Re: Homologous Recombination is Very Rare or Absent in Human Influenza A Virus
Here is the recombinant. It is OBVIOUS recombination with half of the sequence from contemporary sequences from the late 1990's for the first half, and sequences from two decades earlier for the second half. The recombinant sequences is 2341 BP which is a FULL sequence. This paper has MAJOR problems (i.e. excludes data it doesn't like or simply is not what it says it is). The authors can argue all they want about this being some kind of contamination, but the paper appears to indicate that this recombinant doesn't exist, which is false. As noted below, complete CDS means it is a full sequence (and is human).
LOCUS AF258842 2341 bp RNA linear VRL 13-SEP-2004
DEFINITION Influenza A virus (A/Hong Kong/498/97(H3N2)) RNA polymerase (PB2)
gene, complete cds.
ACCESSION AF258842
VERSION AF258842.1 GI:13274643
KEYWORDS .
SOURCE Influenza A virus (A/Hong Kong/498/97(H3N2))
ORGANISM
Influenza A virus (A/Hong Kong/498/97(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2341)
AUTHORS Cooper,L.A. and Subbarao,K.
TITLE A simple restriction fragment length polymorphism-based strategy
that can distinguish the internal genes of human H1N1, H3N2, and
H5N1 influenza A viruses
JOURNAL J. Clin. Microbiol. 38 (7), 2579-2583 (2000)
PUBMED
10878047
REFERENCE 2 (bases 1 to 2341)
AUTHORS Shaw,M., Cooper,L., Xu,X., Thompson,W., Krauss,S., Guan,Y.,
Zhou,N., Klimov,A., Cox,N., Webster,R., Lim,W., Shortridge,K. and
Subbarao,K.
TITLE Molecular changes associated with the transmission of avian
influenza a H5N1 and H9N2 viruses to humans
JOURNAL J. Med. Virol. 66 (1), 107-114 (2002)
PUBMED
11748666
REFERENCE 3 (bases 1 to 2341)
AUTHORS Shaw,M.W., Cooper,L.A., Xu,X., Thompson,W.W., Krauss,S.L., Guan,Y.,
Zhou,N.N., Klimov,A., Cox,N.J., Webster,R.G., Lim,W.,
Shortridge,K.F. and Subbarao,K.
TITLE Direct Submission
JOURNAL Submitted (02-MAR-2001) Influenza Branch, Centers for Disease
Control and Prevention, Mailstop G-16, Atlanta, GA 30333, USA
FEATURES Location/Qualifiers
source 1..2341
/organism="Influenza A virus (A/Hong Kong/498/97(H3N2))"
/mol_type="genomic RNA"
/strain="A/Hong Kong/498/97"
/specific_host="Homo sapiens"
/db_xref="taxon:
153970"
/note="isolated from nasopharyngeal swab/tracheal aspirate
subtype: H3N2"
gene 28..2307
/gene="PB2"
CDS 28..2307
/gene="PB2"
/codon_start=1
/product="RNA polymerase"
/protein_id="
AAK18016.1"
/db_xref="GI:13274644"
/translation="MERIKELRNLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPS
LRMKWMMAMKYPITADKRITEMVPERNEQGQTLWSKMSDAGSDRVMVSPLAVTWWNRN
GPVTSTVTHPKVYKTYFDKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQ
DVIMEVVFPNEVGARILTSESQLTITKEKKEELEDCKISPLMVAYMLERELVRKTRFL
PVAGGTSSIYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRAAVSADP
LASLLEMCHSTQIGGTRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTS
GSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKATRRLVQLIVSGRDEQ
SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG
IEHIDNVMGMVGVLPDMTPSTEMSMRGIRVSKMGVDEYSSTERVVVSIDRFLRVRDQR
GNVLLSPEEVSETHGTERLTITYSSSMMWEINGPESVLVNTYQWIIRNWETVKIQWSQ
NPTMLYNKMEFEPFQSLVPKAIRGQYSGFVRTLFQQMRDVLGTFDTTQIIKLLPFAAA
PPKQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKTTKRLTILGKDAGTLIEDPDES
TSGVESAVLRGFLILGKEDRRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRD
SSILTDSQTATKRIRMAIN"
ORIGIN
1 agcaaaagca ggtcaattat attcaatatg gaaagaataa aagaactacg gaacctgatg
61 tcgcagtctc gcactcgcga gatactaaca aaaaccacag tggaccatat ggccataatt
121 aagaagtaca catcagggag acaggaaaag aacccgtcac ttaggatgaa atggatgatg
181 gcaatgaaat atccaatcac tgctgacaaa aggataacag aaatggttcc ggagagaaat
241 gaacaaggac aaactctatg gagtaaaatg agtgatgctg ggtcagatcg agtgatggta
301 tcacctttgg ctgtgacatg gtggaataga aatggacccg tgacaagtac ggtcactcac
361 ccaaaagtat acaagactta ttttgacaaa gtcgaaaggt taaaacatgg aacctttggc
421 ccagttcatt ttagaaatca agtcaagata cgccgaagag tagacataaa ccctggtcat
481 gcagacctca gtgccaagga ggcacaagat gtaattatgg aagttgtttt tcccaatgaa
541 gtgggagcca ggatactaac atcggaatca caattaacaa taaccaaaga gaaaaaagaa
601 gaactcgaag attgcaaaat ttctccactg atggttgcat acatgttaga gagagaactt
661 gtccgaaaaa caagatttct cccagttgct ggcggaacaa gcagtatata cattgaagtt
721 ttacatttga ctcaaggaac gtgttgggaa caaatgtaca ctccaggtgg agaagtgagg
781 aatgacgatg ttgaccaaag cctaattatt gcagccagga acatagtaag aagagccgca
841 gtatcagcag atccactagc atctttattg gagatgtgcc acagcacaca aattggtggg
901 acaagaatgg tggacattct tagacagaac ccgactgaag aacaagctgt ggatatatgc
961 aaggctgcaa tgggattgag aatcagctca tccttcagtt ttggtggatt tacatttaaa
1021 agaacaagcg ggtcatcagt caaaagagag gaagaagtgc ttacaggcaa tctccaaaca
1081 ttgaaaataa gagtacatga agggtacgag gagttcacaa tggtggggaa aagggcaaca
1141 gctatactca gaaaagcaac caggagattg gttcagctta tagtgagtgg aagggacgag
1201 cagtcaatag ccgaagcgat aattgtagcc atggtgtttt cacaagagga ttgcatgata
1261 aaagcagtta gaggtgacct gaatttcgtt aacagggcaa atcagcggtt gaatcccatg
1321 catcaacttt taaggcattt tcagaaagat gcgaaagtgc tttttcagaa ttggggaatt
1381 gaacatattg acaatgtgat gggaatggtt ggagtattac cagacatgac tccaagcaca
1441 gagatgtcaa tgagaggaat aagagtcagc aaaatgggcg tggatgaata ctccagcaca
1501 gagagggtag tggttagcat tgatcggttt ttgagagttc gagaccaacg tgggaatgta
1561 ttactatctc ctgaggaggt cagtgaaaca catgggacag agagactgac aataacttac
1621 tcatcgtcaa tgatgtggga gattaatggc cctgagtcag tgttggtcaa tacctatcaa
1681 tggatcatca gaaattggga aactgttaaa attcaatggt ctcagaatcc tacaatgttg
1741 tacaacaaaa tggaatttga gccatttcag tctttagttc ctaaggccat tagaggccaa
1801 tacagtggat ttgtcagaac tctattccaa caaatgaggg atgtacttgg gacatttgat
1861 accacccaga taataaagct tctccccttt gcagccgccc caccaaagca aagtagaatg
1921 cagttctctt cattgactgt gaatgtgagg ggatcaggga tgagaatact tgtaaggggc
1981 aattctcctg tattcaacta caacaagacc actaaaagac taacaattct cggaaaagat
2041 gctggcactt taattgaaga cccagatgaa agcacatccg gagtggagtc cgctgttttg
2101 agaggatttc tcattctagg taaggaagat agaagatacg gaccagcatt aagcatcaat
2161 gaactgagca accttgcaaa aggagaaaag gctaatgtgc taattgggca aggagacgtg
2221 gtgttggtaa tgaaacgaaa acgggactct agcatactta ctgacagcca gacagcgacc
2281 aaaagaattc ggatggccat caattaatgt tgaatagttt aaaaacgacc ttgtttctac
2341 t
