Abstract
In December 2020, UK authorities warned of the rapid spread of a new SARS-CoV-2 variant, belonging to the B.1.1.7 lineage, known as the Alpha variant. This variant is characterized by 17 mutations and 3 deletions. The deletion 69–70 in the spike protein can be detected by commercial platforms, allowing its real-time spread to be known. From the last days of December 2020 and over 4 months, all respiratory samples with a positive result for SARS-CoV-2 from patients treated in primary care and the emergency department were screened to detect this variant based on the strategy S gene target failure (SGTF). The first cases were detected during week 53 (2020) and reached >90% of all cases during weeks 15–16 (2021). During this period, the B.1.1.7/SGTF variant spread at a rapid and constant replacement rate of around 30–36%. The probability of intensive care unit admission was twice higher among patients infected by the B.1.1.7/SGTF variant, but there were no differences in death rate. During the peak of the third pandemic wave, this variant was not the most prevalent, and it became dominant when this wave was declining. Our results confirm that the B.1.1.7/SGTF variant displaced other SARS-CoV-2 variants in our healthcare area in 4 months. This displacement has led to an increase in the burden of disease.
Highlights
In the last days of December 2019, the first cases of a pneumonia of unknown origin were described, and only 1 month later, the World Health Organization (WHO) declared a public health emergency of international concern
27,633 respiratory samples coming from 20 PC centers and the emergency department of Hospital Universitario Ramón y Cajal were processed for diagnosing COVID-19 infection: 20,870 samples (75.5%) were received from primary care and 6763 (24.5%) samples were received from patients admitted to the emergency department
The screening started in week of 2020, and only four cases were detected in week in two PC centers, but they were not included in this analysis
Summary
In the last days of December 2019, the first cases of a pneumonia of unknown origin were described, and only 1 month later, the World Health Organization (WHO) declared a public health emergency of international concern. A pandemic caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started, causing great disruption on a global scale [1,2]. SARS-CoV-2 virus, closely related to other lethal coronaviruses such as MERS-CoV (Middle East respiratory syndrome) and SARS-CoV-1, has shown a higher capacity of transmission than its known relatives. Each replication event is a biological opportunity for mutation, and each transmission event is an opportunity for the spreading of these emerged mutants. The diversification of SARS-CoV-2 variants has grown continuously, evolving towards a complex description of lineages
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