Rapid Spread of the SARS-CoV-2 Variant of Concern 202012/01 in Southern Italy (December 2020–March 2021)

Abstract

Epidemiological and virological studies have revealed that SARS-CoV-2 variants of concern (VOCs) are emerging globally, including in Europe. The aim of this study was to evaluate the spread of B.1.1.7-lineage SARS-CoV-2 in southern Italy from December 2020–March 2021 through the detection of the S gene target failure (SGTF), which could be considered a robust proxy of VOC B.1.1.7. SGTF was assessed on 3075 samples from week 52/2020 to week 10/2021. A subset of positive samples identified in the Apulia region during the study period was subjected to whole-genome sequencing (WGS). A descriptive and statistical analysis of the demographic and clinical characteristics of cases according to SGTF status was performed. Overall, 20.2% of samples showed SGTF; 155 strains were confirmed as VOC 202012/01 by WGS. The proportion of SGTF-positive samples rapidly increased over time, reaching 69.2% in week 10/2021. SGTF-positive cases were more likely to be symptomatic and to result in hospitalization (p < 0.0001). Despite the implementation of large-scale non-pharmaceutical interventions (NPIs), such as the closure of schools and local lockdowns, a rapid spread of VOC 202012/01 was observed in southern Italy. Strengthened NPIs and rapid vaccine deployment, first among priority groups and then among the general population, are crucial both to contain the spread of VOC 202012/01 and to flatten the curve of the third wave.

Severe COVID-19 by SARS-CoV-2 Lineage B.1.1.7 in Vaccinated Solid-Organ Transplant Recipients: New Preventive Strategies Needed to Protect Immunocompromised Patients

“…Real-time PCR for SARS-CoV-2 on samples from the three cases showed cycle threshold (Ct) values <20 and S-gene target failure (SGTF), which is considered a robust proxy for the SARS-CoV-2 B.1.1.7 lineage [ 19 ]. In all three cases, prolonged viral shedding was reported ( Table 1 ).…”

“…It has been demonstrated that subjects infected by SARS-CoV-2 VOC 202012/01 are at a higher risk of severe COVID-19, hospitalization, and death [ 19 , 20 ]. Therefore, the severity of COVID-19 in the SOT recipients, as described here, could be related to infection with the B.1.1.7 variant.…”

Case Report: Discovery a Novel SARS-CoV-2 Variant in a Six-Months Long-Term Swab Positive Female Suffering From Non-Hodgkin Lymphoma

“…Among the limits of our paper, we can report the following: a) only a late timepoint was analyzed for this patient in terms of virus sequencing: therefore, we it cannot formally be proven that variation originated in this specific individual, although it is likely. In this regard, we underline as methods of massive parallel sequencing have not been immediately implemented in laboratory tracing in our region as it happened either in other Italian areas or countries ( 26 , 27 ): b) the functional impact of our alteration has been extrapolated by data regarding other point alteration falling in the same domain. Further studies have been planned to better characterize this new variant, possibly in animal or cellular models: these experimental procedures take time and are also expensive.…”

A systematic review of the impact of the Alpha and Gamma variants of concern on hospitalization and symptomatic rates of SARS-CoV-2

“…Finally, a study using data from Southern Italy estimated an adjusted odds ratio of 3.44 (1.76, 6.75) for hospitalization for Alpha with respect to original wildtype (21), and did not directly report on the presence or absence of an age trend.…”

“…Of the included studies, four were conducted in England (15)(16)(17)(18), and will be numbered in the tables that follow. One study was conducted in Denmark (19), one in Ontario, Canada (20), one in Southern Italy (21), and one in Northwest Spain (22). One includes data from seven European national surveillance systems (23).…”