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Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II

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A special issue of Journal of Clinical Medicine (ISSN 2077-0383). This special issue belongs to the section "Epidemiology & Public Health".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 44020

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Prof. Dr. Hiroshi Nishiura

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Kyoto University School of Public Health, Kyoto, Japan
Interests: infectious disease epidemiology; mathematical model; transmission dynamics
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Special Issue Information

Dear Colleagues,

It has been one year since the emergence of coronavirus disease 2019 (COVID-19). Since we first launched our Special Issue Part I on this topic back in January 2020 (https://www.mdpi.com/journal/jcm/special_issues/Novel_Coronavirus), COVID-19 has swiftly spread around the world, affecting all aspects of our normal life. The pandemic has not yet been brought under control with specific preventive measures, but vaccination is starting around the world. The Special Issue Part I acted as one of the earliest special volumes on COVID-19 study papers across the world, clarifying essential aspects of the natural history and transmission dynamics, and moreover offering an analysis of early interventions which are mostly classified as public health and social measures (PHSM). Many of them have since attracted more than 200 citations, and the earliest estimation study of the incubation period had been cited 650 times as of 24 December 2020.

Given the enormous success of the Part I issue, I believe that it is time to move forward to Special Issue Part II, collecting additional insights into the epidemiology and infection dynamics of COVID-19, especially including those handling specific prevention and treatment. Part II is very keen to attract a global audience, welcoming any contributions on this subject from around the world.

Let us customize and update the original research questions. What kind of people are mainly affected and vulnerable to severe illness? How important is each route of transmission? How transmissible is the disease, and what characteristics determine its transmissibility? How should we measure the immune fraction of the population? How many cases have been missed from confirmatory diagnosis in which age and risk groups? How should we evaluate the establishment of herd immunity? To respond to the outbreak in a timely manner, it is vital that research responses to the pandemic focusing on the abovementioned subjects are published in the public domain as quickly as possible. As such, and just as its predecessor, this Special Issue will offer a very swift peer review, acting as a publication medium to attract many clinical and epidemiological studies on this pandemic, ensuring a fast turnaround time for high-quality studies.

We particularly welcome articles providing new insights into (i) the clinical characteristics of the novel coronavirus; (ii) infection and transmission dynamics of the disease; and (iii) evaluation of the impact of interventions, including pharmaceutical and non-pharmaceutical approaches.

We welcome both solicited and unsolicited submissions that will contribute to this goal.

Prof. Dr. Hiroshi Nishiura
Guest Editor

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. Journal of Clinical Medicine is an international peer-reviewed open access semimonthly 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 2600 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

Novel coronavirus
Clinical studies
Critical care and management
Natural history
Asymptomatic cases
Transmission
Severity
Risk assessment
Enhanced surveillance
Interventions

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Published Papers (12 papers)

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Editorial

Jump to: Research

3 pages, 719 KiB

Open AccessEditorial

Relative Reproduction Number of SARS-CoV-2 Omicron (B.1.1.529) Compared with Delta Variant in South Africa

by Hiroshi Nishiura, Kimihito Ito, Asami Anzai, Tetsuro Kobayashi, Chayada Piantham and Alfonso J. Rodríguez-Morales

J. Clin. Med. 2022, 11(1), 30; https://doi.org/10.3390/jcm11010030 - 23 Dec 2021

Cited by 113 | Viewed by 12708

Abstract

The world identified the rapidly increasing incidence of the causative variant of SARS-CoV-2 Pangolin B [...] Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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Research

Jump to: Editorial

12 pages, 2149 KiB

Open AccessArticle

Computational Simulation Model to Predict Behavior Changes in Inflammatory Bowel Disease Patients during the COVID-19 Pandemic: Analysis of Two Regional Japanese Populations

by Gen Suzuki, Ryuichi Iwakiri, Eri Udagawa, Sindy Ma, Ryoko Takayama, Hiroshi Nishiura, Koshi Nakamura, Samuel P. Burns, Paul Michael D’Alessandro and Jovelle Fernandez

J. Clin. Med. 2023, 12(3), 757; https://doi.org/10.3390/jcm12030757 - 18 Jan 2023

Cited by 1 | Viewed by 2474

Abstract

Managing inflammatory bowel disease (IBD) is a major challenge for physicians and patients during the COVID-19 pandemic. To understand the impact of the pandemic on patient behaviors and disruptions in medical care, we used a combination of population-based modeling, system dynamics simulation, and linear optimization. Synthetic IBD populations in Tokyo and Hokkaido were created by localizing an existing US-based synthetic IBD population using data from the Ministry of Health, Labor, and Welfare in Japan. A clinical pathway of IBD-specific disease progression was constructed and calibrated using longitudinal claims data from JMDC Inc for patients with IBD before and during the COVID-19 pandemic. Key points considered for disruptions in patient behavior (demand) and medical care (supply) were diagnosis of new patients, clinic visits for new patients seeking care and diagnosed patients receiving continuous care, number of procedures, and the interval between procedures or biologic prescriptions. COVID-19 had a large initial impact and subsequent smaller impacts on demand and supply despite higher infection rates. Our population model (Behavior Predictor) and patient treatment simulation model (Demand Simulator) represent the dynamics of clinical care demand among patients with IBD in Japan, both in recapitulating historical demand curves and simulating future demand during disruption scenarios, such as pandemic, earthquake, and economic crisis. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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14 pages, 659 KiB

Open AccessArticle

Antibodies to the Spike Protein Receptor-Binding Domain of SARS-CoV-2 at 4–13 Months after COVID-19

by Evgeniia A. Kolosova, Olga N. Shaprova, Daniil V. Shanshin, Valentina S. Nesmeyanova, Iuliia A. Merkuleva, Svetlana V. Belenkaya, Anastasiya A. Isaeva, Artem O. Nikitin, Ekaterina A. Volosnikova, Yuliya A. Nikulina, Marina A. Nikonorova, Dmitry N. Shcherbakov and Svetlana A. Elchaninova

J. Clin. Med. 2022, 11(14), 4053; https://doi.org/10.3390/jcm11144053 - 13 Jul 2022

Cited by 2 | Viewed by 1823

Abstract

Identification of factors behind the level and duration of persistence of the SARS-CoV-2 antibodies in the blood is assumed to set the direction for studying humoral immunity mechanisms against COVID-19, optimizing the strategy for vaccine use, antibody-based drugs, and epidemiological control of COVID-19. Objective: This study aimed to study the relationship between clinical and demographic characteristics and the level of IgG antibodies to the RBD of SARS-CoV-2 spike protein after COVID-19 in the long term. Residents of the Altai Region of Western Siberia of Russia, Caucasians, aged from 27 to 93 years (median 53.0 years), who recovered from COVID-19 between May 2020 and February 2021 (n = 44) took part in this prospective observational study. The titer of IgG antibodies to the RBD of SARS-CoV-2 spike protein was measured repeatedly in the blood at 4–13 months from the beginning of the clinical manifestation of COVID-19 via the method of enzyme-linked immunosorbent assay. The antibody titer positively correlated with age (p = 0.013) and COVID-19 pneumonia (p = 0.002) at 20–40 and 20–24 weeks from the onset of COVID-19 symptoms, respectively. Age was positively associated with antibody titer regardless of history of COVID-19 pneumonia (beta regression coefficient p = 0.009). The antibody titer decreased in 15 (34.1%) patients, increased in 10 (22.7%) patients, and did not change in 19 (43.2%) patients from the baseline to 48–49 weeks from the onset of COVID-19 symptoms, with seropositivity persisting in all patients. Age and COVID-19 pneumonia are possibly associated with higher IgG antibodies to the spike protein RBD of SARS-CoV-2 following COVID-19 in the long term. Divergent trends of anti-RBD IgG levels in adults illustrate inter-individual differences at 4–13 months from the onset of COVID-19 symptoms. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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8 pages, 1245 KiB

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Proportion of Pre-Symptomatic Transmission Events Associated with COVID-19 in South Korea

by Youngji Song and Eunha Shim

J. Clin. Med. 2022, 11(14), 3925; https://doi.org/10.3390/jcm11143925 - 6 Jul 2022

Cited by 2 | Viewed by 1683

Abstract

Pre-symptomatic transmission potentially reduces the effectiveness of symptom-onset-based containment and control strategies for the coronavirus disease (COVID-19). Despite evidence from multiple settings, the proportion of pre-symptomatic transmission varies among countries. To estimate the extent of pre-symptomatic transmission in South Korea, we used individual-level COVID-19 case records from the Korea Disease Control and Prevention Agency and Central Disease Control Headquarters. We inferred the probability of symptom onset per day since infection based on the density distribution of the incubation period to stratify the serial interval distribution in Period 1 (20 January–10 February 2020) and Period 2 (25 July–4 December 2021), without and with expanded testing or implementation of social distancing strategies, respectively. Assuming both no correlation as well as positive and negative correlations between the incubation period and the serial interval, we estimated the proportion of pre-symptomatic transmission in South Korea as 43.5% (accounting for correlation, range: 9.9–45.4%) and 60.0% (56.2–64.1%) without and with expanded testing, respectively, during the Delta variant’s predominance. This study highlights the importance of considering pre-symptomatic transmission for COVID-19 containment and mitigation strategies because pre-symptomatic transmission may play a key role in the epidemiology of COVID-19. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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5 pages, 532 KiB

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The Seroprevalence of SARS-CoV-2 IgG Antibodies in Children Hospitalized for Reasons Other Than COVID-19

by Justyna Franczak, Justyna Moppert, Małgorzata Sobolewska-Pilarczyk and Małgorzata Pawłowska

J. Clin. Med. 2022, 11(13), 3819; https://doi.org/10.3390/jcm11133819 - 1 Jul 2022

Cited by 8 | Viewed by 1621

Abstract

The aim of the study was to assess the seroprevalence of SARS-CoV-2 IgG antibodies in children hospitalized for reasons other than COVID-19. The study was conducted among 686 children, aged 2 weeks to 18 years, hospitalized in the Department of Paediatrics, Infectious Diseases, and Hepatology in Bydgoszcz, Poland, in the period from 1 June 2021 to 30 April 2022. The presence of anti-SARS-CoV-2 antibodies was detected in 392 (57%) children. Since December 2021, a significantly larger proportion of children with a positive titer of anti-SARS-CoV-2 antibodies has been observed, constituting as much as 87.5% of patients hospitalized in April 2022. In total, 69% of children with detected anti-SARS-CoV-2 antibodies were children under 5 years of age. The highest mean amounts of titers of anti-SARS-CoV-2 antibodies were observed in children over 10 years of age. The conducted studies showed the presence of anti-SARS-CoV-2 antibodies in a significant group of hospitalized children and an increase in the percentage of these children during the fourth and fifth wave of COVID-19 in Poland caused by the Delta and Omicron variants, respectively. The vast majority of parents of the studied children had no knowledge of the COVID-19 infection in their charges, which may indicate asymptomatic infection or mild course of the disease. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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13 pages, 1366 KiB

Open AccessArticle

Clinical Time Delay Distributions of COVID-19 in 2020–2022 in the Republic of Korea: Inferences from a Nationwide Database Analysis

by Eunha Shim, Wongyeong Choi and Youngji Song

J. Clin. Med. 2022, 11(12), 3269; https://doi.org/10.3390/jcm11123269 - 7 Jun 2022

Cited by 10 | Viewed by 2247

Abstract

Epidemiological distributions of the coronavirus disease 2019 (COVID-19), including the intervals from symptom onset to diagnosis, reporting, or death, are important for developing effective disease-control strategies. COVID-19 case data (from 19 January 2020 to 10 January 2022) from a national database maintained by the Korea Disease Control and Prevention Agency and the Central Disease Control Headquarters were analyzed. A joint Bayesian subnational model with partial pooling was used and yielded probability distribution models of key epidemiological distributions in Korea. Serial intervals from before and during the Delta variant’s predominance were estimated. Although the mean symptom-onset-to-report interval was 3.2 days at the national level, it varied across different regions (2.9–4.0 days). Gamma distribution showed the best fit for the onset-to-death interval (with heterogeneity in age, sex, and comorbidities) and the reporting-to-death interval. Log-normal distribution was optimal for ascertaining the onset-to-diagnosis and onset-to-report intervals. Serial interval (days) was shorter before the Delta variant-induced outbreaks than during the Delta variant’s predominance (4.4 vs. 5.2 days), indicating the higher transmission potential of the Delta variant. The identified heterogeneity in region-, age-, sex-, and period-based distributions of the transmission dynamics of COVID-19 will facilitate the development of effective interventions and disease-control strategies. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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17 pages, 2164 KiB

Open AccessArticle

Analysis of COVID-19 Spread in Tokyo through an Agent-Based Model with Data Assimilation

by Chang Sun, Serge Richard, Takemasa Miyoshi and Naohiro Tsuzu

J. Clin. Med. 2022, 11(9), 2401; https://doi.org/10.3390/jcm11092401 - 25 Apr 2022

Cited by 6 | Viewed by 1633

Abstract

In this paper, we introduce an agent-based model together with a particle filter approach to study the spread of COVID-19. Investigations are mainly performed on the metropolis of Tokyo, but other prefectures of Japan are also briefly surveyed. A novel method for evaluating the effective reproduction number is one of the main outcomes of our approach. Other unknown parameters are also evaluated. Uncertain quantities, such as, for example, the probability that an infected agent develops symptoms, are tested and discussed, and the stability of our computations is examined. Detailed explanations are provided for the model and for the assimilation process. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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9 pages, 1400 KiB

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Correlation between the Level of Social Distancing and Activity of Influenza Epidemic or COVID-19 Pandemic: A Subway Use-Based Assessment

by Hye Seong, Jin-Wook Hong, Hak-Jun Hyun, Jin-Gu Yoon, Ji-Yun Noh, Hee-Jin Cheong, Woo-Joo Kim, Jae-Hun Jung and Joon-Young Song

J. Clin. Med. 2021, 10(15), 3369; https://doi.org/10.3390/jcm10153369 - 29 Jul 2021

Cited by 9 | Viewed by 2520

Abstract

Social distancing is an effective measure to mitigate the spread of novel viral infections in the absence of antiviral agents and insufficient vaccine supplies. Subway utilization density may reflect social activity and the degree of social distancing in the general population.; This study aimed to evaluate the correlations between subway use density and the activity of the influenza epidemic or coronavirus disease 2019 (COVID-19) pandemic using a time-series regression method. The subway use-based social distancing score (S-SDS) was calculated using the weekly ridership of 11 major subway stations. The temporal association of S-SDS with influenza-like illness (ILI) rates or the COVID-19 pandemic activity was analyzed using structural vector autoregressive modeling and the Granger causality (GC) test. During three influenza seasons (2017–2020), the time-series regression presented a significant causality from S-SDS to ILI (p = 0.0484). During the COVID-19 pandemic in January 2020, S-SDS had been suppressed at a level similar to or below the average of the previous four years. In contrast to the ILI rate, there was a negative correlation between COVID-19 activity and S-SDS. GC analysis revealed a negative causal relationship between COVID-19 and S-SDS (p = 0.0098).; S-SDS showed a significant time-series association with the ILI rate but not with COVID-19 activity. When public transportation use is sufficiently suppressed, additional social mobility restrictions are unlikely to significantly affect COVID-19 pandemic activity. It would be more important to strengthen universal mask-wearing and detailed public health measures focused on risk activities, particularly in enclosed spaces. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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16 pages, 2619 KiB

Open AccessArticle

Vaccine Effects on Susceptibility and Symptomatology Can Change the Optimal Allocation of COVID-19 Vaccines: South Korea as an Example

by Wongyeong Choi and Eunha Shim

J. Clin. Med. 2021, 10(13), 2813; https://doi.org/10.3390/jcm10132813 - 25 Jun 2021

Cited by 4 | Viewed by 2868

Abstract

The approved coronavirus disease (COVID-19) vaccines reduce the risk of disease by 70–95%; however, their efficacy in preventing COVID-19 is unclear. Moreover, the limited vaccine supply raises questions on how they can be used effectively. To examine the optimal allocation of COVID-19 vaccines in South Korea, we constructed an age-structured mathematical model, calibrated using country-specific demographic and epidemiological data. The optimal control problem was formulated with the aim of finding time-dependent age-specific optimal vaccination strategies to minimize costs related to COVID-19 infections and vaccination, considering a limited vaccine supply and various vaccine effects on susceptibility and symptomatology. Our results suggest that “susceptibility-reducing” vaccines should be relatively evenly distributed among all age groups, resulting in more than 40% of eligible age groups being vaccinated. In contrast, “symptom-reducing” vaccines should be administered mainly to individuals aged 20–29 and ≥60 years. Thus, our study suggests that the vaccine profile should determine the optimal vaccination strategy. Our findings highlight the importance of understanding vaccine’s effects on susceptibility and symptomatology for effective public health interventions. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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15 pages, 2113 KiB

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Investigation of the Efficiency of Mask Wearing, Contact Tracing, and Case Isolation during the COVID-19 Outbreak

by Tatiana Filonets, Maxim Solovchuk, Wayne Gao and Tony Wen-Hann Sheu

J. Clin. Med. 2021, 10(13), 2761; https://doi.org/10.3390/jcm10132761 - 23 Jun 2021

Cited by 7 | Viewed by 5817

Abstract

Case isolation and contact tracing are two essential parts of control measures to prevent the spread of COVID-19, however, additional interventions, such as mask wearing, are required. Taiwan successfully contained local COVID-19 transmission after the initial imported cases in the country in early 2020 after applying the above-mentioned interventions. In order to explain the containment of the disease spread in Taiwan and understand the efficiency of different non-pharmaceutical interventions, a mathematical model has been developed. A stochastic model was implemented in order to estimate the effectiveness of mask wearing together with case isolation and contact tracing. We investigated different approaches towards mask usage, estimated the effect of the interventions on the basic reproduction number (R₀), and simulated the possibility of controlling the outbreak. With the assumption that non-medical and medical masks have 20% and 50% efficiency, respectively, case isolation works on 100%, 70% of all people wear medical masks, and R₀ = 2.5, there is almost 80% probability of outbreak control with 60% contact tracing, whereas for non-medical masks the highest probability is only about 20%. With a large proportion of infectiousness before the onset of symptoms (40%) and the presence of asymptomatic cases, the investigated interventions (isolation of cases, contact tracing, and mask wearing by all people), implemented on a high level, can help to control the disease spread. Superspreading events have also been included in our model in order to estimate their impact on the outbreak and to understand how restrictions on gathering and social distancing can help to control the outbreak. The obtained quantitative results are in agreement with the empirical COVID-19 data in Taiwan. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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11 pages, 996 KiB

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Estimation of the Actual Incidence of Coronavirus Disease (COVID-19) in Emergent Hotspots: The Example of Hokkaido, Japan during February–March 2020

by Andrei R. Akhmetzhanov, Kenji Mizumoto, Sung-Mok Jung, Natalie M. Linton, Ryosuke Omori and Hiroshi Nishiura

J. Clin. Med. 2021, 10(11), 2392; https://doi.org/10.3390/jcm10112392 - 28 May 2021

Cited by 8 | Viewed by 3005

Abstract

Following the first report of the coronavirus disease 2019 (COVID-19) in Sapporo city, Hokkaido Prefecture, Japan, on 14 February 2020, a surge of cases was observed in Hokkaido during February and March. As of 6 March, 90 cases were diagnosed in Hokkaido. Unfortunately, many infected persons may not have been recognized due to having mild or no symptoms during the initial months of the outbreak. We therefore aimed to predict the actual number of COVID-19 cases in (i) Hokkaido Prefecture and (ii) Sapporo city using data on cases diagnosed outside these areas. Two statistical frameworks involving a balance equation and an extrapolated linear regression model with a negative binomial link were used for deriving both estimates, respectively. The estimated cumulative incidence in Hokkaido as of 27 February was 2,297 cases (95% confidence interval (CI): 382–7091) based on data on travelers outbound from Hokkaido. The cumulative incidence in Sapporo city as of 28 February was estimated at 2233 cases (95% CI: 0–4893) based on the count of confirmed cases within Hokkaido. Both approaches resulted in similar estimates, indicating a higher incidence of infections in Hokkaido than were detected by the surveillance system. This quantification of the gap between detected and estimated cases helped to inform the public health response at the beginning of the pandemic and provided insight into the possible scope of undetected transmission for future assessments. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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20 pages, 1992 KiB

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Adverse Life Trajectories Are a Risk Factor for SARS-CoV-2 IgA Seropositivity

by Cyrielle Holuka, Chantal J. Snoeck, Sophie B. Mériaux, Markus Ollert, Rejko Krüger, Jonathan D. Turner and the CON-VINCE Consortium

J. Clin. Med. 2021, 10(10), 2159; https://doi.org/10.3390/jcm10102159 - 17 May 2021

Viewed by 3698

Abstract

Asymptomatic individuals, called “silent spreaders” spread SARS-CoV-2 efficiently and have complicated control of the ongoing COVID-19 pandemic. As seen in previous influenza pandemics, socioeconomic and life-trajectory factors are important in disease progression and outcome. The demographics of the asymptomatic SARS-CoV-2 carriers are unknown. We used the CON-VINCE cohort of healthy, asymptomatic, and oligosymptomatic individuals that is statistically representative of the overall population of Luxembourg for age, gender, and residency to characterise this population. Gender (male), not smoking, and exposure to early-life or adult traumatic experiences increased the risk of IgA seropositivity, and the risk associated with early-life exposure was a dose-dependent metric, while some other known comorbidities of active COVID-19 do not impact it. As prior exposure to adversity is associated with negative psychobiological reactions to external stressors, we recorded psychological wellbeing during the study period. Exposure to traumatic events or concurrent autoimmune or rheumatic disease were associated with a worse evolution of anxiety and depressive symptoms throughout the lockdown period. The unique demographic profile of the “silent spreaders” highlights the role that the early-life period plays in determining our lifelong health trajectory and provides evidence that the developmental origins of health and disease is applicable to infectious diseases. Full article

(This article belongs to the Special Issue Real Time Clinical and Epidemiological Investigations on Novel Coronavirus - Part II)

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