Table 3

Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR

David Bonsall, William F. Gregory, Camilla L.C. Ip, Sharyne Donfield, James Iles, M. Azim Ansari, Paolo Piazza, Amy Trebes, Anthony Brown, John Frater, Oliver G. Pybus, Phillip Goulder, Paul Klenerman, Rory Bowden, Edward D. Gomperts, Eleanor Barnes, Amit Kapoor, Colin P. Sharp, and Peter Simmonds

Author affiliations: University of Oxford, Oxford, UK (D. Bonsall, C.L.C. Ip, J. Iles, M.A. Ansari, P. Piazza, A. Trebes, A. Brown, J. Frater, O.G. Pybus, P. Goulder, P. Klenerman, R. Bowden, E. Barnes, P. Simmonds); University of Edinburgh Easter Bush, Edinburgh, Scotland, UK (W.F. Gregory, C.P. Sharp); Rho, Inc., Chapel Hill, North Carolina, USA (S. Donfield); The Childrens' Hospital, Los Angeles, California, USA (E.D. Gomperts); The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA (A. Kapoor)

Main Article

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).

Main Article

Page created: March 15, 2016

Page updated: March 15, 2016

Page reviewed: March 15, 2016

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