Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Mutational Pattern in the Fourth Pandemic Phase in Greece

Panagiotis Halvatsiotis; Sofia Vassiliu; Panagiotis Koulouvaris; Kalliopi Chatzantonaki; Konstantinos Asonitis; Ekatherina Charvalos; Argyris Siatelis; Dimitra Houhoula

doi:10.3390/cimb44010024

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Mutational Pattern in the Fourth Pandemic Phase in Greece

Curr Issues Mol Biol. 2022 Jan 11;44(1):329-335. doi: 10.3390/cimb44010024.

Authors

Panagiotis Halvatsiotis¹, Sofia Vassiliu², Panagiotis Koulouvaris³, Kalliopi Chatzantonaki⁴, Konstantinos Asonitis⁵, Ekatherina Charvalos⁴, Argyris Siatelis⁶, Dimitra Houhoula⁷

Affiliations

¹ 2nd Propaedeutic Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, "ATTIKON" University Hospital, 12461 Chaidari, Greece.
² School of Medicine, National and Kapodistrian University of Athens, 11527 Goudi, Greece.
³ 1st Department of Orthopaedics, School of Medicine, National and Kapodistrian University of Athens, "ATTIKON" University Hospital, 12461 Chaidari, Greece.
⁴ Invitrolabs SA Leventi 9, 12132 Attiki, Greece.
⁵ Division of Hematology and Central Hematology Laboratory, Lausanne, Department of Hematology University Hospital (CHUV) and University of Lausanne (UNIL), 1011 Lausanne, Switzerland.
⁶ 3rd Department of Urologist, School of Medicine, National and Kapodistrian University of Athens, "ATTIKON" University Hospital, 12461 Chaidari, Greece.
⁷ Department of Food Science and Technology, University of West Attica, Agiou Spyridonos 28, 12243 Aigaleo, Greece.

Abstract

The aim of this study is to investigate the circulating variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Athens and from rural areas in Greece during July and August 2021. We also present a rapid review of literature regarding significant SARS-CoV-2 mutations and their impact on public health. A total of 2500 nasopharyngeal swab specimens were collected from suspected COVID-19 cases (definition by WHO 2021b). Viral nucleic acid extraction was implemented using an automatic extractor and the RNA recovered underwent qRT-PCR in order to characterize the specimens as positive or negative for SARS-CoV-2. The positive specimens were then used to identify specific Spike gene mutations and characterize the emerging SARS-CoV-2 variants. For this step, various kits were utilized. From the 2500 clinical specimens, 220 were tested positive for SARS-CoV-2 indicating a prevalence of 8.8% among suspected cases. The RT-PCR Ct (Cycle threshold) Value ranged from 19 to 25 which corresponds to medium to high copy numbers of the virus in the positive samples. From the 220 positive specimens 148 (67.3%) were from Athens and 72 (32.7%) from Greek rural areas. As far as the Spike mutations investigated: N501Y appeared in all the samples, D614G mutation appeared in 212 (96.4%) samples with a prevalence of 87.2% in Athens and 98.6% in the countryside, E484K had a prevalence of 10.8% and 12.5% in Athens and the rural areas, respectively. K417N was found in 18 (12.2%) samples from Athens and four (5.6%) from the countryside, P681H was present in 51 (34.5%) Athenian specimens and 14 (19.4%) specimens from rural areas, HV69-70 was carried in 32.4% and 19.4% of the samples from Athens and the countryside, respectively. P681R had a prevalence of 87.2% in Athens and 98.6% in rural areas, and none of the specimens carried the L452R mutation. 62 (28.2%) samples carried the N501Y, P681H, D614G and HV69-70 mutations simultaneously and the corresponding variant was characterized as the Alpha (UK) variant (B 1.1.7). Only six (2.7%) samples from the center of Athens had the N501Y, E484K, K417N and D614G mutations simultaneously and the virus responsible was characterized as the Beta (South African) variant (B 1.351). Our study explored the SARS-CoV-2 variants using RT-PCR in a representative cohort of samples collected from Greece in July and August 2021. The prevalent mutations identified were N501Y (100%), D614G (96.4%), P681R (90.1%) and the variants identified were the Delta (90.1%), Alpha (28.2%) and Beta (2.7%).

Keywords: COVID-19; Greece; RT-PCR; S gene; SARS-CoV-2; mutations; variants.