- This week new H1 swine sequences from
Canada were placed on deposit at GenBank in association with the publication,
" Identification of Human H1N2 and Human-Swine Reassortant H1N2 and
H1N1 Influenza A Viruses among Pigs in Ontario, Canada (2003 to 2005)"
Seven of the isolates, listed below had an avian PB2 gene and as indicated
earlier, several were recombinants and had sequences matching portions
of three swine isolates from 1977, 1998, and 2002, also listed below:
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- A/swine/Alberta/56626/03(H1N1)
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- A/swine/Ontario/11112/04(H1N1)
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- A/swine/Ontario/23866/04(H1N1)
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- A/swine/Ontario/48235/04(H1N2)
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- A/swine/Ontario/53518/03(H1N1)
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- A/swine/Ontario/55383/04(H1N2)
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- A/swine/Ontario/57561/03(H1N1)
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- A/Swine/Korea/CY02/02(H1N2)
- A/Swine/Tennessee/24/77 (H1N1)
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- A/Swine/North_Carolina/35922/98(H3N2)
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- As noted earlier, Ontario/11112 was
an exact match with North Carolina/35922 for positions 756 through at least
1601 (only a partial sequences from North Carolina was available - sequence
numbers adjusted to reflect longer sequences).. Ontario/53518 similarly
was an exact match with Korea/CY02 from position 568 to the end of the
sequence. Ontario/23866 matched Onraio/53518 through position 568
and then matched Tennessee/24 for positions 1008-1326. These data
showed that each of the above recent isolates exactly matched an earlier
isolate indicating each was a recombinant. The data also provided
evidence for absolute fidelity in copying a large gene segment for 6 years
and a shorter segment for 26 years. These data raised serious questions
that attributed rapid influenza evolution to random mutation.
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- Analysis of the remaining sequences
eliminated "random mutations" as a viable mechanism for the rapid
influenza development observed on an annual basis. The remain isolates
all contained an exact match with the 1977 isolate from Tennessee.
Ontario/561 had an exact match over the same 318 BP region as Ontario/57561.
Ontario/23866 matched Tennessee/24 for a larger region, 768-1354 which
overlapped the 318 BP region. This 586 BP region has been copied
with absolute fidelity for over 26 years, and this larger region includes
sequences not essential for the other two Ontario isolates.
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- However, the remaining two isolates
have even longer regions which exactly matched Tennessee/24. Ontario/48235
was an exact match over position 274-1880 while Ontario/55383 was an exact
match over positions 274-1931. Thus each of these two isolates matched
the 1977 sequences exactly for over 1600 BP. Maintaining an exact
match for over 26 years in these five isolates for over 26 years is not
a property of an error prone polymerase that produces evolving genes via
random mutation. The regions maintained in these two isolates are
not immutable, because most of the 1600 BP has been replaced in the other
isolates, eliminating arguments invoking differential evolution.
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- These data show that all seven isolates
evolved via recombination and random mutations were rare or non-existent
over this time period. The recombination mechanism was supported
by analysis of the PA, which was also a recombinant in all seven sequences,
and six of the seven had exact matches with the same 1977 sequence from
Tennessee. The regions of identity ranged from 598 to 1866BP.
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- The above data destroys the rapid evolution
by random mutation hypothesis repeatedly stated by WHO and consultants.
WHO does not analyze H5N1 bird flu sequences for homolgous recombination,
which is the primary driver of H5N1 evolution. Most recombinants
in H5N1 involve shorter sequences in part because of the high frequency
of recombination, which reduces the length of the exact matches.
Most of the differences in the recombined regions are reduced to single
nucleotide changes. However, these small changes can be used to track
where the isolates have been and where they are going. Moreover,
since the parental strains are frequently known, future recombined sequences
can be determined.
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- Determining future recombinants requires
a robust and current database. WHO has sequestered many of the most
recent H5N1 sequences, including human sequences from Turkey and most of
the H5N1 sequences from Europe. These sequences are controlled by
the WHO affiliated lab at Weybridge. Similarly, the WHO affiliated
lab in Hong Kong has sequestered all human H5N1 sequences from Indonesia.
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- It is time for the WHO to obtain permission
to release these data. If these labs are unwilling to release the
existing data, the WHO should seek alternative labs that are willing to
release data from samples received in the mail. The existing situation
significantly delays the proper analysis of these valuable sequences.
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- © 2006 Recombinomics. All
rights reserved.
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