Table 2.
Applications of 454/Roche pyrosequencing and Illumina NGS technologies in clinical virology.
| Virus | Study | NGS platform | NGS approach | Basis of analysis | References |
|---|---|---|---|---|---|
| CMV | Epidemiology | 454/Roche | Amplicon-based | Reads | Gorzer et al., 2010 |
| CMV | Epidemiology | 454/Roche | Shotgun | Consensus sequence | Jung et al., 2011 |
| EBV | Epidemiology | Illumina | Shotgun | SNV, consensus sequence | Liu et al., 2011 |
| EBV | Epidemiology | Illumina | Shotgun (amplicons) | SNV | Kwok et al., 2012 |
| HBV | Drug resistance | 454/Roche | Amplicon-based | Reads, SNV | Solmone et al., 2009; Homs et al., 2011; Rodriguez-Frías et al., 2012 |
| HBV | Drug resistance | 454/Roche | Amplicon-based | SNV | Margeridon-Thermet et al., 2009; Ko et al., 2012; Sede et al., 2012 |
| HBV | Drug resistance | Illumina | Shotgun | SNV | Nishijima et al., 2012 |
| HCV | Drug resistance | 454/Roche | Amplicon-based | Reads | Bolcic et al., 2012; Fonseca-Coronado et al., 2012 |
| HCV | Drug resistance | Illumina | Shotgun (cDNA) | SNV | Hiraga et al., 2011 |
| HCV | Drug resistance | 454/Roche | Shotgun (amplicons) | SNV, consensus sequences | Lauck et al., 2012 |
| HCV | Drug resistance | Illumina | Paired-end (amplicons) | SNV | Nasu et al., 2011 |
| HCV | Drug resistance | 454/Roche | Amplicon-based | SNV | Powdrill et al., 2011 |
| HCV | Epidemiology | 454/Roche | Amplicon-based | Reads | Escobar-Gutiérrez et al., 2012; Forbi et al., 2012 |
| HCV | Epidemiology | Illumina | Shotgun (cDNA) | SNV, consensus sequences | Ninomiya et al., 2012 |
| HIV | Drug resistance | 454/Roche | Amplicon-based | SNV | Hoffmann et al., 2007; Wang et al., 2007; Mitsuya et al., 2008; Le et al., 2009; Simen et al., 2009; Varghese et al., 2009; Lataillade et al., 2010, 2012; Alteri et al., 2011; D'Aquila et al., 2011; Delobel et al., 2011; Gianella et al., 2011; Ji et al., 2011; Kozal et al., 2011; Moorthy et al., 2011; Stelzl et al., 2011; Fisher et al., 2012; Messiaen et al., 2012 |
| HIV | Drug resistance | 454/Roche | Amplicon-based | Reads, SNV | Hedskog et al., 2010; Ji et al., 2010; Mild et al., 2011; Mukherjee et al., 2011; Armenia et al., 2012 |
| HIV | Epidemiology | 454/Roche | Shotgun (amplicons) | Consensus sequence | Bruselles et al., 2009 |
| HIV | Epidemiology | 454/Roche | Amplicon-based | Consensus sequence | Eshleman et al., 2011 |
| HIV | Epidemiology | 454/Roche | Amplicon-based | Reads | Redd et al., 2012 |
| HIV | Tropism | 454/Roche | Amplicon-based | Reads | Archer et al., 2009; Rozera et al., 2009; Abbate et al., 2011; Swenson et al., 2010; Vandenbroucke et al., 2010; Baatz et al., 2011; Bunnik et al., 2011; Raymond et al., 2011; Saliou et al., 2011; Svicher et al., 2011; Swenson et al., 2011a,b; Vandekerckhove et al., 2011 |
| Influenza A virus | Epidemiology | Illumina | Shotgun (amplicons) | SNV | Kuroda et al., 2010; Kampmann et al., 2011 |
| Influenza A virus | Epidemiology | 454/Roche | Shotgun (amplicons) | SNV | Bartolini et al., 2011 |
| Influenza A virus | Epidemiology | 454/Roche | Shotgun | Reads | Lorusso et al., 2011 |
| norovirus | Epidemiology | 454/Roche | Shotgun (amplicons) | SNV, haplotype recon-struction | Bull et al., 2012 |
| rhinovirus | Epidemiology | Illumina | Shotgun (amplicons) | SNV, consensus sequences | Tapparel et al., 2011 |
| rotavirus | Epidemiology | 454/Roche | Shotgun (cDNA) | Consensus sequences | Jere et al., 2011 |
| VZV | Epidemiology | 454/Roche | Shotgun (amplicons) | Consensus sequences | Zell et al., 2012 |
BAL, bronchoalveolar lavage; CMV, cytomegalovirus; EBV, Epstein Barr virus; HBV, hepatitis B virus; HCV, hepatitis C virus; HIV, human immunodeficiency virus; SNV, single nucleotide variant; VZV, varicella zoster virus.