Challenges of the Unknown: Clinical Application of Microbial Metagenomics

Table 1

Identification of the 25 target viruses within the viral sample using the two taxonomic classification approaches. Genome lengths based on reference genome used within the study and relative viral load shown by qPCR cycle threshold (Ct). If Ct > 37 this is shown as ND (not detectable). Percentages are based on the total reads within each dataset after preprocessing stages.

Target virus	Length (bp)	Ct	Mapping approach		Kmer approach
			Number of reads	%	Number of reads	%
Adenovirus 2	35,937	29.71	262,395	2.3	263,857	2.3
Adenovirus 41	34,188	ND	0	0.0	0	0.0
Astrovirus	6,813	30.53	19,190	0.2	17,227	0.2
Coronavirus 229E	27,317	36.48	0	0.0	0	0.0
Coxsackievirus B4	7,397	30.72	20,706	0.2	14,422	0.1
Cytomegalovirus	230,290	28.95	580,431	5.2	584,018	5.2
Epstein-Barr virus	171,823	31.27	43,600	0.4	43,882	0.4
Herpes simplex virus 1	152,261	30.59	10,189	0.1	10,220	0.1
Herpes simplex virus 2	154,675	32.48	36,786	0.3	36,865	0.3
Influenza A H1N1	10,982	32.02	157	0.0	451	0.0
Influenza A H3N2	12,990	ND	0	0.0	4	0.0
Influenza B virus	14,452	ND	0	0.0	1	0.0
Metapneumovirus A	13,335	31.86	30,256	0.3	30,588	0.3
Norovirus GI	7,623	ND	0	0.0	0	0.0
Norovirus GII	7,535	ND	3	0.0	0	0.0
Parainfluenza virus 1	15,600	34.43	37,489	0.3	33,569	0.3
Parainfluenza virus 2	15,646	33.87	5,226	0.0	5,091	0.0
Parainfluenza virus 3	15,462	ND	309	0.0	270	0.0
Parainfluenza virus 4	17,304	31.83	9,272	0.1	8,728	0.1
Parechovirus 3	7,322	29.35	3,985,296	35.4	2,371,771	21.1
Respiratory syncytial virus A	15,158	34.33	1,530	0.0	1,551	0.0
Rhinovirus A39	7,137	31.16	13,335	0.1	13,797	0.1
Rotavirus A RVA	18,562	24.49	655	0.0	13	0.0
Sapovirus	7,429	33.37	1,455	0.0	507	0.0
Varicella-zoster virus	125,144	29.02	1,398,178	12.4	1,409,763	12.5
Total classified			6,456,450	57.3	4,846,595	43.0