Table 3. Virological profile of influenza A(H1N1)pdm09 specimens contributing to interim 2018/19 vaccine effectiveness evaluation, Canadian Sentinel Practitioner Surveillance Network, 5 November 2018–4 January 2019 (n = 240).
| Nextstrain subgroup [8] |
Genetic cladea with subgroup substitutionsb | British Columbiac | Albertad | Ontarioe | Quebecf | Overallg | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| n | % | n | % | n | % | n | % | n | % | ||
| 6b1.A | 6B.1 + I286V + I372V | 0 | 0 | 2 | 2 | 0 | 0 | 1 | 3 | 3 | 1 |
| 6B.1 + S183P + K302T + I404M + E506D + N523S |
10 | 13 | 4 | 4 | 10 | 38 | 10 | 29 | 34 | 14 | |
| 6b1.A1 | 6B.1 + S183P + R45G + P282A + I298V + H126Y | 0 | 0 | 0 | 0 | 1 | 4 | 0 | 0 | 1 | 0 |
| 6B.1 + S183P + N451T + P137S (Ca2) | 0 | 0 | 0 | 0 | 1 | 4 | 0 | 0 | 1 | 0 | |
| 6B.1 + S183P + N451T + T185I (Sb) | 26 | 35 | 72 | 69 | 0 | 0 | 0 | 0 | 98 | 41 | |
| 6b1.A2 | 6B.1 + S183P + N129D + N260D + T185I (Sb) | 2 | 3 | 7 | 7 | 5 | 19 | 16 | 47 | 30 | 13 |
| 6B.1 + S183P + N129D + N260D + T185I (Sb) + V479I |
2 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | |
| 6B.1 + S183P + N129D + N260D + R205K (Ca1) + K443R |
4 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 2 | |
| 6B.1 + S183P + N129D + N260D + R205K (Ca1) + R74I (Cb) |
2 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | |
| 6B.1 + S183P + E235D (Ca1) + N260D + V520A + T185I (Sb) | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 18 | 6 | 3 | |
| 6B.1 + S183P + E235D (Ca1) + N260D + V520A + N156D (Ca2) + K160M (Sa) + T216K + S478N |
0 | 0 | 0 | 0 | 4 | 15 | 1 | 3 | 5 | 2 | |
| 6b1.A3 | 6B.1 + S183P + T120A | 9 | 12 | 0 | 0 | 1 | 4 | 0 | 0 | 10 | 4 |
| 6B.1 + T120A + P183S (reversion) | 6 | 8 | 3 | 3 | 0 | 0 | 0 | 0 | 9 | 4 | |
| 6b1.A4 | 6B.1 + S183P + L233I + R74G (Cb) | 5 | 7 | 2 | 2 | 0 | 0 | 0 | 0 | 7 | 3 |
| 6b1.A5 | 6B.1 + L161I (Sa) + I404M + N455T + D501E |
9 | 12 | 15 | 14 | 4 | 15 | 0 | 0 | 28 | 12 |
| Total A(H1N1)pdm09 viruses sequenced | 75 | 100 | 105 | 100 | 26 | 100 | 34 | 100 | 240 | 100 | |
a Unless otherwise stated in the subgroup substitutions, all 6B.1 viruses also bear the substitutions S74R (Cb), S164T (Sa) and I295V relative to the cell-passaged vaccine strain A/Michigan/45/2015 plus M209K and R223K (receptor-binding site) relative to the egg-adapted version (X-275). Compared to the alternate egg-passaged vaccine strain (A/Singapore/GP1908/2015 IVR-180), viruses additionally bore T120A (except in those subgroups already bearing T120A), plus M209K and A225G (receptor-binding site), the latter instead of R223K.
b Antigenic site substitutions are shown in bold, and the antigenic site follows in brackets. H1 numbering is based on influenza A(H1N1)pdm09 with the signal peptide removed. Genetic variants displayed here have been aligned with nextstrain subgrouping [8], recognising differences in numbering approaches (HA1 and HA2).
c HA sequences available for 75 of 87 (86%) A(H1N1)pdm09 viruses contributing to analyses, with specimen collection dates spanning 9 November 2018–4 January 2019.
d HA sequences available for 105 of 219 (48%) A(H1N1)pdm09 viruses contributing to analyses with specimen collection dates spanning 5 November–14 December 2018.
e HA sequences available for 26 of 179 (15%) A(H1N1)pdm09 viruses contributing to analyses with specimen collection dates spanning 12 November–7 December 2018.
f HA sequences available for 34 of 100 (34%) A(H1N1)pdm09 viruses contributing to analyses with specimen collection dates spanning 13 November–28 December 2018.
g HA sequences available for 240 of 585 (41%) A(H1N1)pdm09 viruses contributing to analyses with specimen collection dates spanning 5 November 2018–4 January 2019.