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

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.

Keywords: B.1.1.7; Italy; P.1; SARS-Cov-2; epidemic; variant of concern.

Figure 1

Number of SARS-CoV-2 genomes sampled over time in Italy. (a) Bars show the number of cases reported in Italy between 1 January 2020–1 March 2021. Horizontally aligned circles show the number of sequences sampled for each day in North (blue), Central (yellow), South (red) Italy. The size of the circle is equivalent to the total number of sequences (max = 256). Italian regions are coloured according to their macro areas: blue = North (Valle d’Aosta, Piemonte, Liguria, Lombardia, Emilia-Romagna, Veneto, Friuli-Venezia-Giulia, and Trentino-Alto Adige), yellow = Central (Lazio, Marche, Toscana, Umbria, and Abruzzo), red = South (Puglia, Basilicata, Calabria, Campania, Molise, Sicilia, and Sardegna). (b) Number of sequences sampled in Italy for the lineages B.1. B.1.1.74, B.1.177, B.1.1.7, and P.1 for North (top), Central (middle), and South (bottom) Italy. The total number of sequences per day (circles) and the time range between first and most recent sequence (dotted line) is shown (max = 146).

Figure 2

Genomic epidemiology of SARS-CoV-2 lineage B.1.1.7. Maximum likelihood phylogeny of SARS-CoV-2 full genome sequences. Due to the large amount of data for B.1.1.7 (>100,000 sequences), a random subset of 3000 B.1.1.7 sequences sampled globally were incorporated (2900 after data cleaning). Branches are colored according to the macro area: grey = global, blue = North Italy, yellow = Central Italy, red = South Italy. Branch length is scaled according to the number of nucleotide substitutions per site. Lineage B.1.351 and P.1 were used as an outgroup (B.1.351 = EPI_ISL_660190, P.1 = EPI_ISL_833137). Arrows indicate examples of large Italian clades with limited inter-region transmission; bootstrap node support is indicated. One clade with increased inter-region transmission is shown enlarged on the right.

Figure 3

Genomic epidemiology of SARS-CoV-2 lineage P.1. (a) Maximum likelihood phylogeny of SARS-CoV-2 full genome sequences (n = 503 global, n = 111 Italian). Lineage B.1.351 was used as an outgroup (EPI_ISL_660190). Branch lengths are scaled according to the number of nucleotide substitutions per site and are colored according to geographic macro area: grey = global, blue = North Italy, yellow = Central Italy, red = South Italy. The node containing the T to C mutation in ORF1ab is marked with a yellow box (clade I). (b) (bottom) Enlargement of this node and additional clades and their nucleotide or amino acid substitutions are indicated. Bootstrap node support for clades I-III is shown. Note, a single sequence containing also the S813N mutation but falling in clade I is marked with an asterisk. Branches without a tip circle represent sequences from Germany. (top) Schematic view of the spike protein alignment for different reference sequences as well as the clade containing the S813N substitution. The protein structural regions are marked: S1 NTD = N-terminal domain of the S1 subunit, S1 RBD = receptor binding domain of S1, S1–S2 S2 = S1/S2 cleavage region and S2 fusion subunit. A detailed view of the protein alignment can be found in Supplementary Figure S2.