Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy.

Francesca Di Giallonardo,Joanna C A Cobbin,Cesare Cammà,Paolo Calistri,Ilaria Puglia,Iolanda Mangone,Edward C Holmes,Valentina Curini,Alessio Lorusso

doi:10.3390/v13050794

Abstract

Italy’s second wave of SARS-CoV-2 has hit hard, with more than three million cases and over 100,000 deaths, representing an almost ten-fold increase in the numbers reported by August 2020. Herein, we present an analysis of 6515 SARS-CoV-2 sequences sampled in Italy between 29 January 2020 and 1 March 2021 and show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became the dominant variant in November 2020, when cases peaked at 40,000 a day, but since January 2021 this is being replaced by the B.1.1.7 ‘variant of concern’. In addition, we report a sudden increase in another documented variant of concern—lineage P.1—from December 2020 onwards, most likely caused by a single introduction into Italy. We again highlight how international importations drive the emergence of new lineages and that genome sequencing should remain a top priority for ongoing surveillance in Italy.

Highlights

COVID-19, caused by infection with severe respiratory coronavirus 2 (SARS-CoV-2), has had a devastating global impact, with an estimated 116 million cases and 2.5 million deaths [1]
The B.1.351 lineage was first reported in South Africa and shares similar substitutions to B.1.1.7 including N501Y but not the 69/70 deletion [6], while the P.1 lineage was first identified in Brazil and shares two substitutions with B.1.351—E484K and N501Y in the spike protein [4]
Sequence sampling was not equal between North, Central, and South Italy, as a large proportion of SARS-CoV-2 sequence data from North Italy was only available for the beginning of the pandemic (March–May 2020) and again the most recent months (Januar–March 2021) (Figure 1a) Despite this, the time range of data availability overlaps between these three macro areas, minimizing the effect of sampling bias

Summary

Introduction

COVID-19, caused by infection with severe respiratory coronavirus 2 (SARS-CoV-2), has had a devastating global impact, with an estimated 116 million cases and 2.5 million deaths [1]. Of these reported infections, more than 78% have occurred between September. 2020–March 2021, greatly outnumbering the 25 million cases and ~800 k deaths reported globally prior to 31 August 2020 [2] This second wave of infections is characterized by the emergence of numerous new lineages of SARS-CoV-2, three of which are commonly referred to global ‘variants of concern’—B.1.1.7, B.1.351, and P.1 [3].

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Conclusion