Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020

Kostaki, Evangelia Georgia; Pavlopoulos, Georgios A.; Verrou, Kleio-Maria; Ampatziadis-Michailidis, Giannis; Harokopos, Vaggelis; Hatzis, Pantelis; Moulos, Panagiotis; Siafakas, Nikolaos; Pournaras, Spyridon; Hadjichristodoulou, Christos; Chatzopoulou, Fani; Chatzidimitriou, Dimitrios; Panagopoulos, Periklis; Lourida, Panagiota; Argyraki, Aikaterini; Lytras, Theodoros; Sapounas, Spyros; Gerolymatos, Gerasimos; Panagiotakopoulos, Georgios; Prezerakos, Panagiotis; Tsiodras, Sotirios; Sypsa, Vana; Hatzakis, Angelos; Anastassopoulou, Cleo; Spanakis, Nikolaos; Tsakris, Athanasios; Dimopoulos, Meletios A.; Κοτανίδου, Αναστασία; Sfikakis, Petros P.; Κόλλιας, Γεώργιος; Magiorkinis, Gkikas; Paraskevis, Dimitrios

doi:10.1128/msphere.00180-21

Cited by 9 publications

(11 citation statements)

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“…Epidemiological information from the Mexican Health Ministry in the early stages of the pandemic in Mexico, together with the results from this study, suggest that the pandemic in Mexico was maintained by community transmission, following the importation of variants mainly from the United States, Europe, and South America. This same phenomenon has been reported in other countries in Europe, Asia, Africa and South America ( Al Nahid and Ghosh, 2021 ; Al-Mahruqi et al, 2021 ; Elizondo et al, 2021 ; Engelbrecht et al, 2021 ; Giovanetti et al, 2021 ; Kostaki et al, 2021 ; Richter et al, 2021 ).…”

Section: Discussionsupporting

confidence: 87%

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

et al. 2022

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BackgroundThe advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs).ObjectiveThis study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs.Methods30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed.Results148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes.ConclusionThe COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.

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Section: Discussionsupporting

confidence: 87%

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

et al. 2022

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“…Our study, albeit analyzing a small cohort of patients, contributes to the very few data that have been published about Greece. A total of 41% of transmission in Greece was attributed to imported lineages [ 129 ], and viral importation has occurred via multiple routes [ 130 ]. This could explain the fact that a lot of the mutations we detected have also been characterized in other regions around the world, as mentioned above.…”

Section: Discussionmentioning

confidence: 99%

“…Regarding the rest of the mutations of our analysis, no references were found in previous data derived from our geographic region. After the first wave, the importation of the virus was limited in our country [ 129 ].…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic

et al. 2022

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility rate, albeit a lower case fatality rate, which results in accumulation of a significant number of mutations and a faster evolution rate. Genomic studies on the mutation rate of the virus, as well as the identification of mutations that prevail and their impact on disease severity, are of great importance for pandemic surveillance and vaccine and drug development. Here, we aim to identify mutations on the SARS-CoV-2 viral genome and their effect on the proteins they are located in, in Greek patients infected in the first wave of the pandemic. To this end, we perform SARS-CoV-2 amplicon-based NGS sequencing on nasopharyngeal swab samples from Greek patients and bioinformatic analysis of the results. Although SARS-CoV-2 is considered genetically stable, we discover a variety of mutations on the viral genome. In detail, 18 mutations are detected in total on 10 SARS-CoV-2 isolates. The mutations are located on ORF1ab, S protein, M protein, ORF3a and ORF7a. Sixteen are also detected in patients from other regions around the world, and two are identified for the first time in the present study. Most of them result in amino acid substitutions. These substitutions are analyzed using computational tools, and the results indicate minor or major impact on the proteins’ structural stability, which could probably affect viral transmissibility and pathogenesis. The correlation of these variations with the viral load levels is examined, and their implication for disease severity and the biology of the virus are discussed.

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“…Most of these tools were used for subtyping/classification, alignment, sequence similarity, phylogenetic, phylogeographic and phylodynamic analysis. Specifically, she has been involved in studies related to the investigation of how transmission networks associate with social networks, the estimation of transmission dynamics, dispersal patterns, and spatiotemporal characteristics of viral infections, as well as outbreak investigation [ 162 , 163 , 164 , 165 , 166 ].…”

Section: Women In the Evbcmentioning

confidence: 99%

Women in the European Virus Bioinformatics Center

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Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing “Big Data” offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

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Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020

Cited by 9 publications

References 30 publications

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic

Women in the European Virus Bioinformatics Center

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