On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy

Abstract

Background: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020.

Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020.

Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions.

Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.

Keywords: SARS-CoV-2; genome; transmission.

Figure 1

(a) The blue line represents the daily new COVID-19 positive cases in Trentino in 2020, while the red line is the percentage of positive daily swabs. The second epidemic wave is characterized by an increase in the number of tests, resulting in a reduction of the ratio between new positive cases and number of tests, but an increase of the absolute number of new positive cases. (b) Number of mutations compared to the Wuhan reference genome as a function of sampling date for a selection of sequences from the GISAID database and for the sequences generated in this study (red dots). (c) Relationship between the number of sequenced genomes classified according to the Pangolin classification scheme and mobility data monitored in Trentino. The diameter of each circle is proportional to the number of sequenced samples that belong to each lineage.

Figure 2

Frequency (a) and temporal distribution (b) of the Pangolin lineages in Trentino. (c) Most common mutations found in the first and second epidemic wave. In gray, we show the sequences where the mutation position was not sequenced. Only mutations present in more than 10 sequences are shown.

Figure 3

Phylogeny of 386 genomes of SARS-CoV-2, 253 from Trentino and 133 from GISAID. Red branches identify sequences from Trentino from samples collected in the first epidemic wave (spring 2020), while blue branches identify sequences from Trentino from the second epidemic wave (autumn 2020). Black dots mark nodes with high posterior probability (pp ≥ 80%), while gray dots mark nodes with intermediate posterior probability (50% < pp < 80%).

Figure 4

Minimum spanning network of the major lineages sampled from Trentino and other areas across the world. Nodes represent genomes, and the size of the nodes is proportional to the number of samples sharing that sequence. Edges connect two nodes if the most internal node has a subset of mutations from the external one. Colors represent the date of first sampling of each genome, and the transparency of the links is inversely proportional to the number of mutations differentiating the two connected genomes (lighter links correspond to a higher number of mutations). Different symbols represent the origin of the samples of each genome: only from Trentino (diamonds), only from outside Trentino (squares), or from both (circles). Nodes are labelled with the location of the first (in terms of sampling date) detection of a genome. Possible entry and exit points of the virus in Trentino are indicated as “IN” and “OUT”.