A main event and multiple introductions of SARS‐CoV‐2 initiated the COVID‐19 epidemic in Greece

Spanakis, Nikolaos; Kassela, Katerina; Dovrolis, Nikolas; Bampali, Maria; Gatzidou, Elisavet; Kafasi, Athanasia; Froukala, Elisavet; Stavropoulou, Anastasia; Λιλάκος, Κωνσταντίνος; Veletza, Stavroula; Tsiodras, Sotirios; Tsakris, Athanasios; Karakasiliotis, Ioannis

doi:10.1002/jmv.26778

Cited by 15 publications

(9 citation statements)

References 40 publications

(80 reference statements)

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“…The use of next-generation sequencing technology can be beneficial in several steps of an epidemic response [13], among them, pathogen identification [14], tracing the origins of the agent [15][16][17], and monitoring its spread [18][19][20][21][22][23] and evolution [17,24,25], as well as supporting development of diagnostic solutions and new therapeutic target discovery [26]. Even though there are different approaches to full-genome sequencing, the multiplex PCR amplicon method is currently one of the cheapest, while also proving to be superior to capture-based sequencing in the analysis of challenging samples [4].…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

Szargut

Cytacka

Serwin

et al. 2022

Viruses

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The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.

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Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

Szargut

Cytacka

Serwin

et al. 2022

Viruses

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“…Our study data comprised of 389 unique full-genome SARS-CoV-2 sequences, of which 280 were newly generated and 109 were available on the GISAID database, collected in Attica until December 1, 2020 [35]. The vast majority of our samples had been collected in Attica (Ν=353, 90.7%).…”

Section: Resultsmentioning

confidence: 99%

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

Pavlopoulos

Verrou

et al. 2021

Preprint

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Molecular epidemiology has provided an additive value to traditional public health tools by identifying SARS-CoV-2 clusters, or providing evidence that clusters based on virus sequences and contact tracing are highly concordant. Our aim was to infer the levels of virus importation and to estimate the impact of public health measures related to travel restrictions to local transmission in Greece. Our phylogenetic and phylogeographic analyses included 389 SARS-CoV-2 sequences collected during the first 7 months of the pandemic in Greece and a random collection in 5 replicates of 3,000 sequences sampled globally, as well as the best hits to our dataset identified by BLAST. Phylogenetic analyses revealed the presence of 70 genetically distinct viruses identified as independent introductions into Greece. The proportion of imported strains was 41%, 11.5%, and 8.8% during the three periods of sampling, namely, March (no travel restrictions), April to June (strict travel restrictions), and July to September (lifting of travel restrictions based on a thorough risk assessment), respectively. These findings reveal low levels of onward transmission from imported cases during summer and underscore the importance of targeted public health measures that can increase the safety of international travel during a pandemic.

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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%

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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A main event and multiple introductions of SARS‐CoV‐2 initiated the COVID‐19 epidemic in Greece

Cited by 15 publications

References 40 publications

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

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

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

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