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From where did the 2009 'swine-origin' influenza A virus (H1N1) emerge?

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The swine-origin influenza A (H1N1) virus that appeared in 2009 and was first found in human beings in Mexico, is a reassortant with at least three parents. Six of the genes are closest in sequence to those of H1N2 'triple-reassortant' influenza viruses isolated from pigs in North America around 1999-2000. Its other two genes are from different Eurasian 'avian-like' viruses of pigs; the NA gene is closest to H1N1 viruses isolated in Europe in 1991-1993, and the MP gene is closest to H3N2 viruses isolated in Asia in 1999-2000. The sequences of these genes do not directly reveal the immediate source of the virus as the closest were from isolates collected more than a decade before the human pandemic started. The three parents of the virus may have been assembled in one place by natural means, such as by migrating birds, however the consistent link with pig viruses suggests that human activity was involved. We discuss a published suggestion that unsampled pig herds, the intercontinental live pig trade, together with porous quarantine barriers, generated the reassortant. We contrast that suggestion with the possibility that laboratory errors involving the sharing of virus isolates and cultured cells, or perhaps vaccine production, may have been involved. Gene sequences from isolates that bridge the time and phylogenetic gap between the new virus and its parents will distinguish between these possibilities, and we suggest where they should be sought. It is important that the source of the new virus be found if we wish to avoid future pandemics rather than just trying to minimize the consequences after they have emerged. Influenza virus is a very significant zoonotic pathogen. Public confidence in influenza research, and the agribusinesses that are based on influenza's many hosts, has been eroded by several recent events involving the virus. Measures that might restore confidence include establishing a unified international administrative framework coordinating surveillance, research and commercial work with this virus, and maintaining a registry of all influenza isolates.
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Virology Journal
Research
From where did the 2009 'swine-origin' influenza A virus
(H1N1) emerge?
Adrian J Gibbs*1, John S Armstrong1 and Jean C Downie2
Address: 1Australian National University Emeritus Faculty, ACT, 0200, Australia and 2CIDMLS, ICPMR, Westmead Hospital, NSW, 2145, Australia
Email: Adrian J Gibbs* - adrian_j_gibbs@hotmail.com; John S Armstrong - j_s_armstrong@hotmail.com;
Jean C Downie - jean.downie@bigpond.com.au
* Corresponding author
Abstract
The swine-origin influenza A (H1N1) virus that appeared in 2009 and was first found in human
beings in Mexico, is a reassortant with at least three parents. Six of the genes are closest in
sequence to those of H1N2 'triple-reassortant' influenza viruses isolated from pigs in North
America around 1999-2000. Its other two genes are from different Eurasian 'avian-like' viruses of
pigs; the NA gene is closest to H1N1 viruses isolated in Europe in 1991-1993, and the MP gene is
closest to H3N2 viruses isolated in Asia in 1999-2000. The sequences of these genes do not directly
reveal the immediate source of the virus as the closest were from isolates collected more than a
decade before the human pandemic started. The three parents of the virus may have been
assembled in one place by natural means, such as by migrating birds, however the consistent link
with pig viruses suggests that human activity was involved. We discuss a published suggestion that
unsampled pig herds, the intercontinental live pig trade, together with porous quarantine barriers,
generated the reassortant. We contrast that suggestion with the possibility that laboratory errors
involving the sharing of virus isolates and cultured cells, or perhaps vaccine production, may have
been involved. Gene sequences from isolates that bridge the time and phylogenetic gap between
the new virus and its parents will distinguish between these possibilities, and we suggest where they
should be sought. It is important that the source of the new virus be found if we wish to avoid
future pandemics rather than just trying to minimize the consequences after they have emerged.
Influenza virus is a very significant zoonotic pathogen. Public confidence in influenza research, and
the agribusinesses that are based on influenza's many hosts, has been eroded by several recent
events involving the virus. Measures that might restore confidence include establishing a unified
international administrative framework coordinating surveillance, research and commercial work
with this virus, and maintaining a registry of all influenza isolates.
Introduction
A novel H1N1 influenza virus, Swine-Origin Influenza
Virus (S-OIV), was first isolated in mid-April 2009 and, by
the end of the month, the first complete genomic
sequences were published, and the virus shown to be of a
novel re-assortant [1]. The virus spread fast in the human
population, and the resulting pandemic has already
proved to be a significant and very costly cause of mortal-
ity and morbidity in the human population. It has created
intense interest worldwide. Several hundred research
papers, reports, reviews and summaries [2,3] have been
published about this virus in the last six months. Many
Published: 24 November 2009
Virology Journal 2009, 6:207 doi:10.1186/1743-422X-6-207
Received: 29 July 2009
Accepted: 24 November 2009
This article is available from: http://www.virologyj.com/content/6/1/207
© 2009 Gibbs et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Virology Journal 2009, 6:207 http://www.virologyj.com/content/6/1/207
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discuss its genealogy deduced from its gene sequences,
however it seems that we have no clearer evidence of its
immediate origins than we have of the influenzas that
caused past influenza pandemics. So the search for its
source must be intensified while the clues are still fresh.
The possibility that human activity may have had some
role in its origins should not be dismissed without a dis-
passionate analysis of all available evidence. If we wish to
avoid future pandemics, rather than just minimizing the
damage they cause, we must better understand what con-
ditions produce them.
Several phylogenetic studies of the gene sequences of S-
OIV and other influenzas have now been reported [4-10].
In these studies the sequences have been compared using
various techniques (e.g. statistical inference (SI), neigh-
bour-joining, maximum parsimony and principal compo-
nents analyses), and have involved various selections of
the very large number of influenza gene sequences that are
now publicly available. Most phylogenetic studies com-
pared nucleotide sequences, and at least one compared
the encoded amino acid sequences.
All studies have concluded that S-OIV emerged into the
human population on a single occasion, probably around
January 2009 [8,11]. They agree that six of its genes, those
encoding the polymerase proteins (PB2, PB1 and PA), the
haemagglutinin (HA), the nucleoprotein (NP) and the
non-structural proteins (NS), show a clear affinity with
those of the 'triple-reassortant' influenza viruses first
found in North American pigs around 1998, whereas the
other two genes, those encoding the neuraminidase (NA)
and matrix proteins (MP), are from the Eurasian 'avian-
like' virus lineage first isolated in Europe around 1979
[12-19]. Neither the 'triple- reassortant' viruses nor their
individual genes have previously been found in Europe
nor, likewise, have those of the 'avian-like' lineage been
found in North America. However, viruses of both line-
ages have been found more recently in South East Asia
[20,21], but reasortants intermediate between S-OIV and
its parental lineages have not [22].
Discussion
Phylogenetic Studies
One of the most intriguing findings of the phylogenetic
studies is that each S-OIV gene is connected to its respec-
tive phylogenetic tree by a noticeably long branch. This
indicates that, immediately before its emergence, each
had a period of "unsampled ancestry", which Smith and
his colleagues estimated to be between 9.2 and 17.2 years
long for the different genes [8]. Garten and her colleagues
concluded however that "Though long, these branch
lengths are not unusual for swine viruses; there are 52
other similar or longer branch lengths in the swine phylo-
genetic trees" that they published. However, Garten and
her colleagues compared viruses collected over nine dec-
ades under a wide range of sampling intensities. It would
be more appropriate to compare phylogenetically close
isolates collected around the same time. We looked at
branch lengths in a maximum likelihood tree of 160 HA
nucleotide sequences most closely related to those of S-
OIV, and found that after the long branch to the S-OIV HA
gene cluster, the next longest branch was 79 isolates away
and the next a further 21. There is a clear contrast between
the branch lengths in trees of diverse sequences, and those
in sister and cousin lineages.
Another unusual feature of the long S-OIV branches [8] is
that the lengths and error ranges of the branches of seven
of the genes estimated by Smith and colleagues (Table 1
in [8]) form a single broadly overlapping cluster (Fig. 1)
with a mean length of 11.02 +/- 1.05 years, whereas those
of the NA gene are significantly longer and indicate that it
had not been sampled for more than 17.15 +/- 1.74 years.
Thus although the NA and MP genes of S-OIV were both
from the Eurasian avian-like lineage of influenza viruses,
they probably first became associated with the S-OIV lin-
eage on separate occasions, and hence came from two dif-
ferent viruses. We conclude therefore that S-OIV probably
had at least three immediate parents, not two.
The reports of the phylogenetic studies disagree most
obviously in the sequences found to be closest to those of
S-OIV. This is not surprising because the studies analysed
different sets of sequences selected in different ways and
different analytical techniques were used. Furthermore,
the statistical inference methods used by some may not be
ideal for identifying close neighbours in large datasets;
evolution is stochastic, and close relationships are not sta-
tistical, and so a tree fitted statistically to a very large
number of sequences [8] probably confounds close phyl-
ogenetic relationships, especially when those relation-
ships have been globally optimized [7]. We therefore
checked whether more consistent information about S-
OIV's immediate parental lineages could be obtained
from its gene sequences by using a more selective and
direct approach. We first used SWeBLAST [23], a variant of
BLAST, to select from the Genbank database only the
sequences closest to those of S-OIV, then inferred their
relationships using a maximum likelihood method, and
finally ranked the sequences by their patristic distances
within the trees using PATRISTIC [24].
Our analyses showed that almost all the closest genes
came from pig isolates. The NA genes closest to the 04/
2009 NA were all from 'avian-like' H1N1 isolates from
Europe sampled around 1991 (Figure 2) and Additional
file 1; closest were A/swine/Spain/WVL6/1991 (H1N1)
(0.0706 nucleotide substitutions/site: ns/s), A/swine/Eng-
land/WVL7/1992 (H1N1) (0.0718ns/s) and A/swine/
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England/WVL10/1993 (H1N1) (0.0753ns/s). The MP
genes closest to the 04/2009 MP gene were also from
'avian-like' isolates but collected in Asia around 1999
(Figure 3); closest were A/swine/Hong Kong/5200/1999
(H3N2), A/swine/Hong Kong/51901999 (H3N2) and A/
swine/Hong Kong/5212/1999 (H3N2) (all 0.0254 ns/s).
The other six genes, including the HA gene (Figure 4),
were closest to those of North American 'triple-reassor-
tant' isolates sampled around or soon after 1999; most
were H1N2 isolates from pigs, although a few of the
polymerase genes were close to H3N2 isolates (data not
shown). We narrowed the search for the triple reassortant
parent by assuming, as is likely, that the six S-OIV genes
came from a single triple reassortant rather than two or
more. We found that there were five triple-reassortant iso-
lates with four or five genes that were among the twenty
closest to those of 04/2009 (Table 1). Closest of all were
A/swine/Indiana/9K035/1999 (H1N2), A/swine/Indiana/
P12439/2000 (H1N2) and A/swine/Minnesota/55551/
2000 (H1N2).
So, in summary, our analyses provide consistent evidence
that the immediate parents were swine viruses. The sam-
pling dates of those isolates are congruent with the esti-
mated lengths of 'unsampled ancestry' of the parents [8]
and, together with differences in provenance support the
conclusion that S-OIV had three parents; one from North
America, one from Europe and the third from Asia.
Hypotheses
The results of the phylogenetic analyses outlined above
can be used to construct plausible scenarios of the ways in
which S-OIV might have originated. This is a useful exer-
cise as it may focus the search for new clues. Some of the
crucial evidence provided by the phylogenetic analyses is
that:
1) S-OIV emerged into the human population on a
single occasion, probably in Mexico.
2) S-OIV is a reassortant with at least three parental
viruses, all of them viruses of pigs.
3) the parents of S-OIV were last sampled directly in
three very distant parts of the world.
4) the parental genes were last sampled more than a
decade ago. Two were sampled around 11 years ago,
the third 17 years ago, whereas their sister and cousin
lineages have been sampled frequently.
S-OIV could have been generated by natural means. The
parental isolates could, for example, have been assembled
in one place by migratory birds, however the consistent
link of S-OIV's immediate ancestors with pigs suggests
that human activity of some sort was involved in bringing
together the parental viruses. At least two contrasting the-
ories are congruent with this possibility and the available
clues:
1) The "unsampled pig herd" theory was suggested by
Smith and his colleagues [8], who concluded that "the
progenitor of the S-OIV epidemic originated in pigs",
and the "long unsampled history observed for every
segment" of the S-OIV genome "suggests that the reas-
sortment of Eurasian and North American swine line-
ages may not have occurred recently, and it is possible
that this single reassortant lineage has been cryptically
circulating rather than two distinct lineages of swine
flu", and that "Movement of live pigs between Eurasia
and North America seems to have facilitated the mix-
ing of diverse swine influenzas, leading to the multiple
reassortment events associated with the genesis of the
S-OIV strain."
This theory was implicitly supported by Trifonov and
his colleagues in their report of a study of the numbers
of gene sequences deposited in Genbank from human
and pig influenzas sampled around the world in dif-
ferent years [25]. They had found that, although the
number of influenza sequences deposited had
increased greatly in the last decade, there were four
times as many human as pig influenza sequences. Fur-
thermore, whereas the sequenced human isolates
came from all over the world, the pig isolates came
Graph showing the duration of the "unsampled ancestry of different S-OIV genesFigure 1
Graph showing the duration of the "unsampled
ancestry of different S-OIV genes. The data is from
Table 1 of [8], and the error bars give the "95% credible
intervals". The data from the lineage of the triple reassortant
parent are in blue, those from the Eurasian 'avian-like' swine
virus lineage in red. The black triangles indicate the mean and
standard deviation of the values for the triple reassortant and
MP lineage genes combined.
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only from North America, Asia, and Europe, and none
from Africa, Oceania, or South America. They con-
cluded that, given "the lack of sampling" of pigs "in
certain parts of the world, it is perhaps not surprising
that the ancestors of the new human influenza A
(H1N1) virus have gone unnoticed for almost two
decades." [26].
It is important to note that this theory depends on the
intercontinental movement of live infected pigs, and
requires at least two quarantine-breaching incursions
involving three different countries. It is likely that
quarantine control of the spread of swine influenzas
around the world varies greatly in its efficacy. However
viruses of the Eurasian 'avian-like' lineage, and their
genes, have never been found in North America before
S-OIV appeared, even though they have been common
in Europe for over three decades, and similarly 'triple
reassortant' viruses and their genes have not been iso-
lated in Europe, although they have been the domi-
nant swine influenza virus in North America for more
than a decade.
2) The "laboratory error" theory. We note that influ-
enza viruses survive well in virus laboratories, that lab-
oratories are not subject to routine surveillance, and
that there are probably many laboratories in the world
that share and propagate a range of swine influenza
viruses from different sources and continents, and also
share and use immortalized lines of cultured cells. The
viruses are used for research, diagnostic tests and for
making vaccines, and the cells are used for propagat-
ing the viruses. Thus if S-OIV had been generated by
laboratory activity, when one host was simultaneously
infected with strains from the different parental line-
ages, this would explain most simply why S-OIV's
genes had escaped surveillance for over a decade, and
how viruses last sampled in North America, Europe
and Asia became assembled in one place and gener-
ated a reassortant.
So what sort of laboratory event might produce mixed
infections with different strains of influenza, and
thereby generate S-OIV? The simplest is that S-OIV is a
reassortant produced during research. There is also the
possibility that it was generated during the production
of multivalent vaccines. Multivalent 'killed' vaccines
are mixtures of virions that have been grown in hen's
eggs and then chemically sterilized. Thus a reassortant
might be produced if insufficient sterilant, usually for-
maldehyde or propiolactone, is added to the virion
mixture. The live mixture could then infect pigs 'vacci-
nated' with it, and the growing viruses could reassort,
infect piggery staff and hence spread to the broader
human population. Finally, it is possible that serially
passaged cells, such as the Madin-Darby canine kidney
(MDCK) cells now widely used in influenza laborato-
ries, became latently and serially infected with differ-
ent strains of influenza as a result of lax laboratory
practices. This process could generate reassortants, and
infect staff.
Circumstantial Evidence
There are clear historical precedents for most of the events
described in the above scenarios. Viruses do 'escape' from
laboratories, even high security facilities. The H1N1 influ-
enza lineage that circulated in the human population for
four decades after the 1918 Spanish influenza epidemic,
disappeared during the 1957 Asian influenza pandemic,
was absent for two decades, but then reappeared in 1977.
Gene sequences of the 1977 isolate and others collected in
the 1950s were almost identical, indicating that the virus
had not replicated and evolved in the interim, and had
probably been held in a laboratory freezer between 1950
and 1977 and 'escaped' during passaging. The suggestion
that persistently infected cells might be involved is also
Table 1: Distances between genes of A/California/04/2009 (H1N1) and those of the closest H1N2 isolates.
PB21PB1 PA HA NP NS3
A/swine/Indiana/P12439/2000 0.0368*20.0430 0.0474 0.0525 0.0360* 0.0533
A/swine/Indiana/9K035/1999 0.0406 0.0395* 0.0498 0.0513* 0.0387 0.0439
A/swine/Minnesota/55551/2000 0.0372 0.0451 0.0450* 0.1224 0.0408 0.0427*
A/swine/Illinois/100084/2001 0.0446 0.0434 0.0451 0.0597 0.0404 0.0528
A/swine/Illinois/100085A/2001 0.0453 0.0420 0.0486 0.0578 0.0404 0.0539
1 Genes: PB2, PB1 and PA, polymerase genes; HA, haemagglutinin; NP, nucleoprotein; NS, non-structural proteins 1 and 2
2 Patristic distances; nucleotide substitutions/site. The isolate that gave the shortest distance for each gene is marked with an asterisk.
3 All five NS1 genes encode a slightly truncated (219 amino acids) NS1 protein as does the NS1 gene of S-OIV.
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Unrooted maximum likelihood tree of the neuraminidase gene sequences of S-OIV and the most closely related sequences in GenbankFigure 2
Unrooted maximum likelihood tree of the neuraminidase gene sequences of S-OIV and the most closely
related sequences in Genbank. The ten closest are marked with red arrows. Details of the sequence selection and tree
inference methods used are in Additional File 1.
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Unrooted maximum likelihood tree of the gene sequences of the matrix proteins of S-OIV and the most closely related sequences in GenbankFigure 3
Unrooted maximum likelihood tree of the gene sequences of the matrix proteins of S-OIV and the most
closely related sequences in Genbank. The ten closest are marked with red arrows. Details of the sequence selection and
tree inference methods used are in Additional File 1.
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Unrooted maximum likelihood tree of the haemagglutinin gene sequences of S-OIV and the most closely related sequences in GenbankFigure 4
Unrooted maximum likelihood tree of the haemagglutinin gene sequences of S-OIV and the most closely
related sequences in Genbank. The ten closest are marked with red arrows. Details of the sequence selection and tree
inference methods used are in Additional File 1.
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not outlandish; influenza virus can persistently and
latently infect MDCK cells [27], and viruses do travel
between laboratories in cells [28].
Multivalent 'killed' vaccines are widely used to control
swine influenzas, particularly in North American piggeries
[29], indeed one of the viruses identified by us and others
(e.g. [30]) as closest to S-OIV, A/swine/Indiana/P12439/
2000 (H1N2), seems to be the "2000 Indiana strain" used
in commercial vaccines in North America [31]. We also
note that isolates selected from the three clusters of viruses
we find to be closest to S-OIV would probably make a use-
ful trivalent vaccine for international use as they would
provide a mixture of haemagglutinins of the swine H3, H1
'classical swine' and H1 'Eurasian avian-like' lineages.
The patchy occurrence of S-OIV infections in piggeries
over the past six months is interesting and may be signifi-
cant. Pigs have been shown to be fully susceptible to S-
OIV. They shed the virus and readily transmit it between
themselves, but whereas S-OIV has been reported in
humans worldwide, it has not yet been reported from a
pig farm in the USA (October 2009). By contrast it has
been found in two piggeries each in Australia, Canada and
Ireland, and one each in Argentina, Indonesia and Japan.
In the outbreaks in Argentina, Australia and Canada, at
least, the pigs had not been vaccinated (Jorge H. Dillon, J.
Keenliside and Alain Laperle, personal communication),
and became infected from infected farm staff. The appar-
ent immunity to S-OIV of pigs in the USA and Mexico, but
not elsewhere, may indicate that the swine influenza vac-
cines currently used in the USA and Mexico contain an
immunogen that either protects against S-OIV infection or
mitigates its symptoms.
Circumstantial evidence must always be treated with cau-
tion. One major uncertainty in trying to determine the ori-
gin of S-OIV is that one cannot predict which characters of
the parental viruses have remained or changed during the
reassortment process that produced S-OIV. If, for exam-
ple, the significant infectiousness of S-OIV is an 'emer-
gent' property of S-OIV, and not shown by its parents,
then one could conclude that the final reassortment prob-
ably occurred at about the time it emerged in early 2009.
However it is not yet known whether S-OIV's infectious-
ness is novel; the reassortment may have occurred a dec-
ade ago, and a recent mutation may have enhanced its
infectiousness. Another widely reported feature of S-OIV
is that it replicates poorly in embryonated eggs, but again
this may be merely a specific feature of S-OIV and not its
immediate parents. Similarly the fact that the evolution-
ary rate of all of the genes of S-OIV seem to be 'normal'
during their unsampled pre-emergent period [8,11]] does
not prove that the virus or its parents have been main-
tained in "unsampled" pig herds and precluded the possi-
bility of human involvement, as viruses grown for
vaccines evolve, and indeed might be expected to show an
increased evolutionary rate [32,33] while adapting to
eggs, a new host, although such an increase may have
been offset by the practice of storing 'seed stocks' for use
in several 'production cycles' in vaccine production, so
that the evolutionary age of a vaccine virus may be less
than its sidereal age, and the average could then appear to
be 'normal'. Finally there is the report that the first human
S-OIV infections were in Perote, a small Mexican town
with a very large number of large piggeries, although it
was also reported that none of the pigs showed signs of
influenza. Among the earliest cases were some in Oaxaca,
290 kms to the south [34]. Perote is an unlikely place for
an infected migratory pig to arrive from an interconti-
nental trip, as the town is in a remote high valley sur-
rounded by mountains, 200 kms to the east of Mexico
City where there is the nearest major airport, and 130 kms
from the nearest port at Vera Cruz. The four month differ-
ence between 'The Most Recent Common Ancestor' date
for S-OIV estimated from its phylogeny [8,11], and its ear-
liest detection in the human population makes it more
difficult to make specific conclusions about its prove-
nance.
Motifs and Sequence Signatures
We have also checked whether any extra information
about the origin of S-OIV can be gleaned from gene
sequence features reported to be associated with host
adaptation, virulence, etc. Such sequence signatures must
be interpreted with caution as although Genbank records
the source host of influenza isolates, it rarely records their
passage hosts and passage history. Influenza viruses are
nowadays mostly isolated in MDCK cells, but early influ-
enza isolates were mostly grown in embryonated hen's
eggs, and adaptation to eggs is known to cause protein
sequence changes [32,33,35,36]. Therefore we compared
sequence signatures and motifs in S-OIV with those of
their closest relatives.
Subbarao and his colleagues [37] were first to show that
amino acid 627 of the PB2 protein was almost always
glutamate in bird isolates and lysine in human isolates.
We checked 142 PB2 sequences, about one third each of
isolates from birds, pigs and human beings, and found
glutamate in contrast to lysine at this site in 98% and 70%
of the bird and pig isolates. The only human isolates that
had glutamate were all five S-OIVs, and three other
human isolates; A/Hong Kong/156/1997(H5N1) and A/
Hong Kong/1073/1999(H9N2) both from human beings
infected from birds, and A/Hong Kong/1774/
1999(H3N2) which came from a person infected from
pigs. Chen and colleagues [38] made a much more exten-
sive survey of sequences and found 51 more sites in 10 of
the 11 proteins of influenza virus that discriminated
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between bird and human isolates as well as, or better
than, PB2-627. Unfortunately they did not report simi-
larly specific sites for swine isolates, but we have checked
whether any of those 52 sites (Table 1 in [38]) also distin-
guish S-OIV and its closest relatives, and found that only
two of the 52 sites, PA-356 and NP-313, did. At 29 of the
sites, the amino acids of the 'S-OIV cluster' (i.e. S-OIV and
the swine viruses closest to it) are avian-like, at 16 they are
human-like, at 6 (in the matrix proteins) they are novel,
and the single recognised site in some NS1s has been lost
by truncation. However, surprisingly, all the five recog-
nised sites in the PB1-F2 protein of the S-OIV cluster have
human-like residues, whereas the other 11 human-like
residues are spread over 40 sites in eight proteins.
Another oddity of the S-OIV genome is that its PB1-F2
gene is truncated. In most influenza viruses the PB1 gene
encodes three proteins [39,40]. The primary ORF encodes
the PB1 and PB1-N40 proteins, and the PB1-F2 ORF,
which encodes a proapoptotic protein of 90 amino acids,
is in the second (+1) reading frame of the gene starting at
nt 95. In a small number of influenzas, including all S-
OIVs, the PB1-F2 ORF is truncated by termination codons
at positions 12, 58 and 88, and its absence is associated
with avirulence in mice [41-43]. Trifonov and colleagues
have reported statistical tests of various features of the
PB1-F2 region [26], and concluded "that PB1-F2 is of little
or no evolutionary significance for the virus".
We compared the PB1-F2 genes of S-OIV with those most
closely related to them. Four of the five triple-reassortants
closest to S-OIV (Table 1) have a complete PB1-F2, but
one, A/swine/Minnesota/55551/2000, terminates at
codon 58 and so is partly truncated. The PB1-F2 of
another isolate, A/swine/Minnesota/3236/2007 (H1N2)
has termination codons 12, 26 and 58 and, together with
A/swine/Ohio/75004/2004 (H1N1), which has termina-
tion codon 58, forms a distant sister group to the S-OIVs
in a ML tree of the complete PB1 genes. A survey of the
individual S-OIV PB1-F2 termination codons in 7644
PB1-F2 sequences (Genbank; August 2009) established
that one might expect to find, at random, 0.46 sequences
with all three termination codons in a dataset of that size,
whereas they were found not only in S-OIV but also in the
unrelated A/mallard/Alberta/300/1977 (H1N1) and A/
Siena/9/1989 (H1N1). The termination codons in the S-
OIV PB1-F2 originate as silent mutations to valine or leu-
cine (VL) codons of the main PB1 ORF, but whereas VL
codons are evenly distributed throughout the PB1 protein,
the termination mutations in the +1 frame are not; three
of the eleven VL codons have mutated in the PB1-F2
region, which is 90 codons long, but only in two of the 82
VL codons in the remaining 665 codons have mutated. It
seems that the peculiarities of the S-OIV PB1-F2 gene, the
human-like signature sites and its selectively super-
imposed termination codons, probably reflect the out-
come of selection rather than being of "little or no evolu-
tionary significance".
Finally, we examined the NS1 protein, which in c. 80% of
over 3000 sequences obtained from Genbank (July 2009)
were full length, and at the C-terminus had an intact '-
ESEV' motif or a similar sequence, which has been linked
with virulence [44]. 7% of the NS1s were, like that of S-
OIV, only 219 amino acids long and terminating in '-QK';
most of them (66%) had come from pig isolates, 20%
from human, 8% birds, 5% horses and fewer than 1%
from mink and dogs, but none were as short as the NS1
protein experimentally truncated to 126 amino acids to
attenuate the virus for use in a live vaccine [45].
Thus our examination of sequence signatures and motifs
in the S-OIV genome has not clarified our knowledge of
its origins, but has certainly raised many new questions.
Conclusion
Influenza virus is a very significant zoonotic pathogen.
Public confidence in influenza research, and the agribusi-
nesses that are based on influenza's many hosts, has been
eroded by several recent events. Measures that might
restore confidence include establishing both a unified
international administrative framework coordinating all
surveillance, research and commercial work with this
virus, and also a detailed registry of all influenza isolates
held for research and vaccine production.
The phylogenetic information presently available does
not identify the source of S-OIV, however it provides some
clues, which can be translated into hypotheses of where
and how it might have originated. Two contrasting possi-
bilities have been described and discussed in this com-
mentary, but more data are needed to distinguish between
them. It would be especially valuable to have gene
sequences of isolates filling the time and phylogenetic gap
between those of S-OIV and those closest to it. We believe
that these important sequences are most likely to be
found in isolates from as-yet-unsampled pig populations
or as-yet-unsampled laboratories, especially those hold-
ing isolates of all three clusters of viruses closest to those
of S-OIV, and involved in vaccine research and produc-
tion. Quarantine and trade records of live pigs entering
North America could probably focus the search for the
unsampled pig population. It is likely that further infor-
mation about S-OIV's immediate ancestry will be
obtained when the unusual features of its PB1-F2 gene are
understood.
Abbreviations
BLAST: Basic Local Alignment Search Tool; ORF: open
reading frame.
Virology Journal 2009, 6:207 http://www.virologyj.com/content/6/1/207
Page 10 of 11
(page number not for citation purposes)
Competing interests
The work reported here was unfunded, and the authors
have no competing financial or intellectual property inter-
ests.
Authors' contributions
The work was planned as a result of discussions and
projects involving all the authors. Analyses were done by
AJG, all authors contributed to the manuscript.
Additional material
Acknowledgements
We thank the two anonymous reviewers for their comments, and also
many colleagues, especially Gillian Air, Richard Carter, Joe Dudley, Bill Gal-
laher, Mark Gibbs, Simon Ho, John Mackenzie, John Maindonald, Matt Phil-
lips and John Trueman, for very helpful comments and suggestions during
the protracted gestation of this paper.
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Taxonomic methods and sequence Accession Codes. Details of the meth-
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Codes of all the sequences used in the analyses.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1743-
422X-6-207-S1.DOC]
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