Table 2 Distribution of SARS-CoV-2 local clusters, according to lineages, timing of diagnosis, and reported risk.

From: Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

 

tMRCAa

Earliest and most closely related strains outside Lombardyb

Before March 8

After March 8

N (%)

Age, median IQR

Provinces, N (%)

International Travels, N (%)c

Covid-19 contact, N (%)d

N (%)

Age, median IQR

Provinces, N (%)

International Travels, N (%)c

Covid-19 contact, N (%)d

Lineage B.1

            

 Cluster A

Feb, 14 (Feb, 5–Feb, 20)

None

10 (40.0)

66 (47–78)

Bergamo: 8 (80.0) Como: 1 (10.0) Lecco: 1 (10.0) Milan: 0 (0.0)

0

0

15 (60.0)

58 (51–80)

Bergamo: 1 (6.6) Como: 4 (26.7) Lecco: 3 (20.0) Milan: 7 (46.7)

0

2

Lineage B.1.5

            

 Cluster B

Feb, 12 (Feb, 6–Feb, 23)

China: 1 (Zhejiang)

9 (39.1)

70 (61–86)

Cremona: 1 (11.1) Milan: 1 (11.1) Pavia: 7 (77.8)

0

0

14 (60.9)

78 (60–86)

Como: 1 (7.1) Milan: 1 (7.1) Pavia: 11 (78.6) Other: 1 (7.1)

0

3

Lineage B.1.1

            

 Cluster C

March, 1 (Feb, 27–March, 6)

None

2 (33.3)

36

Pavia: 1 (50.0) Como: 1 (50.0)

0

0

4 (66.7)

81 (64–81)

Como: 4 (100.0)

0

0

 Cluster D

Feb, 27 (Feb, 20–Feb, 28)

NoAm: 1 (Atlanta)

3 (50.0)

80 (51–82)

Bergamo: 1 (33.3) Como: 1 (33.3) Lecco: 1 (33.3)

0

0

3 (50.0)

68 (37–79)

Bergamo: 2 (66.7) Lecco: 1 (33.3)

0

1

  1. Time of the most recent common ancestors and most closely related strains were also reported for each cluster.
  2. aTime of the most recent common ancestors (TMRCA) of lineages and local clusters characterized by a posterior probability ≥0.98 in the Bayesian Tree. TMRCA are represented in the order of date/month/year. The values in parentheses represent the 95% HPD intervals.
  3. bThe SARS-CoV-2 genomes most closely related to lineages and clusters identified in Lombardy by the Bayesian Tree.
  4. cData available for 51 patients.
  5. dData available for 24 patients.
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