A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic

Chrysostomou, Andreas; Vrancken, Bram; Koumbaris, George; Themistokleous, George; Aristokleous, Antonia; Masia, Christina; Eleftheriou, Christina; Iοannou, Costakis; Stylianou, Dora C.; Ioannides, Marios; Petrou, Panagiotis; Georgiou, Vasilis; Hatziyianni, Amalia; Lemey, Philippe; Vandamme, Anne‐Mieke; Patsalis, Philippos P; Kostrikis, Leondios G.

doi:10.3390/v13061098

Cited by 13 publications

(31 citation statements)

References 78 publications

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“…D1118H: This mutation was detected first in the B.1.1.7 UK variant. The D1118H substitution is also present in the S2 subunit of the S protein ( Chrysostomou et al., 2021 ). It has been suggested that this mutation can alter the stability and dynamics of trimer assembly ( Zhao et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach

Mohammad

Choudhury

Habib

et al. 2021

Front. Cell. Infect. Microbiol.

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A continual rise in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease (COVID-19) has become a global threat. The main problem comes when SARS-CoV-2 gets mutated with the rising infection and becomes more lethal for humankind than ever. Mutations in the structural proteins of SARS-CoV-2, i.e., the spike surface glycoprotein (S), envelope (E), membrane (M) and nucleocapsid (N), and replication machinery enzymes, i.e., main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) creating more complexities towards pathogenesis and the available COVID-19 therapeutic strategies. This study analyzes how a minimal variation in these enzymes, especially in S protein at the genomic/proteomic level, affects pathogenesis. The structural variations are discussed in light of the failure of small molecule development in COVID-19 therapeutic strategies. We have performed in-depth sequence- and structure-based analyses of these proteins to get deeper insights into the mechanism of pathogenesis, structure-function relationships, and development of modern therapeutic approaches. Structural and functional consequences of the selected mutations on these proteins and their association with SARS-CoV-2 virulency and human health are discussed in detail in the light of our comparative genomics analysis.

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Section: Discussionmentioning

confidence: 99%

Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach

Mohammad

Choudhury

Habib

et al. 2021

Front. Cell. Infect. Microbiol.

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“…Cyprus was no exception with regard to this pattern of lineage replacement, with certain lineages causing surges of new infections, reaching a distinct peak and then a decline; this peaks-and-valleys pattern is referred to as ‘waves’ [ 27 , 28 ]. Specifically, in our previous study covering the period of April 2020 to January 2021, we determined that despite polyphyletic infection in Cyprus with 34 different lineages, there were three consecutive waves characterized by specific lineages [ 29 ]: B.1.1, specifically B.1.1.29, comprising the first wave with sequences from April 2020 to June 2020; B.1.258 & sublineages comprising the second wave, with sequences from September 2020 to January 2021; and Alpha (B.1.1.7 & Q. sublineages), comprising the beginning of the third wave, with sequences from December 2020 until the end of the sampling period in January 2021 [ 29 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Chrysostomou¹,

Vrancken²,

Haralambous³

et al. 2022

Viruses

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.

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“…Vaccination campaigns against SARS-CoV-2 have been gathering momentum, but most countries remain months away from reaching group immunity [ 1 - 4 ], provided that such immunity can be attained [ 5 , 6 ]. The almost incessant emergence of new variants is concerning [ 7 ]—all the more so as some variants have been shown to evade the immune response acquired by vaccination or by prior infection [ 8 , 9 ]. Viral dissemination may even be facilitated, if normal social interactions are restored and social distancing measures are eliminated, as countries face ever increasing social and economic pressures [ 10 - 12 ].…”

Section: Introductionmentioning

confidence: 99%

Nationwide Deployment of a Serious Game Designed to Improve COVID-19 Infection Prevention Practices in Switzerland: Prospective Web-Based Study

Suppan¹,

Stuby²,

Harbarth³

et al. 2021

JMIR Serious Games

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Background Lassitude and a rather high degree of mistrust toward the authorities can make regular or overly constraining COVID-19 infection prevention and control campaigns inefficient and even counterproductive. Serious games provide an original, engaging, and potentially effective way of disseminating COVID-19 infection prevention and control guidelines. Escape COVID-19 is a serious game for teaching COVID-19 infection prevention and control practices that has previously been validated in a population of nursing home personnel. Objective We aimed to identify factors learned from playing the serious game Escape COVID-19 that facilitate or impede intentions of changing infection prevention and control behavior in a large and heterogeneous Swiss population. Methods This fully automated, prospective web-based study, compliant with the Checklist for Reporting Results of Internet E-Surveys (CHERRIES), was conducted in all 3 main language regions of Switzerland. After creating an account on the platform, participants were asked to complete a short demographic questionnaire before accessing the serious game. The only incentive given to the potential participants was a course completion certificate, which participants obtained after completing the postgame questionnaire. The primary outcome was the proportion of participants who reported that they were willing to change their infection prevention and control behavior. Secondary outcomes were the infection prevention and control areas affected by this willingness and the presumed evolution in the use of specific personal protective equipment items. The elements associated with intention to change infection prevention and control behavior, or lack thereof, were also assessed. Other secondary outcomes were the subjective perceptions regarding length, difficulty, meaningfulness, and usefulness of the serious game; impression of engagement and boredom while playing the serious game; and willingness to recommend its use to friends or colleagues. Results From March 9 to June 9, 2021, a total of 3227 accounts were created on the platform, and 1104 participants (34.2%) completed the postgame questionnaire. Of the 1104 respondents, 509 respondents (46.1%) answered that they intended to change their infection prevention and control behavior after playing the game. Among the respondents who answered that they did not intend to change their behavior, 86.1% (512/595) answered that they already apply these guidelines. Participants who followed the German version were less likely to intend to change their infection prevention and control behavior (odds ratio [OR] 0.48, 95% CI 0.24-0.96; P=.04) and found the game less engaging (P<.001). Conversely, participants aged 53 years or older had stronger intentions of changing infection prevention and control behavior (OR 2.07, 95% CI 1.44-2.97; P<.001). Conclusions Escape COVID-19 is a useful tool to enhance correct infection prevention and control measures on a national scale, even after 2 COVID-19 pandemic waves; however, the serious game's impact was affected by language, age category, and previous educational training, and the game should be adapted to enhance its impact on specific populations.

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A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic

Cited by 13 publications

References 78 publications

Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach

Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Nationwide Deployment of a Serious Game Designed to Improve COVID-19 Infection Prevention Practices in Switzerland: Prospective Web-Based Study

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