Table 1 Demographic and clinical findings of the 346 SARS-CoV-2-infected patients according to lineages.

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

 

Overall, N = 346

Lineages

P-valueb

B.1, N = 179

B.1.1, N = 126

B.1.5, N = 34

Othera, N = 7

Demographics and clinical characteristics

      

Age, years

72 (54–84)

68 (54–83)

74 (55–84)

74 (60–85)

72 (46–84)

0.815

 18–39

30 (8.7)

17 (9.5)

9 (7.1)

4 (11.8)

0 (0.0)

0.484

 40–49

36 (10.4)

20 (11.2)

11 (8.7)

3 (8.8)

2 (28.6)

0.374

 50–59

48 (13.9)

31 (17.3)

16 (12.7)

1 (2.9)

0 (0.0)

0.082

 60–69

46 (13.3)

23 (12.8)

16 (12.7)

6 (17.6)

1 (2.2)

0.915

 70–79

64 (18.5)

24 (13.4)

30 (23.8)

8 (23.5)

2 (28.6)

0.101

 ≥80

122 (35.3)

64 (35.8)

44 (34.9)

12 (35.3)

2 (28.6)

0.978

Sex, male

195 (56.4)

87 (48.6)

80 (63.5)

23 (67.6)

5 (71.4)

0.018

Residency

      

 Milan

75 (21.7)

46 (25.7)

24 (19.0)

3 (8.8)

2 (28.6)

0.108

 Como

68 (19.7)

26 (14.5)

40 (31.7)

2 (5.9)

0 (0.0)

<0.001

 Pavia

61 (17.6)

20 (11.2)

15 (11.9)

23 (67.6)

3 (42.9)

<0.001

 Bergamo

36 (10.4)

12 (6.7)

23 (18.3)

1 (2.9)

0 (0.0)

0.003

 Lecco

30 (8.7)

9 (5.0)

21 (16.7)

0 (0.0)

0 (0.0)

0.001

 Lodi

33 (9.5)

30 (16.8)

1 (0.8)

0 (0.0)

2 (28.6)

<0.001

 Cremona

26 (7.5)

23 (12.8)

0 (0.0)

3 (8.8)

0 (0.0)

<0.001

 Otherc

17 (4.9)

13 (7.3)

2 (1.6)

2 (5.9)

0 (0.0)

0.135

Chronic comorbiditiesd

155 (52.4)

80 (51.3)

57 (53.3)

14 (46.7)

4 (66.7)

0.759

 Hypertension

107 (35.8)

52 (33.3)

42 (39.3)

11 (36.7)

2 (33.3)

0.530

 Obesity

23 (7.8)

9 (5.8)

11 (10.3)

2 (6.7)

1 (16.7)

0.477

 Diabetes

31 (10.5)

14 (9.0)

14 (13.1)

2 (6.7)

1 (16.7)

0.591

 Cardiovascular disease

98 (33.1)

46 (29.5)

40 (37.4)

10 (33.3)

2 (33.3)

0.635

 Chronic obstructive lung disease

42 (14.2)

16 (10.3)

19 (17.8)

5 (16.7)

2 (33.3)

0.175

 Malignancies

35 (11.8)

21 (13.5)

11 (10.3)

2 (6.7)

1 (16.7)

0.639

 Chronic kidney disease

23 (7.8)

8 (5.1)

9 (8.4)

3 (10.0)

3 (50.0)

0.868

 Chronic liver disease

4 (1.4)

3 (1.9)

1 (0.9)

0 (0.0)

0 (0.0)

0.788

 Othere

28 (9.7)

15 (9.7)

9 (8.7)

4 (13.3)

0 (0.0)

0.765

Symptoms at admissionf

      

 Fever

150 (65.2)

73 (59.3)

52 (68.4)

19 (67.9)

6 (100.0)

0.174

 Cough

106 (46.1)

51 (41.5)

35 (46.1)

15 (53.6)

5 (83.3)

0.204

 Dyspnea

93 (40.4)

44 (35.8)

32 (42.1)

14 (50.0)

3 (50.0)

0.571

Time from symptoms-onset to SARS-CoV-2 diagnosis, weeks

0.29 (0.14–0.57)

0.29 (0.14–0.50)

0.33 (0.17–0.69)

0.26 (0.00–0.37)

0.17 (0.00–0.57)

0.244

SARS-CoV-2 diagnosis (month, day)

March, 14

March, 11

March, 15

March, 10

March, 18

0.138

March, 06–March, 20

March, 05–March, 21

March, 09–March, 20

March, 05–March, 20

March, 10–March, 23

 Before March, 8

106 (30.6)

63 (35.2)

27 (21.4)

15 (44.1)

1 (14.3)

0.987

 After March, 8

240 (69.4)

116 (64.8)

99 (78.6)

19 (54.9)

6 (85.7)

Disease severityg

      

 Mild

119 (50.9)

71 (57.3)

37 (47.4)

12 (41.4)

2 (33.3)

0.314

 Moderate

52 (22.2)

30 (24.2)

14 (17.9)

7 (24.1)

1 (16.7)

0.732

 Severe

53 (22.6)

19 (15.3)

22 (28.2)

9 (31.0)

3 (50.0)

0.117

 Critical

10 (4.3)

4 (3.2)

5 (6.4)

1 (3.4)

0 (0.0)

0.674

Evidence of Interstitial Pneumoniah

116 (49.6)

54 (43.5)

41 (52.6)

17 (58.6)

4 (66.7)

0.372

Contact tracing

      

COVID-19 contacti

25 (21.0)

13 (22.0)

8 (15.7)

3 (42.9)

1 (50.0)

0.269

International travelj

4 (1.7)

2 (1.8)

2 (2.2)

0 (0.0)

0 (0.0)

0.898

SARS-CoV-2 rtPCR

      

Mean cycle thresholdsk

18.8 (16.8–20.1)

19.1 (17.2–20.3)

18.1 (16.5–19.9)

19.2 (17.8–20.6)

19.0 (16.3–21.3)

0.050

Local clusters

      

Sequences in cluster

60 (17.3)

25 (14.0)

12 (9.5)

23 (67.6)

0 (0.0)

<0.001

Cluster A

25 (7.2)

25 (14.0)

0 (0.0)

0 (0.0)

0 (0.0)

–

Cluster B

23 (6.6)

0 (0.0)

0 (0.0)

23 (67.6)

0 (0.0)

–

Cluster C

6 (1.7)

0 (0.0)

6 (4.8)

0 (0.0)

0 (0.0)

–

Cluster D

6 (1.7)

0 (0.0)

6 (4.8)

0 (0.0)

0 (0.0)

–

SNP in SARS-CoV-2 genome

      

14408, C to T, non-syn P to L (RdRp)

344 (99.4)

179 (100.0)

126 (100.0)

34 (100.0)

5 (71.4)

0.002

20268, A to G, syn (nsp15)

11 (3.2)

0 (0.0)

0 (0.0)

11 (32.3)

0 (0.0)

<0.001

23403, A to G, non-syn D to G (S)

344 (99.4)

179 (100.0)

126 (100.0)

34 (100.0)

5 (71.4)

0.002

23575, C to T, non-syn T to I (S)

24 (6.9)

1 (0.6)

0 (0.0)

23 (67.6)

0 (0.0)

<0.001

26530, A to G, non-syn D to G (M)

25 (7.2)

25 (14.0)

0 (0.0)

0 (0.0)

0 (0.0)

<0.001

28881-28883, GGG to AAC, non-syn RG to KR (N)

130 (37.6)

0 (0.0)

126 (100.0)

0 (0.0)

4 (57.1)

<0.001

  1. Data are expressed as median (IQR), or N (%).
  2. aIncluding A.2 (n = 1), B (n = 1), B.1.1.1 (n = 4), B.1.8 (n = 1).
  3. bTwo-sided P-values were calculated by Kruskal–Wallis test, or Chi-square test for trend, as appropriate.
  4. cOther includes Brescia, Mantua, Monza and Brianza, Sondrio and Varese.
  5. dData available for 309 patients.
  6. eIncluding: Crohn’s disease (n = 1), Hashimoto’s thyroiditis (n = 3), familial lipid disorders (n = 9), rheumatoid arthritis (n = 3), amyotrophic lateral sclerosis (n = 1), cognitive disorders (n = 11).
  7. fData available for 180 patients.
  8. gData available for 237 patients.
  9. hDiagnosed by X Ray or CT Scan. Data available for 232 patients.
  10. iData available for 119 patients.
  11. jData available for 231 patients.
  12. kReal-time reverse transcription PCR Ct (cycle threshold) values ranged from 9 to 35 (GeneFinderTM COVID-19 Plus RealAmp Kit, ELITech; AllplexTM 2019-nCoV Assay, Seegene; Corman et al.46).
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