Table 5. Description of viral strains.
| Virus Strain | Virus Description | Representative Accessions * | Sequence Alterations | Description Source |
|---|---|---|---|---|
| A/California/04/2009 (H1N1) | A/California/04/2009 (H1N1) - An isolate of the 2009 influenza pandemic | 1=FJ966079, 2=FJ966080, 3=FJ966081, 4=FJ966082, 5=FJ966083, 6=FJ966084, 7=FJ969513, 8=FJ966086 | None Specified | Josset et al., 2012 6 |
| MERS-CoV | MERS-CoV - A member of the betacoronavirus genus isolated from patients in the Middle East that causes severe acute respitory syndrome (SARS) fomerly known as vHuman coronavirus EMC 2012 (HCoV-EMC) [PMID: 23631916] | NC_019843 | None Specified | Josset et al., 2013 5 |
| A/Vietnam/1203/2004 (H5N1) | A/Vietnam/1203/2004 (H5N1)–Highly pathogenic avian influenza (HPAI) H5N1 | 1=AY651719, 2=AY651665, 3=AY651611, 4=AY651334, 5=AY651499, 6=AY651447, 7=AY651388, 8=AY651553, | None Specified | Li et al., 2011 4 |
| A/Netherlands/602/2009 (H1N1) | A/Netherlands/602/2009 (H1N1) - An isolate of the 2009 influenza pandemic | 1=CY046940, 2=CY046941, 3=CY046942, 4=CY039527, 5=CY046943, 6=CY039528, 7=CY046944, 8=CY046945 | None Specified | Mitchell et al., 2013 11 |
| A/New Jersey/8/1976 (H1N1) | A/New Jersey/8/76 (H1N1) - Isolated from throat swab material of a young military recruit during an outbreak at Fort Dix, NJ, in 1976. | 1=CY130125, 2=CY130124, 3=CY130123, 4=CY130118, 5=CY130121, 6=CY130120, 7=CY130119, 8=CY130122 | None Specified | Josset et al., 2012 6 |
| A/Mexico/4482/2009 (H1N1) | A/Mexico/4482/2009 (H1N1) - An Isolate from the 2009 H1N1 pandemic that caused severe respiratory illness in humans | 1=CY098505, 2=GQ149675, 3=GQ149676, 4=GQ149671, 5=GQ149673, 6=GQ149675, 7=GQ149669, 8=GQ379818, | None Specified | Josset et al., 2012 6 |
| Reconstructed 1918 (H1N1) | Reconstructed 1918 (H1N1) - The r1918 influenza virus segments were derived from the published sequences of strains A/South Carolina/1/18 (H1N1) HA, and A/Brevig Mission/1/1918 (H1N1) NA, M, NS, NP, PA, PB1 and PB2. The 1918 recombinant viruses also contained the 5′ and 3′ non-coding regions from strain A/WSN/1933 (H1N1). | 1=DQ208309, 2=DQ208310 3=DQ208311, 4=AF117241, 5=AY744935, 6=AF250356, 7=AY130766, 8=AF333238 | 5′ and 3′ non-coding regions were supplied by strain A/WSN/1933 (H1N1) | Kash et al., 2006 23 |
| A/Brisbane/59/2007 (H1N1) | A/Brisbane/59/2007 (H1N1) - H1N1 used in trivalent vaccine from 2008-2010 in Northern Hemisphere | 1=CY058484, 2=CY058485, 3=CY058486, 4=CY058487, 5=CY058488, 6=CY058489, 7=CY058490, 8=CY058491 | None Specified | Josset et al., 2012 6 |
| A/Vietnam/1203-CIP048_RG1 (H5N1) | A/Vietnam/1203-CIP048_RG1 (H5N1) - The H5N1 VN1203-HAavir mutant virus harbors an altered multi-basic cleavage site – a virulence factor important for expanded tissue range – and exhibits restricted systemic viral spread due to limited HA susceptibility to furin protease activity. | Parent Strain: A/Vietnam/1203/2004 (H5N1) | hemagglutinin (HA) surface protein poly-basic cleavage site (RERRRKKR↓G) was mutated to (RETR↓G) | Tchitchek et al., 2013 8 |
| A/Vietnam/1203-CIP048_RG2 (H5N1) | A/Vietnam/1203-CIP048_RG2 (H5N1) - The H5N1 VN1203-PB2627E mutant possesses an amino acid substitution (Lys-to-Glu) at position 627 in the PB2 polymerase subunit. This mutation is known to confer increased polymerase activity in mammalian cells, and also modulates anti-viral activity, apoptosis, and viral clearance. | Parent Strain: A/Vietnam/1203/2004 (H5N1) | PB2: K627E | Tchitchek et al., 2013 8 |
| A/Vietnam/1203-CIP048_RG3 (H5N1) | A/Vietnam/1203-CIP048_RG3 (H5N1) - H5N1 VN1203-PB1F2del mutant lacks expression of the PB1-F2 protein, potentially impacting an array of functions. PB1-F2 is a viral pathogenicity factor in mammals and birds, and has been shown to modulate viral polymerase activity, enhance lung inflammation, modulate innate immune responses, and demonstrate pro-apoptotic activity. | Parent Strain: A/Vietnam/1203/2004 (H5N1) | PB1 gene segment: T120C, C153G, G291A (all stops) | Tchitchek et al., 2013 8 |
| A/Vietnam/1203-CIP048_RG4 (H5N1) | A/Vietnam/1203-CIP048_RG4 (H5N1) - H5N1 VN1203-NS1trunc mutant virus produces a 91 amino acid C-terminal truncation in the effector domain of the NS1 host response antagonist protein. The NS1 protein inhibits RIG-I activation and cellular mRNA processing, and also promotes PI3K activation. The truncation results in the loss of the NS1 nuclear localization signal, a PI3K-binding motif, and binding domains. | Parent Strain: A/Vietnam/1203/2004 (H5N1) | NS1: 124(Stop), NS Gene segment: T400A | Tchitchek et al., 2013 8 |
| MA1-A/ California/04/2009 (H1N1) | MA1-A/ California/04/2009 (H1N1) - Mouse adapted MA-CA/04 contains five genetic mutations (in HA, G155E, S183P, and D222G; in PB2, E158G; and in NP, D101G) and is associated with a dramatic increase in virulence in mice | Parent Strain: A/California/04/2009 (H1N1) | PB2: E158GPA: L295PHA: G155E S183P R221R D222GNP: D101G | Ilyushina NA et al., 2010 27 |
| A/Aichi/02/68 (HA, NA) x A/Puerto Rico/8/34 (X31) | A/Aichi/02/68 (HA, NA) x A/Puerto Rico/8/34 (HKx31) - A reassortant virus that combines the surface HA and NA from an H3N2 virus (A/HK/x-31) with the 6 internal genes of PR8. Despite containing the same replication proteins as PR8, it is significantly less pathogenic in mice. | 1=CY009451, 2=CY009450, 3=CY009449, 4=AB295605, 5=CY009447, 6=AB295606, 7=CY009445, 8=CY009448 | None Specified | Askovich et al. 9 |
| A/Puerto Rico/8/1934 (H1N1) | A/Puerto Rico/8/34 (H1N1) - The H1N1 influenza virus A/Puerto Rico/34 (PR8) has been adapted to grow efficiently in the airways of mice, and is lethal at relatively low doses. | 1=CY009451, 2=CY009450, 3=CY009449, 4=CY009444, 5=CY009447, 6=CY009446, 7=CY009445, 8=CY009448 | None Specified | Askovich et al., 2013 9 |
| A/Vietnam/1203/04 (HA Vn1203, NA) x A/Puerto Rico/8/34 (VN6+2) | A/Vietnam/1203/04 (HA Vn1203, NA) x A/Puerto Rico/8/34 (VN6+2) - This H5N1 reassortant virus, designated rg/VN1203(6+2) contains the 6 internal genes from PR8 and the HA and NA from VN1203. The HA of this virus has had its polybasic cleavage site removed to restrict replication to the lung and airway epithelium. This virus is more pathogenic than PR8 and serves as a murine model for infection with a highly pathogenic strain. | 1=CY009451, 2=CY009450, 3=CY009449, 4=AY651334, 5=CY009447, 6=AY651447, 7=CY009445, 8=CY009448 | None Specified | Askovich et al., 2013 9 |
| icSARS Bat SRBD | SARS Bat SRBD - A SARS-CoV like virus isolated from bats that contains the receptor binding domain RBD from wild type SARS-CoV Urbani | FJ211859 | Bat-SCoV RBD (amino acid 323–505) was replaced with the SARS-CoV RBD (amino acid 319–518): FJ211860 | Becker, M.M., 2008 28 |
| icSARS CoV Urbani | icSARS CoV Urbani - Wild type infectious clone of SARS-CoV derived from genome fragments that were amplified in E. coli, ligated, and purified prior to in vitro transcription reactions to synthesize full length genomic RNA which were transfected into VeroE6 cells. | NC_004718* | Numerous alterations were made, see publications for details. Breifly, alterations included removal of one endogenous BglI site and the addition of three. Nucleotide alterations included an A to G at position 6460, T to C at position 14178, T to C at position 15740, C to T at position 19814, A to G at position 20528, and a T to C at position 20555. | Yount, B. et al., 2003 30 |
| icSARS dORF6 | icSARS dORF6 - infectious clone of a mutant Urbani SARS CoV in which the ORF6 protein is not expressed | Parent Strain icSARS CoV Urbani | Entire ORF6 deleted (nucleotides 27,074-27265) | Sims et al., 2013 12 |
| SARS CoV MA15 | SARS CoV MA15 - The mouse-adapted SARS-CoV (MA15) | FJ882957 | Gralinski et al., 2013 7 | |
| icSARS dNSP16 | icSARS dNSP16 - Genetic modification of non-structural protein 16 in SARS-CoV was shown to give rise to enhanced susceptibility to type I and III interferon responses | Parent Strain icSARS CoV Urbani | NSP16: K46A, K170A, D130A | Menachery et al., 2014 13 |
*Strains used were not directly sequenced. Accessions given are representative sequences with necessary details for recreating the strain used given in the ‘Sequence Alterations’ column.