Figure 1.
Estimated case numbers & laboratory-confirmed cases of pandemic and seasonal influenza, England, 2009.
The estimated number of symptomatic cases with ILI due to pandemic influenza was calculated each week using a statistical model which relies on data from various surveillance systems: the primary care-based QSurveillance scheme, sentinel virological surveillance schemes and data from the National Pandemic Flu Service (NPFS) [61]. Number of pandemic H1N1 viruses selected for sequencing of HA per week is also shown.
Figure 2.
Phylogenetic relationship of full length HA sequences of pandemic influenza viruses isolated in the UK.
Viruses from an illustrative subset of 100 were included, as well as additional 50 worldwide viruses, all collected between April and December, 2009. Tips are tagged and coloured according to whether viruses were isolated during the first or second wave. The tree was rooted with A/California/07/2009 as the outgroup. Branch lengths are drawn to scale. Signature amino acid changes are annotated at the nodes of each cluster.
Figure 3.
Amino acid changes seen in UK viruses, April – December, 2009.
Sites are described using H1 numbering with the HA protein sequence of the vaccine strain A/California/07/2009 used as reference sequence. The logo describes the amino acid changes by displaying the one-letter symbol that codes each amino acid (according to IUPAC – IUB nomenclature) in the proportion seen amongst the analysed viruses. The number of viruses presenting each change is indicated below the logos, with frequencies in brackets.
Figure 4.
Antigenic reactivities of influenza H1N1 viruses isolated in the UK.
Percentage of viruses with different antigenic reactivities as per reduction in HI titres against: a) A/California/07/2009 (pandemic H1N1 2009) antiserum. b) A/Solomon Islands/3/06 (seasonal H1N1) antiserum.
Table 1.
Antigenic reactivity of pandemic influenza (H1N1) 2009 viruses from UK (n = 227).
Figure 5.
Surface representation of the hemagglutinin hetero-trimer from a pandemic (H1N1) 2009 strain [17].
Antigenic sites Ca (Orange), Cb (Blue), Sa (Pink) and Sb (Cyan) and residues of interest (56A [seq:73] (red), 84A [seq:101] (purple), 203A [seq:220) (dark green), 370B (HA2 43) [seq:387] (yellow) and 374B (HA2 47) [seq:391] (light green) are highlighted. Residue 203 is in a buried position only visible when residues 218, 238 & 239 are removed.