Molecular epidemiology of SARS-CoV-2 in Cyprus

Richter, Jan; Fanis, Pavlos; Tryfonos, Christina; Koptides, Dana; Krashias, George; Bashiardes, Stavros; Hadjisavvas, Andreas; Loizidou, Maria A.; Oulas, Anastasis; Alexandrou, Denise; Kalakouta, Olga; Panayiotidis, Mihalis Ι.; Spyrou, George M.; Christodoulou, Christina

doi:10.1371/journal.pone.0248792

Cited by 10 publications

(5 citation statements)

References 39 publications

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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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“…The succession of the different waves observed in Tunisia is similar to the global picture of COVID-19 infection (https:// covid19.who.int/ (accessed on 30 August 2021)). In addition, the same picture of the circulation of several viral lineages has been reported in several countries around the world, such as the Czech Republic, Cyprus, the UK, Russia, South Africa and countries from the Middle East and North Africa (MENA) region [23][24][25][26][27][28].…”

Section: Discussionsupporting

confidence: 59%

“…This phenomenon is characteristic of airborne viruses. Countries that have succeeded in stopping their transmission are those that have applied drastic measures, such as China and South Korea, or other countries that were able to contain the virus during the first phases of the pandemic with full containment, border closures and the minimization of any contact, even between non-infected people [23][24][25][26][27][28].…”

Section: Discussionmentioning

confidence: 99%

Virological Diagnosis of SARS-CoV-2 in a Tunisian Orthopedic Institute

2023

TMOA

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Background: The objective of this study was to investigate the epidemiological profile of the virological diagnosis of COVID 19 at Mohamed Kassab Institute of Orthopedics. Methods: The virological diagnosis was performed by RT-PCR from november 2020 to september 2021 on 33505 nasopharyngeal swabs which different reagent kits were used: Allplex® 2019 nCoV Assay, WANTAI® SARS-CoV-2 RT-PCR, WONDFO® 2019- nCoV Real-Time RT-PCR Assay, GENESIG® Real time PCR coronavirus (COVID-19), GENESIG® COVID-19 2G . The duration from onset to laboratory test in COVID-19 suspected cases and contact individuals ranged from 0 to 14 days with a median of 3 days. The present study provides some genetic information on the lineages of SARS-CoV-2 that circulated in Tunisia over 6 months from april to september 2021. Lineages were assigned for 13 samples using whole-genome sequencing, partial S gene sequencing. Results: A total of 33505 PCR tests were performed from five governorates including Manouba which represented 88.2% (29560). The positive samples were 35% (11695) and 57% (19223) were negative. The sex ratio of confirmed cases was 0.9 (5540/6155). The age group 20-65 years was the most represented with 65.9%. For sequencing her we describe the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains. Conclusion: This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.

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“…The succession of the different waves observed in Tunisia is similar to the global picture of COVID-19 infection ( (accessed on 30 August 2021)). In addition, the same picture of the circulation of several viral lineages has been reported in several countries around the world, such as the Czech Republic, Cyprus, the UK, Russia, South Africa and countries from the Middle East and North Africa (MENA) region [ 28 , 29 , 30 , 31 , 32 , 33 ]. The exchange between countries has played a crucial role in the importation of new lineages and their rapid spread across countries.…”

Section: Discussionmentioning

confidence: 57%

Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19

Chouikha

Laamari

Haddad-Boubaker

et al. 2022

Viruses

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Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.

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Molecular epidemiology of SARS-CoV-2 in Cyprus

Cited by 10 publications

References 39 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

Virological Diagnosis of SARS-CoV-2 in a Tunisian Orthopedic Institute

Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19

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