Published Date: 2009-05-29 15:00:05
Subject: PRO/AH/EDR> Influenza A (H1N1) - worldwide (51): dynamics
Archive Number: 20090529.1999
INFLUENZA A (H1N1) - WORLDWIDE (51): DYNAMICS
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[The following 2 reports concern estimation of the transmission rate in a
school outbreak in the United States , and investigation of the origins
of the 2009 A (H1N1) influenza virus by cluster analysis .
The transmission rate estimate comes out at the lower end of previous
estimates and is in line with that published by Fraser and colleagues.
The cluster analysis supports the hypotheses derived from phylogenetic
approaches that the 2009 pandemic influenza A (H1N1) virus derives from one
or multiple reassortment(s) between influenza A viruses circulating in
swine in Eurasia and in North America. - Mod.CP]
 Transmission rate
Date: Fri 29 May 2009
From: Bev Paterson <Bev.Paterson@hnehealth.nsw.gov.au>
Transmission rate of influenza A (H1N1) 2009 infection calculated from a
A key determinant of the success of influenza containment is the
transmission rate of the novel strain. Fraser et al (1) estimated the basic
reproduction number (R0) of the Mexican outbreak of influenza A (H1N1) to
be in the range of 1.4-1.6. R0 is a key measure of transmissibility and
estimates the number of secondary cases in a completely susceptible
population. Their findings were comparable to lower estimates for the 1918
pandemic, where R0 ranged from 2-3 (2).
To further investigate the transmissibility of this novel virus we
conducted a secondary analysis of the largest reported cluster of influenza
A (H1N1) (3). Survey data from students of the St Francis Preparatory
School outbreak in the United States were used to calculate the outbreak
effective reproduction number (R) in a school-based setting. R is the
average number of secondary cases generated by an infectious case during an
epidemic and is comparable to R0. This survey collected data on
self-reported ILI (influenza-like illness -- fever AND either cough or sore
throat) between 8 Apr 2009 and 28 Apr 2009.
We used the method proposed by Vynncky et al (4), to calculate R using the
growth rate of the epidemic. Parameter assumptions were based on estimates
for seasonal influenza commonly reported in the literature, as the values
for this novel virus are not yet available. These were as follows:
incubation period of 2 days; infectious period of 3 days; and a calculated
serial interval of 5 days. The serial interval is the time between the
onset of symptoms for 1st and 2nd generation cases. Using daily data from
the outbreak growth phase, R was calculated at 2.69 (95 per cent, CI
2.20-3.22). Increasing the estimated infectious period to 5 days results in
an R of 3.45 (95 per cent, CI 2.74-4.28). The confidence interval [CI] for
R was derived from a Monte Carlo simulation based on the uncertainty of the
slope estimate. Estimates of R were relatively insensitive to the use of
data from the growth phase or entire outbreak.
Our calculated R is specific to this school setting and transmission rates
in the community are likely to be lower (2). The use of parameters
estimated from seasonal influenza will need confirmation for the 2009
influenza A H1N1 virus. Our analysis supports the findings from Fraser et
al (1) that this H1N1 virus has a transmission rate comparable to the lower
R0 estimates of the 1918 pandemic.
1. C Fraser, et al. Pandemic potential of a strain of influenza A (H1N1):
early findings. [Published online May 14 2009; 10.1126/science.1176062
(Science Express Reports); available from
2. G Chowell, H Nishiura, L Bettencourt. Comparative estimation of the
reproduction number for pandemic influenza from daily case notification
data. J R Soc Interface 22 Feb 2007; 4(12): 155-66; doi:
10.1098/rsif.2006.0161 [available from
3. New York City Department of Health and Mental Hygiene - St Francis Prep
Update: Swine Flu Outbreak. Available from
(30 Apr 2009, accessed 5 May 2009).
4. E Vynncky, A Trindall, P Mangtani: Estimates of the reproduction numbers
of Spanish influenza using morbidity data. Int J Epidemiol 2007; 36: 881-9;
doi:10.1093/ije/dym071 [available from
Bev Paterson (MAE), David N Durrheim (MD, DrPH), Frank Tuyl (PhD)
Hunter New England Area Health Service
Hunter New England Area Health Service
 Cluster analysis
Date: Thu 28 May 2009
Source: Eurosurveillance edition 2009; 14(21) [edited]
Cluster analysis of the origins of the New Zealand A (H1N1) virus
[Authors: A Solovyov1, G Palacios2, T Briese2, W I Lipkin2, R Rabadan3
1. Physics Department, Princeton University, Princeton, United States
2. Center for Infection and Immunity, Mailman School of Public Health,
Columbia University, New York, United States
3. Department of Biomedical Informatics, Center for Computational Biology
and Bioinformatics, Columbia University College of Physicians and Surgeons,
New York, United States]
In March and April 2009, a new strain of influenza A (H1N1) virus has been
isolated in Mexico and the United States. Since the initial reports more
than 10 000 cases have been reported to the World Health Organization, all
around the world. Several hundred isolates have already been sequenced and
deposited in public databases. We have studied the genetics of the new
strain and identified its closest relatives through a cluster analysis
approach. We show that the new virus combines genetic information related
to different swine influenza viruses. Segments PB2, PB1, PA, HA, NP, and NS
are related to swine H1N2 and H3N2 influenza viruses isolated in North
America. Segments NA and M are related to swine influenza viruses isolated
Influenza A virus is a single stranded RNA virus with a segmented genome.
When different influenza viruses co-infect the same cell, progeny viruses
can be released that contain a novel mix of segments from both parental
viruses. Since the 1st reported pandemic in 1918, there have been 2 other
pandemics in the 20th century. In both cases, the pandemic strains
presented a novel reassortment of genome segments derived from human and
avian viruses (1-3). The origins of the 1918 strain are so not clear,
although different analyses suggest that this virus had an avian origin (4,5).
When and where pandemic reassortments happen remains a mystery. Avian
viruses often undergo reassortment events among different subtypes. Several
reports suggest that reassortments are also frequent between human viruses
(6,7). Swine have been found frequently with co-infections and reassortment
of swine, human, and avian viruses has been reported (8-10,3). In addition,
cell surface oligosaccharide receptors of the swine trachea present both, a
N-acetylneuraminic acid-alpha2,3-galactose (NeuAcalpha2,3Gal) linkage,
preferred by most avian influenza viruses, and a NeuAcalpha2,6Gal linkage,
preferred by human viruses (11). Co-infection combined with co-habitation
of swine and poultry on small family farms all over Asia, and the presence
of avian as well as human receptor types in pigs have led to the "mixing
vessel" conjecture (12,13) that suggests that most of the inter-host
reassortments are produced in pigs.
Recently, a new A (H1N1) subtype strain has been identified initially in
Mexico, then rapidly reported in all continents. As of 27 May 2009, 12 954
cases of the new influenza A (H1N1) virus infection, including 92 deaths
have been reported to WHO (14,15). Several approaches have been used to
understand the origins of this strain. Searches in public databases
containing influenza A genomes using sequence alignment tools indicated
that the closest relatives for each of the 8 genomic segments are from
viruses circulating in swine for the past decade (16-19). These include
genome segments derived from "triple reassortant" swine viruses that
combined in the late 1990s genome segments from viruses previously
identified in humans, birds, and swine (20). Similar conclusions were drawn
by the application of phylogenetic techniques (16,21).
Here we present a cluster analysis using principal component analysis and
unsupervised clustering. Clustering methods are particularly robust under
changes in the underlying evolutionary models. Our results substantiate
previous reports (16,21), and demonstrate that for each of the genome
segments of the new influenza A (H1N1) virus the closest relative was most
recently identified in a swine, compatible with a reassortment of Eurasian
and North American swine viruses (data displayed as figure 1 in the
Materials and methods
Influenza sequences were obtained from the National Center for
Biotechnology Information (NCBI) (22) in the United States. We performed a
search using Basic Local Alignment Search Tool (BLAST) for each of the
eight A/California/04/2009(H1N1) segments separately, recording the 50 best
matches. Then we constructed the union of all these matches, taking the
sequences for all their segments available in the database. We aligned
these sequences using the stretcher algorithm as implemented in the EMBOSS
After the alignment we translate the sequences into the binary data,
comparing them to the reference sequence site by site. A mutation maps to
1, while a nucleotide identical to that in a reference sequence maps to 0.
Whenever there are masks, they map to the corresponding fractional numbers.
Gaps are not counted as polymorphisms. Therefore, if there are the S
sequences restricted to the P polymorphic sites, these data translate to
the SxP matrix. Each row of this matrix can be thought of as a vector in a
P-dimensional space, and it represents one of the sequences.
We perform the principal component analysis (PCA) in order to determine the
most significant coordinates in this P-dimensional space. After this we
leave the principal components, which capture 85 per cent of the total
variance, discard the remaining ones and project the data onto this
relevant coordinate subset.
This procedure is followed by the consensus K-means clustering. Namely, if
one targets for K clusters, one repeats the K-means clustering procedure N
times, and forms the matrix n whose elements nij (i,j=1,,S) represent the
number of times out of the N trials when the i-th and j-th sequences were
clustered together. In our analysis we set N greater than or equal to 100.
The matrix of the distances between the samples is Dij=1-(nij/N)
One then performs the standard hierarchical clustering with this matrix,
targeting for the K clusters. This procedure does not depend on any
assumptions made by the phylogenetic models. Note that these techniques can
be used for inferring phylogenies as well (23), though this is beyond the
scope of the present note.
Sequence comparison of available sequences of the new A (H1N1) virus (as of
27 May 2009) did not identify significant sequence variation, except for a
few point mutations. Hence A/California/04/2009(H1N1) was chosen as the
representative for further analyses. There are many different phylogenetic
techniques, each of them with their own assumptions about evolutionary
models that vary in the way of computing genetic distances, probabilities,
etc. As opposed to phylogenetic techniques, cluster methods do not have a
need for evaluation of a tree, which is a more complicated structure than a
set of clusters. Clustering techniques do not provide a detailed
phylogenetic structure because they analyse group features of the sequence
data. That is why the clustering analysis is more robust to the assumptions
we make, for instance, the choice of genetic distance. Unsupervised methods
provide a way of identifying clusters without relying on previous
information about the origins, host, and time isolation.
Figures 2a-2h show the data projected onto the 1st 2 principal components
with the corresponding percentage of variation. [These figures cannot be
reproduced here. Interested readers should consult the original text at the
source URL above]. The figures clearly show that in all cases the new virus
sequences clustered with those of swine viruses. The closest matches for
each of the segments are summarised in Table 1.
Table 1. Closer clusters to the new influenza A (H1N1) virus
Segment / closest match / years
PB2 / swine, North America / 1998-2007
PB1 / swine, North America / 1998-2007
PA / swine, North America / 1998-2007
HA / swine H1, North America / 1985-2007
NP / swine, North America / 1985-2007
NA / avian/swine N1, Eurasia / 1982-2007
M / swine, Eurasia / 1980 - 2005
NS / swine, North America / 1998-2007
Our analyses support the hypotheses whereby the 2009 pandemic influenza A
(H1N1) virus derives from one or multiple reassortment(s) between influenza
A viruses circulating in swine in Eurasia and in North America.
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