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Vaccines
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Epidemiology of COVID-19
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Epidemiology of COVID-19

A special issue of Vaccines (ISSN 2076-393X). This special issue belongs to the section "COVID-19 Vaccines and Vaccination".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 32164

Special Issue Editors

Prof. Dr. Alberto E. Paniz-Mondolfi

E-Mail Website
Guest Editor
Icahn School of Medicine at Mount Sinai, Department of Pathology, Molecular and Cell-Based Medicine, Clinical Microbiology Laboratory, New York, NY 10029, USA
Interests: virology; clinical microbiology; emergent pathogens; molecular epidemiology
Dr. Emilia Mia Sordillo

E-Mail Website
Guest Editor
Icahn School of Medicine at Mount Sinai, Molecular and Cell-Based Medicine Clinical Microbiology Laboratory, New York, NY 10029, USA
Interests: pathogen surveillance; infection prevention; host-pathogen interaction

Special Issue Information

Dear Colleagues,

The Coronavirus disease- 2019 (COVID-19) pandemic, caused by the novel virus, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has had devastating consequences worldwide, with over one hundred million cases confirmed and nearly 2.3 million deaths reported as of February 3, 2021.  The complex and heterogeneous   expansion of the pandemic has highlighted the critical importance of global surveillance efforts and science-based public health decision-making and policies.  Recently, the description of virus variants and emergent lineages has raised concerns regarding increased infectivity and virulence, potentially reshaping the epidemiologic landscape of this disease.  This special issue will present emerging concepts regarding the epidemiology, prevention and control of SARS-CoV-2 infection, with special focus on ecological & evolutionary factors in virus emergence,  host- virus dynamics,  and the assessment and implementation of therapeutic and immunization efforts to mitigate  disease burden.

Prof. Dr. Alberto E. Paniz-Mondolfi
Dr. Emilia Mia Sordillo
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. Vaccines 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 2700 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

  • SARS-CoV-2 epidemiology
  • disease transmission
  • viral dynamics
  • variants
  • lineages
  • molecular epidemiology
  • immunizations
  • control
  • surveillance.

Published Papers (6 papers)

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8 pages, 248 KiB  
Article
Changing Features of COVID-19: Characteristics of Infections with the SARS-CoV-2 Delta (B.1.617.2) and Alpha (B.1.1.7) Variants in Southern Italy
by Daniela Loconsole, Francesca Centrone, Caterina Morcavallo, Silvia Campanella, Marisa Accogli, Anna Sallustio, Davide Peccarisi, Angela Stufano, Piero Lovreglio and Maria Chironna
Vaccines 2021, 9(11), 1354; https://doi.org/10.3390/vaccines9111354 - 18 Nov 2021
Cited by 17 | Viewed by 3037
Abstract
Differences in the demographic and clinical characteristics of patients infected with the Alpha and Delta SARS-CoV-2 variants of concern in a large region of Southern Italy were assessed. Two cohorts of positive patients were compared. The Alpha group consisted of 11,135 subjects diagnosed [...] Read more.
Differences in the demographic and clinical characteristics of patients infected with the Alpha and Delta SARS-CoV-2 variants of concern in a large region of Southern Italy were assessed. Two cohorts of positive patients were compared. The Alpha group consisted of 11,135 subjects diagnosed between 21 March and 21 April 2021, and the Delta group consisted of 499 positive subjects diagnosed between 21 July and 21 August 2021. A descriptive and statistical analysis of the demographic and clinical characteristics of the two groups was performed. The proportion of patients with mild and moderate infections was significantly higher in the Delta than in the Alpha group (p < 0.001). In fully vaccinated patients, the proportion of symptomatic individuals was significantly higher in the Delta than in the Alpha group. The Delta group showed odds ratios of 3.08 (95% CI, 2.55–3.72) for symptomatic infection and 2.66 (95% CI, 1.76–3.94) for hospitalization. Improving COVID-19 vaccination rates is a priority, since infection with the SARS-CoV-2 Delta variant has a significant impact on patient outcomes. Additional targeted prevention strategies such as social distancing, the use of masks in indoor settings irrespective of vaccination status, and the use of a sanitary passport could be crucial to contain further spread of SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue Epidemiology of COVID-19)
18 pages, 4179 KiB  
Article
Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic
by Sergio Castañeda, Luz H. Patiño, Marina Muñoz, Nathalia Ballesteros, Enzo Guerrero-Araya, Daniel Paredes-Sabja, Carolina Flórez, Sergio Gomez, Carolina Ramírez-Santana, Gustavo Salguero, Juan E. Gallo, Alberto E. Paniz-Mondolfi and Juan David Ramírez
Vaccines 2021, 9(8), 837; https://doi.org/10.3390/vaccines9080837 - 30 Jul 2021
Cited by 10 | Viewed by 3084
Abstract
Current efforts to understand the epidemiology, transmission dynamics and emergence of novel SARS-CoV-2 variants worldwide has enabled the scientific community to generate critical information aimed at implementing disease surveillance and control measures, as well as to reduce the social, economic and health impact [...] Read more.
Current efforts to understand the epidemiology, transmission dynamics and emergence of novel SARS-CoV-2 variants worldwide has enabled the scientific community to generate critical information aimed at implementing disease surveillance and control measures, as well as to reduce the social, economic and health impact of the pandemic. Herein, we applied an epidemic model coupled with genomic analysis to assess the SARS-CoV-2 transmission dynamics in Colombia. This epidemic model allowed to identify the geographical distribution, Rt dynamics and predict the course of the pandemic considering current implementation of countermeasures. The analysis of the incidence rate per 100,000 inhabitants carried out across different regions of Colombia allowed visualizing the changes in the geographic distribution of cases. The cumulative incidence during the timeframe March 2020 to March 2021 revealed that Bogotá (8063.0), Quindío (5482.71), Amazonas (5055.68), Antioquia (4922.35) and Tolima (4724.41) were the departments with the highest incidence rate. The highest median Rt during the first period evaluated was 2.13 and 1.09 in the second period; with this model, we identified improving opportunities in health decision making related to controlling the pandemic, diagnostic testing capacity, case registration and reporting, among others. Genomic analysis revealed 52 circulating SARS-CoV-2 lineages in Colombia detected from 774 genomes sequenced throughout the first year of the pandemic. The genomes grouped into four main clusters and exhibited 19 polymorphisms. Our results provide essential information on the spread of the pandemic countrywide despite implementation of early containment measures. In addition, we aim to provide deeper phylogenetic insights to better understand the evolution of SARS-CoV-2 in light of the latent emergence of novel variants and how these may potentially influence transmissibility and infectivity. Full article
(This article belongs to the Special Issue Epidemiology of COVID-19)
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15 pages, 3439 KiB  
Article
Signatures of the Venezuelan Humanitarian Crisis in the First Wave of COVID-19: Fuel Shortages and Border Migration
by Margarita Lampo, Juan V. Hernández-Villena, Jaime Cascante, María F. Vincenti-González, David A. Forero-Peña, Maikell J. Segovia, Katie Hampson, Julio Castro and Maria Eugenia Grillet
Vaccines 2021, 9(7), 719; https://doi.org/10.3390/vaccines9070719 - 01 Jul 2021
Cited by 9 | Viewed by 5348
Abstract
Testing and isolation have been crucial for controlling the COVID-19 pandemic. Venezuela has one of the weakest testing infrastructures in Latin America and the low number of reported cases in the country has been attributed to substantial underreporting. However, the Venezuelan epidemic seems [...] Read more.
Testing and isolation have been crucial for controlling the COVID-19 pandemic. Venezuela has one of the weakest testing infrastructures in Latin America and the low number of reported cases in the country has been attributed to substantial underreporting. However, the Venezuelan epidemic seems to have lagged behind other countries in the region, with most cases occurring within the capital region and four border states. Here, we describe the spatial epidemiology of COVID-19 in Venezuela and its relation to the population mobility, migration patterns, non-pharmaceutical interventions and fuel availability that impact population movement. Using a metapopulation model of SARS-CoV-2 transmission dynamics, we explore how movement patterns could have driven the observed distribution of cases. Low within-country connectivity most likely delayed the onset of the epidemic in most states, except for those bordering Colombia and Brazil, where high immigration seeded outbreaks. NPIs slowed early epidemic growth and subsequent fuel shortages appeared to be responsible for limiting the spread of COVID-19 across the country. Full article
(This article belongs to the Special Issue Epidemiology of COVID-19)
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15 pages, 2977 KiB  
Article
Perception of COVID-19 Vaccination Amongst Physicians in Colombia
by Jorge L. Alvarado-Socarras, Andrea Liliana Vesga-Varela, Doris Cristina Quintero-Lesmes, Marcela M. Fama-Pereira, Norma C. Serrano-Diaz, Mauricio Vasco, Virgil Carballo-Zarate, Lysien I. Zambrano, Alberto Paniz-Mondolfi and Alfonso J. Rodriguez-Morales
Vaccines 2021, 9(3), 287; https://doi.org/10.3390/vaccines9030287 - 19 Mar 2021
Cited by 27 | Viewed by 9139
Abstract
Introduction: The SARS-CoV-2/COVID-19 pandemic has triggered the need to develop rapidly effective and safe vaccines to prevent infection, particularly in those at-risk populations such as medical personnel. This study’s objective was to assess the perception of COVID-19 vaccination amongst Colombian physicians featuring [...] Read more.
Introduction: The SARS-CoV-2/COVID-19 pandemic has triggered the need to develop rapidly effective and safe vaccines to prevent infection, particularly in those at-risk populations such as medical personnel. This study’s objective was to assess the perception of COVID-19 vaccination amongst Colombian physicians featuring two different scenarios of COVID-19 vaccination. Methods: A cross-sectional analytical study was carried out through an online survey directed at medical staff in several cities in Colombia. The percentage of physicians who have a positive perception to be vaccinated and the associated factors that determine that decision were determined. A binomial regression analysis adjusted for age and sex was carried out, taking as a dependent variable the acceptance of free vaccination with an effectiveness of 60 and 80%. The most significant factors were determined in the non-acceptance of vaccination. Results: Between 77.0% and 90.7% of physicians in Colombia accept COVID-19 vaccination, according to the scenario evaluated where the vaccine’s effectiveness was 60 or 80%, respectively. Medical specialty, having never paid for a vaccine, recommending the administration of the vaccine to their parents or people over 70 years, and dispensing the vaccine to their children, were the factors to consider to be vaccinated for free with an effectiveness of 60% and 80%. Conclusions: There is a high perception of the intention to vaccinate physicians in Colombia against COVID-19, and this is very similar to that of the general population. Full article
(This article belongs to the Special Issue Epidemiology of COVID-19)
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10 pages, 1614 KiB  
Article
Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia
by Juan David Ramírez, Marina Muñoz, Nathalia Ballesteros, Luz H. Patiño, Sergio Castañeda, Carlos A. Rincón, Claudia Mendez, Carolina Oliveros, Julie Perez, Elizabeth K. Márquez, Frank de los Santos Ortiz, Camilo A. Correa-Cárdenas, Maria Clara Duque and Alberto Paniz-Mondolfi
Vaccines 2021, 9(3), 282; https://doi.org/10.3390/vaccines9030282 - 19 Mar 2021
Cited by 16 | Viewed by 4882
Abstract
The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR [...] Read more.
The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR results in a 1–2-month window period, and subsequent phylogenetics and genetic polymorphism analysis of these genomes was performed. Herein, we report, for the first time, genomic evidence of one case of reinfection in Colombia, exhibiting different SARS-CoV-2 lineage classifications between samples (B.1 and B.1.1.269). Furthermore, we report two cases of possible viral persistence, highlighting the importance of deepening our understanding on the evolutionary intra-host traits of this virus throughout different timeframes of disease progression. These results emphasize the relevance of genomic surveillance as a tool for understanding SARS-CoV-2 infection dynamics, and how this may translate effectively to future control and mitigations efforts, such as the national vaccination program. Full article
(This article belongs to the Special Issue Epidemiology of COVID-19)
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11 pages, 4456 KiB  
Case Report
COVID-19 Associated Rhino-Orbital Mucormycosis Complicated by Gangrenous and Bone Necrosis—A Case Report from Honduras
by Elsa Yolanda Palou, María Auxiliadora Ramos, Emec Cherenfant, Adoni Duarte, Itzel Carolina Fuentes-Barahona, Lysien I. Zambrano, Fausto Muñoz-Lara, Sandra Aracely Montoya-Ramirez, Alex Francisco Cardona-Ortiz, Jorge Alberto Valle-Reconco, Juan J. Montenegro-Idrogo, D. Katterine Bonilla-Aldana, Alberto E. Paniz-Mondolfi and Alfonso J. Rodriguez-Morales
Vaccines 2021, 9(8), 826; https://doi.org/10.3390/vaccines9080826 - 27 Jul 2021
Cited by 14 | Viewed by 4356
Abstract
Background: Mucormycosis is a life-threatening invasive fungal infection most commonly observed in immunocompromised patients. Throughout the COVID-19 pandemic, a growing number of Mucorales associated infections, now termed COVID-19 associated mucormycosis (CAM), have been reported. Despite an increase in fatality reports, no cases of [...] Read more.
Background: Mucormycosis is a life-threatening invasive fungal infection most commonly observed in immunocompromised patients. Throughout the COVID-19 pandemic, a growing number of Mucorales associated infections, now termed COVID-19 associated mucormycosis (CAM), have been reported. Despite an increase in fatality reports, no cases of rhino-orbital CAM complicated with gangrenous bone necrosis have been described in the literature to date. Case: A 56-year-old male with a recent COVID-19 diagnosis developed rhino-orbital mucormycosis after 22 days of treatment with dexamethasone. Cultures and histopathological assessment of tissue biopsy confirmed the diagnosis. The patient survived after treatment with amphotericin B. Conclusions: Mucormycosis is an invasive fungal infection affecting mostly immunocompromised patients. Along with the COVID-19 pandemic, the inappropriate use of steroids, in addition to concurrent risk factors, such as diabetes, has led to an increase in the occurrence of these devastating mycoses, leading to the development of severe presentations and complications, as observed in many cases. Early diagnosis and prompt treatment are crucial in order to avoid dissemination and fatal outcomes. Full article
(This article belongs to the Special Issue Epidemiology of COVID-19)
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