Table 3 Factors associated with transmission clustering.

From: A novel methodology for large-scale phylogeny partition

Factor/threshold

1st Percentile (0.04 ns s−1)

15th Percentile (0.07 ns s−1)

30th Percentile (0.08 ns s−1)

 

OR

95% CI

P value

OR

95% CI

P value

OR

95% CI

P value

Calendar year of genotyping (per more recent)

1.04

(1.01–1.06)

0.0011

0.98

(0.96–1)

0.1163

0.98

(0.95–1.01)

0.2626

Italian country area of residence (ref. Central)

Northern

0.52

(0.46–0.6)

<0.0001

0.73

(0.63–0.85)

<0.0001

1.09

(0.85–1.39)

0.4936

Southern

0.58

(0.45–0.75)

<0.0001

0.78

(0.6–1.01)

0.0578

1.07

(0.68–1.68)

0.7860

Unknown

0.86

(0.56–1.34)

0.5151

1.05

(0.63–1.76)

0.8583

0.65

(0.32–1.32)

0.2341

Mode of HIV-1 transmission (ref. IDU)

Heterosexual

1.64

(1.29–2.09)

<0.0001

1.08

(0.86–1.36)

0.4993

0.27

(0.17–0.44)

<0.0001

Male homosexual

1.58

(1.24–2.01)

0.0002

1.05

(0.82–1.33)

0.7112

0.16

(0.1–0.25)

<0.0001

Other/unknown

1.52

(1.19–1.94)

0.0007

1.05

(0.84–1.32)

0.6658

0.33

(0.21–0.52)

<0.0001

Gender (ref. female)

Male

1.88

(1.56–2.26)

<0.0001

1.00

(0.83–1.19)

0.9564

0.54

(0.4–0.73)

<0.0001

Unknown

2.27

(1.73–2.97)

<0.0001

1.08

(0.82–1.42)

0.5801

0.52

(0.32–0.83)

0.0058

Country of birth (ref. Italy)

Other than Italy

0.64

(0.45–0.91)

0.0142

0.53

(0.37–0.75)

0.0004

0.28

(0.18–0.43)

<0.0001

Unknown

1.03

(0.86–1.23)

0.7390

1.13

(0.93–1.36)

0.2096

1.12

(0.82–1.53)

0.4867

Age (ref. >46 years old)

≤36

1.49

(1.23–1.81)

<0.0001

1.20

(0.98–1.47)

0.0790

1.49

(1.1–2.04)

0.0111

>36 and ≤41

1.06

(0.88–1.26)

0.5617

1.00

(0.83–1.21)

0.9656

1.70

(1.26–2.29)

0.0006

>41 and ≤46

0.99

(0.84–1.18)

0.9366

1.00

(0.84–1.19)

0.9965

1.44

(1.1–1.9)

0.0082

Unknown

1.02

(0.82–1.26)

0.8910

1.10

(0.87–1.38)

0.4303

1.50

(1.01–2.21)

0.0424

ART status (ref. ART-naive)

ART-experienced

0.68

(0.56–0.84)

0.0003

1.08

(0.85–1.37)

0.5361

1.18

(0.82–1.7)

0.3708

Unknown

0.72

(0.59–0.89)

0.0020

1.04

(0.82–1.31)

0.7447

0.93

(0.65–1.32)

0.6677

Time from first HIV+ test (ref. >14 years)

≤3 years

2.56

(1.87–3.51)

<0.0001

1.78

(1.3–2.45)

0.0004

1.33

(0.75–2.36)

0.3261

>3 and ≤9 years

1.70

(1.27–2.26)

0.0003

1.14

(0.87–1.5)

0.3524

0.87

(0.52–1.45)

0.6022

>9 and ≤14 years

1.30

(1–1.7)

0.0537

1.18

(0.93–1.51)

0.1804

0.99

(0.62–1.57)

0.9519

Unknown

1.38

(1.04–1.81)

0.0232

0.90

(0.7–1.17)

0.4394

0.77

(0.47–1.24)

0.2809

Presence of at least one drug-resistance mutation*

NRTI

0.68

(0.6–0.78)

<0.0001

0.72

(0.62–0.82)

<0.0001

0.99

(0.8–1.24)

0.9378

NNRTI

0.93

(0.83–1.04)

0.2271

0.99

(0.88–1.12)

0.8875

0.95

(0.78–1.16)

0.6196

PI

0.93

(0.82–1.07)

0.3092

0.80

(0.7–0.92)

0.0012

0.77

(0.61–0.97)

0.0274

HIV-1 RNA per one Log10 copies per ml higher

1.08

(1.01–1.15)

0.0344

1.01

(0.94–1.09)

0.7574

1.04

(0.92–1.17)

0.5722

CD4+ count per 50 cells/mm3 higher

1.03

(1.01–1.04)

0.0002

1.02

(1.01–1.04)

0.0057

1.03

(1–1.06)

0.0616

  1. ART, antiretroviral therapy; CI, confidence interval; IDU, injecting drug user; NNRTI, non-nucleoside reverse transcriptase inhibitors; NRTI, nucleoside/tide reverse transcriptase inhibitors; ns s−1, nucleotide substitutions per site; OR, odds-ratio; PI, protease inhibitors.
  2. *Mixtures of wild-type and resistant mutants are classified as resistant
  3. Adjusted OR of transmission clustering evidence (clustered versus un-clustered isolates) from fitting a multivariable logistic generalized-estimating-equations model, by considering different percentile thresholds.
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