Global Dynamic of Viral Diseases

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 14519

Special Issue Editor

CIRAD, University of Montpellier, Montpellier, France
Interests: emerging diseases; infectious diseases; microbiology; genomics; virus evolution; dynamics of infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The current COVID-19 crisis clearly illustrates that a viral disease, in particular an emerging one, is a complex phenomenon going far beyond the field of medicine. The emergence of the disease per se is only the last step of a whole process. Before emerging as a disease, there is a dynamic of the circulation, evolution, adaptation and amplification of a microorganism. This dynamic is not visible but it has a crucial impact on the future development of a disease. A viral disease cannot be understood and controlled by focusing on the sole medical aspect. Primarily because when a disease emerges, it is too late, the virus has already spread and the apparition of symptoms is only a matter of local amplification and time. Addressing a viral disease the right way is considering altogether the medical and epidemiological aspects and all parameters involved in the “predisease” dynamic. These parameters are relevant to a large range of non-medical topics, such as biology, ecology evolution, entomology, geography, environment, etc. The COVID-19 crisis demonstrated what was known to specialized scientists: there is nothing we can do to prevent the circulation of viruses in the wild, the sylvatic cycle, and acting when the disease has emerged is too late. The right segment to address is the circulation and amplification within the human society. Doing so requires a multidisciplinary and integrative approach. This special issue of Viruses is thus open to any kind of articles (research, review, opinion, etc.), addressing the dynamic of viral diseases beyond the sole field of medicine and epidemiology.

Prof. Dr. Roger Frutos
Guest Editor

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Keywords

  • viral diseases
  • emerging diseases
  • viral evolution
  • epidemiology
  • vector-borne diseases
  • viral ecology
  • medicine
  • ecology
  • GIS
  • modeling
  • environmental factors of disease expansion

Published Papers (6 papers)

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Research

21 pages, 6828 KiB  
Article
Phylodynamic Dispersal of SARS-CoV-2 Lineages Circulating across Polish–German Border Provinces
Viruses 2022, 14(5), 884; https://doi.org/10.3390/v14050884 - 24 Apr 2022
Cited by 2 | Viewed by 1517
Abstract
Introduction: The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evolved into a worldwide outbreak, with significant molecular evolution over time. Large-scale phylodynamic studies allow to map the virus spread and inform preventive strategies. Aim: This study investigates the extent of binational [...] Read more.
Introduction: The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evolved into a worldwide outbreak, with significant molecular evolution over time. Large-scale phylodynamic studies allow to map the virus spread and inform preventive strategies. Aim: This study investigates the extent of binational dispersal and dynamics of SARS-CoV-2 lineages between seven border provinces of the adjacent countries of Poland and Germany to reconstruct SARS-CoV-2 transmission networks. Methods: Following three pandemic waves from March 2020 to the end of May 2021, we analysed a dataset of 19,994 sequences divided into B.1.1.7|Alpha and non-Alpha lineage groups. We performed phylogeographic analyses using the discrete diffusion models to identify the pathways of virus spread. Results: Based on population dynamics inferences, in total, 673 lineage introductions (95% HPD interval 641–712) for non-Alpha and 618 (95% HPD interval 599–639) for B.1.1.7|Alpha were identified in the area. For non-Alpha lineages, 5.05% binational, 86.63% exclusively German, and 8.32% Polish clusters were found, with a higher frequency of international clustering observed for B.1.1.7|Alpha (13.11% for binational, 68.44% German and 18.45% Polish, p < 0.001). We identified key transmission hubs for the analysed lineages, namely Saxony, West Pomerania and Lower Silesia. Conclusions: Clustering patterns between Poland and Germany reflect the viral variant transmission dynamics at the international level in the borderline area. Tracing the spread of the virus between two adjacent large European countries may provide a basis for future intervention policies in cross-border cooperation efforts against the spread of the pandemics. Full article
(This article belongs to the Special Issue Global Dynamic of Viral Diseases)
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12 pages, 1212 KiB  
Article
Characteristics and Factors Associated with SARS-CoV-2 Infections in Individuals That Attended Referral Hospitals from Southern Region of Bahia State, Brazil: A Surveillance Network Retrospective Study
Viruses 2021, 13(12), 2462; https://doi.org/10.3390/v13122462 - 09 Dec 2021
Cited by 4 | Viewed by 1990
Abstract
In December 2019, a novel coronavirus was detected in Wuhan, China, and rapidly spread worldwide. In Brazil, to date, there have been more than 20,000,000 confirmed cases of COVID-19 and more than 550,000 deaths. The purpose of the current study was to determine [...] Read more.
In December 2019, a novel coronavirus was detected in Wuhan, China, and rapidly spread worldwide. In Brazil, to date, there have been more than 20,000,000 confirmed cases of COVID-19 and more than 550,000 deaths. The purpose of the current study was to determine the clinical and epidemiological profile of the population affected by COVID-19 that have attended referral hospitals in Southern region of Bahia State, to better understand the disease and its risk factors in order to enable more appropriate conduct for patients. An observational, descriptive, cross-sectional, exploratory study was conducted using secondary data collected from the Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz (LAFEM/UESC). Chi-squared and Fisher’s exact tests were applied to determine the association between clinical symptoms and laboratory results, and to identify risk factors associated with SARS-CoV-2 infection. A total of 3135 individuals with suspected severe respiratory illness were analyzed and 41.4% of them tested positive for SARS-CoV-2 infection. Male individuals and having comorbidities were risk factors significantly associated with SARS-CoV-2 infection (OR = 1.17 and OR = 1.37, respectively). Interestingly, being a healthcare professional was a significantly protective factor (OR = 0.81, p < 0.001). Our findings highlight the importance of routinely testing the population for early identification of infected individuals, and also provide important information to health authorities and police makers to improve control measures, management, and screening protocols. Full article
(This article belongs to the Special Issue Global Dynamic of Viral Diseases)
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18 pages, 1871 KiB  
Article
Geographic Partitioning of Dengue Virus Transmission Risk in Florida
Viruses 2021, 13(11), 2232; https://doi.org/10.3390/v13112232 - 05 Nov 2021
Cited by 8 | Viewed by 2811
Abstract
Dengue viruses (DENVs) cause the greatest public health burden globally among the arthropod-borne viruses. DENV transmission risk has also expanded from tropical to subtropical regions due to the increasing range of its principal mosquito vector, Aedes aegypti. Focal outbreaks of dengue fever [...] Read more.
Dengue viruses (DENVs) cause the greatest public health burden globally among the arthropod-borne viruses. DENV transmission risk has also expanded from tropical to subtropical regions due to the increasing range of its principal mosquito vector, Aedes aegypti. Focal outbreaks of dengue fever (dengue) in the state of Florida (FL) in the USA have increased since 2009. However, little is known about the competence of Ae. aegypti populations across different regions of FL to transmit DENVs. To understand the effects of DENV genotype and serotype variations on vector susceptibility and transmission potential in FL, we orally infected a colony of Ae. aegypti (Orlando/ORL) with low passage or laboratory DENV-1 through -4. Low passage DENVs were more infectious to and had higher transmission potential by ORL mosquitoes. We used these same DENVs to examine natural Ae. aegypti populations to determine whether spatial distributions correlated with differential vector competence. Vector competence across all DENV serotypes was greater for mosquitoes from areas with the highest dengue incidence in south FL compared to north FL. Vector competence for low passage DENVs was significantly higher, revealing that transmission risk is influenced by virus/vector combinations. These data support a targeted mosquito-plus-pathogen screening approach to more accurately estimate DENV transmission risk. Full article
(This article belongs to the Special Issue Global Dynamic of Viral Diseases)
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11 pages, 3699 KiB  
Article
Genetic Characterizations and Molecular Evolution of the Measles Virus Genotype B3’s Hemagglutinin (H) Gene in the Elimination Era
Viruses 2021, 13(10), 1970; https://doi.org/10.3390/v13101970 - 30 Sep 2021
Viewed by 1608
Abstract
Measles virus (MeV) genotype B3 is one globally significant circulating genotype. Here, we present a systematic description of long-term evolutionary characterizations of the MeV genotype B3’s hemagglutinin (H) gene in the elimination era. Our results show that the B3 H gene can be [...] Read more.
Measles virus (MeV) genotype B3 is one globally significant circulating genotype. Here, we present a systematic description of long-term evolutionary characterizations of the MeV genotype B3’s hemagglutinin (H) gene in the elimination era. Our results show that the B3 H gene can be divided into two main sub-genotypes, and the highest intra-genotypic diversity was observed in 2004. MeV genotype B3’s H gene diverged in 1976; its overall nucleotide substitution rate is estimated to be 5.697 × 10−4 substitutions/site/year, and is slowing down. The amino acid substitution rate of genotype B3’s H gene is also decreasing, and the mean effective population size has been in a downward trend since 2000. Selection pressure analysis only recognized a few sites under positive selection, and the number of positive selection sites is getting smaller. All of these observations may reveal that genotype B3’s H gene is not under strong selection pressure, and is becoming increasingly conservative. MeV H-gene or whole-genome sequencing should be routine, so as to better elucidate the molecular epidemiology of MeV in the future. Full article
(This article belongs to the Special Issue Global Dynamic of Viral Diseases)
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10 pages, 4118 KiB  
Article
A Waterborne Gastroenteritis Outbreak Caused by a GII Norovirus in a Holiday Camp in Catalonia (Spain), 2017
Viruses 2021, 13(9), 1792; https://doi.org/10.3390/v13091792 - 08 Sep 2021
Cited by 8 | Viewed by 2538
Abstract
On 2 February 2017, Epidemiological Surveillance Services were notified of an outbreak of acute gastroenteritis (AGE) among schoolchildren who had taken part of a school trip from 30 January to 3 February 2017 at a holiday camp in Catalonia. A retrospective cohort study [...] Read more.
On 2 February 2017, Epidemiological Surveillance Services were notified of an outbreak of acute gastroenteritis (AGE) among schoolchildren who had taken part of a school trip from 30 January to 3 February 2017 at a holiday camp in Catalonia. A retrospective cohort study was performed to identify the causative agent, estimate the magnitude of the outbreak and identify its source, as well as to determine the route of transmission. Data collected by standardised questionnaires identified 41 episodes of AGE among 174 individuals who attended the camp. Cases had mainly symptoms of abdominal pain (73.8%), nausea (64.3%), vomiting (54.8%), diarrhoea (45.2%) and headache (42.9%). Consumption of water was associated with gastroenteritis (crude RR: 1.72, 95%CI: 1.01–2.92; adjusted RR: 1.88, 95%CI 1.03–3.56). NoV GII was detected in faeces (5 out of 13) and water samples. Additionally, faecal indicator bacteria and protozoa were detected in water samples. The outbreak showed a high attack rate and was caused by a natural water fountain not properly treated and not monitored for safety quality. There could have been a discharge of wastewater at a point close to the fountain; however, the source of contamination of the water could not be identified. Health education may be useful to eliminate risks associated with the consumption of untreated water from natural fountains. Full article
(This article belongs to the Special Issue Global Dynamic of Viral Diseases)
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36 pages, 16936 KiB  
Article
The Evolving Faces of the SARS-CoV-2 Genome
Viruses 2021, 13(9), 1764; https://doi.org/10.3390/v13091764 - 03 Sep 2021
Cited by 12 | Viewed by 2982
Abstract
Surveillance of the evolving SARS-CoV-2 genome combined with epidemiological monitoring and emerging vaccination became paramount tasks to control the pandemic which is rapidly changing in time and space. Genomic surveillance must combine generation and sharing sequence data with appropriate bioinformatics monitoring and analysis [...] Read more.
Surveillance of the evolving SARS-CoV-2 genome combined with epidemiological monitoring and emerging vaccination became paramount tasks to control the pandemic which is rapidly changing in time and space. Genomic surveillance must combine generation and sharing sequence data with appropriate bioinformatics monitoring and analysis methods. We applied molecular portrayal using self-organizing maps machine learning (SOM portrayal) to characterize the diversity of the virus genomes, their mutual relatedness and development since the beginning of the pandemic. The genetic landscape obtained visualizes the relevant mutations in a lineage-specific fashion and provides developmental paths in genetic state space from early lineages towards the variants of concern alpha, beta, gamma and delta. The different genes of the virus have specific footprints in the landscape reflecting their biological impact. SOM portrayal provides a novel option for ‘bioinformatics surveillance’ of the pandemic, with strong odds regarding visualization, intuitive perception and ‘personalization’ of the mutational patterns of the virus genomes. Full article
(This article belongs to the Special Issue Global Dynamic of Viral Diseases)
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