Background
Methods
Design of the study
Subjects and samples
Sample ID
|
Material
|
Diagnosis
|
Origin
|
Year of sampling
|
Age
|
Sex
|
Genotype
|
Plasma viral load gen eq/mL
|
Clinical stage
|
---|---|---|---|---|---|---|---|---|---|
26 K | Biopsy | cKS | Central Italy | 2008 | 73 | M | A | 107 | B IV |
30 K | Biopsy | cKS | South Italy | 2008 | 78 | M | A | 33 | B IV |
33 K | Biopsy | cKS | South Italy | 2008 | 65 | M | A | 563 | B IV |
36 K | Biopsy | cKS | South Italy | 2009 | 61 | F | A | 100 | B IV |
40 K | Biopsy | cKS | Central Italy | 2010 | 38 | F | A | Undetectable | A II |
47 K | Biopsy | cKS | South Italy | 2003 | 68 | M | A | 105 | B IV |
48 K | Biopsy | cKS | South Italy | 2003 | 77 | M | A | 190 | B IV |
4 K | Biopsy | cKS | South Italy | 2003 | 72 | F | A | 100 | B II |
15 K | Biopsy | cKS | South Italy | 2004 | 68 | M | A | 57 | B IV |
18 K | Biopsy | cKS | Central Italy | 2005 | 66 | M | C | 70 | B IV |
20 K | Biopsy | cKS | Central Italy | 2007 | 66 | M | C | 100 | A II |
21 K | Biopsy | cKS | Central Italy | 2007 | 67 | M | C | 231 | B I |
27 K | Biopsy | cKS | Central Italy | 2008 | 87 | M | C | 5 | B IV |
34 K | Biopsy | cKS | South Italy | 2009 | 56 | M | C | 20 | A I |
37 K | Biopsy | cKS | Central Italy | 2009 | 82 | M | C | 400 | B III |
14 K | PBMC | Early MF | Central Italy | 2010 | 41 | M | A | Undetectable | |
3 K | Biopsy | Early MF | South Italy | 2002 | 56 | M | A | Undetectable | |
77 K | Biopsy | Early MF | Central Italy | 2007 | 74 | M | A | Undetectable | |
78 K | Biopsy | Early MF | Central Italy | 2006 | 66 | M | A | Undetectable | |
17 K | PBMC | MF | Central Italy | 2005 | 70 | M | A | 124 | |
13 K | Biopsy | MF | South Italy | 2010 | 72 | M | C | 21200 | |
42 K | Biopsy | MF | Central Italy | 2010 | 66 | M | C | 100 | |
5 K | Biopsy | MF | Central Italy | 2003 | 40 | M | C | 125 | |
1 K | PBMC | Asymptomatic | South Italy | 2000 | 79 | F | A | Undetectable | |
2 K | PBMC | Asymptomatic | South Italy | 2000 | 83 | F | A | Undetectable | |
43 K | PBMC | Asymptomatic | Central Italy | 2000 | 80 | F | C | Undetectable | |
44 K | PBMC | Asymptomatic | Central Italy | 2000 | 61 | M | C | Undetectable |
Laboratory procedures
Anti-HHV-8 antibodies
HHV-8 viral load
ORFK1 sequencing
Genetic analysis
Datasets
Likelihood mapping
Phylogenetic analysis
Bayesian phylogenetic analysis: evolutionary rate estimate and dated tree
Selective pressure analysis
Statistical analysis
Results
Virological parameters
Likelihood mapping
Phylogenetic analysis
Bayesian phylogenetic analysis: evolutionary rate estimate and dated tree
Evolutionary analysis
Negatively selected sites* | 102(Gln) | ||
(ω <1)** | |||
HYPHY software | |||
Positively selected sites* | 44 (Glu,Ala,Thr,His,Ser,Pro) | 58 (Ser,Phe,Trp,Leu,Val) | 60 (Leu,Pro,Met,Ala) |
(ω >1) ** | 62 (Gln, Asp, Lys,Glu,Thr,Arg) | 66 (Leu,Phe,Thr,Asn,Ser,His) | 66 (Leu,Phe,Thr,Asn,Ser,His) |
HYPHY and PAML software | 67 (Val,Pro,Ala,Gly,Ile) | 68 (Gly,Val,Ala,Ser,Leu,Phe,Asp) | 69 (Thr,Asp,Arg,Asn,Ile) |
70 (Ile,Phe,Leu) | 71 (Ile,Ser,Val,Asn,Ala,Thr,His) | 75 (Val,Thr,Ser,Leu) | |
101 (Gly,Ala,Val,Arg) |
Model
|
Free parameters
|
Log likelihood
|
Parameters estimates
|
Avg ω
|
---|---|---|---|---|
M0, one ratio | 1 | −2327.23 | ω = 2.111 | 2.111 |
M1, neutral | 1 | −2336.44 | p0 = 0.149; p1 = 0.851 | 1.000 |
M2, selection | 3 | −2186.37 | p0 = 0.290; p1 = 0.553; p2 = 0.156; ω2 = 12.812 | 2.556 |
M3, discrete | 5 | −2184.71 | p0 = 0.648; p1 = 0.218; p2 = 0.134; ω0 = 0.340; ω1 = 2.954; ω2 = 16.654 | 3.099 |
M7, beta | 2 | −2283.13 | P = 0.005, q = 0.006 | 0.421 |
M8, beta, and ω | 4 | −2186.45 | p0 = 0.843; P = 0.012; q = 0.005; p1 = 0.156; ω = 13.380 | 2.683 |
Statistical analysis of disease association
Clades
|
Clusters
|
KS
|
All
|
Fisher exact test
| |
---|---|---|---|---|---|
No
|
Yes
| ||||
I | IA | 1 (16.7%) | 5 (83.3%) | 6 (100%) | P = 0.08 |
IB | 4 (100%) | 1 (0.0%) | 4 (100%) | ||
II | IIA | 7 (87.5%) | 1 (12.5%) | 8 (100%) | P = 0.05 |
IIB | 0 (0%) | 6 (100%) | 6 (100%) |
Sequence ID
|
Genotype
|
Diagnosis
|
AA codon 44
|
AA codon 58
|
AA codon 60
|
AA codon 62
|
AA codon 66
|
AA codon 67
|
AA codon 68
|
AA codon 69
|
AA codon 70
|
AA codon 71
|
AA codon 75
|
AA codon 101
|
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15 K | A | cKS | Ala | Phe | Pro | Asp | Phe | Pro | Val | Thr | Ile | Ser | Thr | Ala |
18 K | C | cKS | Thr | Phe | Leu | Gln | Thr | Val | Val | Asp | Phe | Val | Ser | Val |
20 K | C | cKS | Thr | Phe | Leu | Gln | Thr | Val | Ala | Arg | Leu | Val | Ser | Arg |
21 K | C | cKS | Thr | Phe | Leu | Gln | Thr | Val | Val | Asn | Leu | Ile | Ser | Gly |
26 K | A | cKS | Ala | Leu | Leu | Glu | Ser | Pro | Val | Thr | Ile | Ala | Thr | Ala |
27 K | C | cKS | Thr | Phe | Leu | Glu | Thr | Val | Val | Asn | Leu | Ile | Ser | Gly |
30 K | A | cKS | His | Trp | Leu | Lys | Asn | Ala | Ser | Thr | Ile | Asn | Leu | Ala |
33 K | A | cKS | Ala | Phe | Leu | Glu | Phe | Pro | Leu | Thr | Ile | Ala | Thr | Ala |
34 K | C | cKS | Glu | Ser | Leu | Gln | Leu | Val | Gly | Thr | Ile | Ile | Val | Gly |
36 K | A | cKS | Ala | Leu | Leu | Lys | Thr | Ala | Val | Thr | Ile | Thr | Thr | Ala |
37 K | C | cKS | Thr | Phe | Met | Gln | Thr | Val | Phe | Asn | Leu | Ile | Ser | Gly |
40 K | A | cKS | Ala | Val | Leu | Glu | Phe | Pro | Val | Thr | Ile | Ala | Thr | Ala |
47 K | A | cKS | Ala | Phe | Ala | Glu | Phe | Pro | Val | Thr | Ile | Ala | Thr | Ala |
48 K | A | cKS | Ala | Trp | Leu | Arg | Thr | Val | Ala | Thr | Ile | Thr | Thr | Ala |
4 K | A | cKS | Thr | Leu | Leu | Thr | His | Gly | Val | Asn | Leu | Thr | Thr | Ala |
14 K | A | eMF | Thr | Trp | Leu | Lys | Thr | Ile | Asp | Ile | Ile | His | Leu | Ala |
3 K | A |
eMF
|
Ser
|
Trp
|
Leu
|
Lys
|
Thr
|
Ile
|
Asp
|
Ile
|
Ile
|
Thr
|
Thr
|
Ala
|
77 K | A |
eMF
|
Ser
|
Trp
|
Leu
|
Lys
|
Thr
|
Ile
|
Asp
|
Ile
|
Ile
|
Thr
|
Thr
|
Ala
|
78 K | A |
eMF
|
Ser
|
Trp
|
Leu
|
Lys
|
Thr
|
Ile
|
Asp
|
Ile
|
Ile
|
Thr
|
Thr
|
Ala
|
13 K | C | MF | Ser | Phe | Leu | Arg | Thr | Val | Val | Asn | Ile | Ser | Leu | Gly |
17 K | A | MF | Pro | Trp | Leu | Lys | Thr | Ile | Asp | Ile | Ile | Asn | Leu | Ala |
42 K | C | MF | Thr | Leu | Leu | Lys | Thr | Val | Val | Thr | Ile | Ile | Ser | Ala |
5 K | C | MF | Thr | Leu | Leu | Lys | Thr | Val | Val | Thr | Leu | Ile | Ser | Gly |
1 K | A | Asympt. | Thr | Trp | Leu | Lys | Thr | Ile | Asp | Ile | Ile | Asn | Leu | Ala |
2 K |
A
|
Asympt.
|
Ser
|
Trp
|
Leu
|
Lys
|
Thr
|
Ile
|
Asp
|
Ile
|
Ile
|
Thr
|
Thr
|
Ala
|
43 K | C | Asympt. | Thr | Leu | Leu | Met | Thr | Val | Asp | Thr | Leu | Ile | Ser | Gly |
44 K | C | Asympt. | Thr | Leu | Leu | Lys | Thr | Ile | Val | Thr | Leu | Ile | Ser | Gly |