This is a re-evaluation of the Pandemic of 1957 and also a test case for reassortment detection methods.
| HA | NA |
|---|---|
 |
 |
| PB2 | PB1 | PA |
|---|---|---|
 |
 |
 |
| NP | M | NS |
 |
 |
 |
Focusing on the pandemic of 1957 and not the pandemic of 1968, genomic information was fetched from IVR for influenza A isolates collected prior to 1966. Fetched sequences were pared down to strains with all 8 gene segments sequenced resulting in a final dataset of 148 strains for gene reassortment analysis.
Nextstrain allows the ability to display tanglegrams between two trees. The same data above was used to create gene segment trees and can be compared in the below table.
| HA | NA | PB2 | PB1 | PA | NP | M | NS | |
|---|---|---|---|---|---|---|---|---|
| HA | equal | reassort | equal | reassort | reassort | reassort | reassort | |
| NA | reassort | equal | reassort | reassort | reassort | reassort | ||
| PB2 | reassort | equal | equal | equal | equal | |||
| PB1 | reassort | reassort | reassort | reassort | ||||
| PA | equal | equal | equal | |||||
| NP | equal | equal | ||||||
| M | equal |
The following references were pulled from the NCBI Genbank Files for the 148 WGS strains and listed chronologically by decade.
1970s
- McCauley J, Bye J, Elder K, Gething MJ, Skehel JJ, Smith A, Waterfield MD. Influenza virus haemagglutinin signal sequence. FEBS letters. 1979 Dec 15;108(2):422-6.
1980s
- Gething MJ, Bye J, Skehel J, Waterfield M. Cloning and DNA sequence of double-stranded copies of haemagglutinin genes from H2 and H3 strains elucidates antigenic shift and drift in human influenza virus. Nature. 1980 Sep;287(5780):301-6.
- Fang R, Jou WM, Huylebroeck D, Devos R, Fiers W. Complete structure of A/duck/Ukraine/63 influenza hemagglutinin gene: animal virus as progenitor of human H3 Hong Kong 1968 influenza hemagglutinin. Cell. 1981 Aug 1;25(2):315-23.
- Winter G, Fields S, Brownlee GG. Nucleotide sequence of the haemagglutinin gene of a human influenza virus H1 subtype. Nature. 1981 Jul;292(5818):72-5.
- Garten W, Kuroda K, Schuy W, Naruse H, Scholtissek C, Klenk HD. Haemagglutinin transport mutants. Vaccine. 1985 Sep 1;3(3):227-9.
- Kawaoka Y, Bean WJ, Webster RG. Evolution of the hemagglutinin of equine H3 influenza viruses. Virology. 1989 Apr 1;169(2):283-92.
- Donis RO, Bean WJ, Kawaoka Y, Webster RG. Distinct lineages of influenza virus H4 hemagglutinin genes in different regions of the world. Virology. 1989 Apr 1;169(2):408-17.
1990s
- Gibson CA, Daniels RS, Oxford JS, McCauley JW. Sequence analysis of the equine H7 influenza virus haemagglutinin gene. Virus research. 1992 Feb 1;22(2):93-106.
- Schaffr JR, Kawaoka Y, Bean WJ, Suss J, Senne D, Webster RG. Origin of the pandemic 1957 H2 influenza A virus and the persistence of its possible progenitors in the avian reservoir. Virology. 1993 Jun 1;194(2):781-8.
- Smeenk CI, Brown EG. The influenza virus variant A/FM/1/47-MA possesses single amino acid replacements in the hemagglutinin, controlling virulence, and in the matrix protein, controlling virulence as well as growth. Journal of virology. 1994 Jan 1;68(1):530-4.
- Connor RJ, Kawaoka Y, Webster RG, Paulson JC. Receptor specificity in human, avian, and equine H2 and H3 influenza virus isolates. Virology. 1994 Nov 15;205(1):17-23.
- Ito T, Couceiro JN, Kelm S, Baum LG, Krauss S, Castrucci MR, Donatelli I, Kida H, Paulson JC, Webster RG, Kawaoka Y. Molecular basis for the generation in pigs of influenza A viruses with pandemic potential. Journal of virology. 1998 Sep 1;72(9):7367-73.
- Reid AH, Fanning TG, Hultin JV, Taubenberger JK. Origin and evolution of the 1918 “Spanish” influenza virus hemagglutinin gene. Proceedings of the National Academy of Sciences. 1999 Feb 16;96(4):1651-6.
2000s
- Schickli JH, Flandorfer A, Nakaya T, Martinez-Sobrido L, Garcia-Sastre A, Palese P. Plasmid-only rescue of influenza A virus vaccine candidates. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences. 2001 Dec 29;356(1416):1965-73.
- Lindstrom SE, Cox NJ, Klimov A. Genetic analysis of human H2N2 and early H3N2 influenza viruses, 1957–1972: evidence for genetic divergence and multiple reassortment events. Virology. 2004 Oct 15;328(1):101-19.
- Obenauer JC, Denson J, Mehta PK, Su X, Mukatira S, Finkelstein DB, Xu X, Wang J, Ma J, Fan Y, Rakestraw KM. Large-scale sequence analysis of avian influenza isolates. Science. 2006 Mar 17;311(5767):1576-80.
2010s
- Zohari S, Metreveli G, Kiss I, Belak S, Berg M. Full genome comparison and characterization of avian H10 viruses with different pathogenicity in Mink (Mustela vison) reveals genetic and functional differences in the non-structural gene. Virology journal. 2010 Dec 1;7(1):145.
- Worobey M, Han GZ, Rambaut A. A synchronized global sweep of the internal genes of modern avian influenza virus. Nature. 2014 Apr;508(7495):254-7.
- Joseph U, Linster M, Suzuki Y, Krauss S, Halpin RA, Vijaykrishna D, Fabrizio TP, Bestebroer TM, Maurer-Stroh S, Webby RJ, Wentworth DE. Adaptation of pandemic H2N2 influenza A viruses in humans. Journal of virology. 2015 Feb 15;89(4):2442-7.
- Noda T, Murakami S, Nakatsu S, Imai H, Muramoto Y, Shindo K, Sagara H, Kawaoka Y. Importance of the 1+ 7 configuration of ribonucleoprotein complexes for influenza A virus genome packaging. Nature communications. 2018 Jan 4;9(1):1-0.