Volume 22, Number 4—April 2016
Research
Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR
Table 3
Read depth and divergence of HPgV sequences obtained by using metagenomic screening*
Virus, ID no. | Case-patient origin | Type† | Length | Coverage, % | Reads | Div, %‡ | dN/dS | MFED, %§ |
---|---|---|---|---|---|---|---|---|
HHpgV-1, n = 2 | ||||||||
D1220 | UK | NA | 9,550 | 99.8 | 247,798 | 4.7 | 0.193 | 7.6 |
D1255 |
UK |
NA |
9,503 |
99.6 |
101,951 |
5.1 |
0.170 |
8.3 |
HPgV, n = 20 | ||||||||
89859249 | UK | 2 | 9,383 | 99.9 | 19,231,581 | 10.0 | 0.031 | 11.4 |
89859262 | UK | 2 | 9,388 | 99.8 | 6,766,497 | 9.9 | 0.029 | 12.4 |
56330218 | South Africa | 5 | 9,364 | 99.7 | 4,242,732 | 13.6 | 0.043 | 11.6 |
56330227 | Australia | 2 | 9,366 | 99.7 | 2,411,508 | 9.9 | 0.031 | 12.0 |
56330281 | DRC | 1 | 9,362 | 99.7 | 2,297,064 | 13.5 | 0.048 | 13.2 |
67845223 | UK | 2 | 9,382 | 99.9 | 1,332,130 | 9.4 | 0.023 | 11.5 |
56330260 | UK | 5 | 9,365 | 99.7 | 1,306,864 | 13.7 | 0.043 | 12.1 |
56330265 | UK | 2 | 9,425 | 99.7 | 1,178,508 | 9.5 | 0.035 | 12.5 |
56330292 | NA | 2 | 9,356 | 99.6 | 1,021,219 | 11.5 | 0.035 | 11.9 |
89860237 | UK | 2 | 9,367 | 99.7 | 953,683 | 9.5 | 0.035 | 11.0 |
56330272 | DRC | 1 | 9,340 | 99.4 | 707,495 | 13.6 | 0.052 | 12.0 |
56330229 | UK | 2 | 9,366 | 99.7 | 698,622 | 11.5 | 0.036 | 12.6 |
56330276 | DRC | 5 | 9,337 | 99.4 | 612,424 | 13.3 | 0.042 | 12.3 |
89860282 | UK | Novel | 8,443 | 89.9 | 574,652 | 13.2 | 0.049 | 10.5 |
89860286 | UK | 2 | 8,923 | 95.0 | 513,420 | 9.6 | 0.035 | 10.3 |
89860260 | UK | 2 | 8,983 | 95.6 | 512,515 | 11.6 | 0.041 | 10.5 |
56330286 | NA | 2 | 9,355 | 99.6 | 454,106 | 9.6 | 0.022 | 12.5 |
56330228 | Australia | ND | 436 | 4.6 | 68,351 | 8.6 | 0.019 | ND |
56330250 | UK | ND | 423 | 4.5 | 38,083 | 11.6 | 0.043 | ND |
89860212 |
UK |
ND |
1,117 |
11.9 |
17,226 |
8.6 |
0.068 |
ND |
*HPgV, human pegivirus; ID, identification; Div, sequence divergence; dN/dS: ratio of nonsynonymous (dN) to synonymous (dS) substitutions; MFED, mean folding energy difference; HHpgV, human hepegivirus; UK, United Kingdom; NA, not applicable (no genotypes of HHpgV-1 are currently assigned); DRC, Democratic Republic of Congo; ND, not done (insufficient sequence length). †Genotype based on phylogenetic analysis of complete genome sequences (Figure 1). ‡Comparison with AK790 prototype sequence (HHPgV-1) or AF121950 (HPgV; genotype 2). §Difference in minimum folding energy of sequences compared with those of sequence order-randomized controls (MFED) (16). |