight that mass testing using rapid diagnostic tests can be used as an effective intervention for countries transitioning from pandemic mitigation to endemic COVID-19. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Communication
Reproduction Number of the Omicron Variant Triples That of the Delta Variant
Viruses 2022, 14(4), 821; https://doi.org/10.3390/v14040821 - 15 Apr 2022
Cited by 11 | Viewed by 1880
Abstract
COVID-19 remains a persistent threat, especially with the predominant Omicron variant emerging in early 2022, presenting with high transmissibility, immune escape, and waning. There is a need to rapidly ramp up global vaccine coverage while enhancing public health and social measures. Timely and [...] Read more.
COVID-19 remains a persistent threat, especially with the predominant Omicron variant emerging in early 2022, presenting with high transmissibility, immune escape, and waning. There is a need to rapidly ramp up global vaccine coverage while enhancing public health and social measures. Timely and reliable estimation of the reproduction number throughout a pandemic is critical for assessing the impact of mitigation efforts and the potential need to adjust for control measures. We conducted a systematic review on the reproduction numbers of the Omicron variant and gave the pooled estimates. We identified six studies by searching PubMed, Embase, Web of Science, and Google Scholar for articles published between 1 January 2020 and 6 March 2022. We estimate that the effective reproduction number ranges from 2.43 to 5.11, with a pooled estimate of 4.20 (95% CI: 2.05, 6.35). The Omicron variant has an effective reproduction number which is triple (2.71 (95% CI: 1.86, 3.56)) that of the Delta variant. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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Communication
Antiviral Efficacy of Molnupiravir for COVID-19 Treatment
Viruses 2022, 14(4), 763; https://doi.org/10.3390/v14040763 - 06 Apr 2022
Cited by 2 | Viewed by 1480
Abstract
The ongoing global pandemic of COVID-19 poses unprecedented public health risks for governments and societies around the world, which have been exacerbated by the emergence of SARS-CoV-2 variants. Pharmaceutical interventions with high antiviral efficacy are expected to delay and contain the COVID-19 pandemic. [...] Read more.
The ongoing global pandemic of COVID-19 poses unprecedented public health risks for governments and societies around the world, which have been exacerbated by the emergence of SARS-CoV-2 variants. Pharmaceutical interventions with high antiviral efficacy are expected to delay and contain the COVID-19 pandemic. Molnupiravir, as an oral antiviral prodrug, is active against SARS-CoV-2 and is now (23 February 2022) one of the seven widely-used coronavirus treatments. To estimate its antiviral efficacy of Molnupiravir, we built a granular mathematical within-host model. We find that the antiviral efficacy of Molnupiravir to stop the growth of the virus is 0.56 (95% CI: 0.49, 0.64), which could inhibit 56% of the replication of infected cells per day. There has been good progress in developing high-efficacy antiviral drugs that rapidly reduce viral load and may also reduce the infectiousness of treated cases if administered as early as possible. Full article
(This article belongs to the Special Issue Infectious Disease Epidemiology and Transmission Dynamics)
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