Table 2
Clade distribution of viruses contributing to influenza vaccine effectiveness (VE) analyses, Canadian Sentinel Practitioner Surveillance Network (SPSN), 1 November 2019–1 February 2020 (n = 628)
Clades with defining substitutions (antigenic site) + extra substitutions (antigenic site)	Number of viruses
Influenza A(H1N1)pdm09	N = 287
6B.1A = 6B + S74R (Cb) + S162N (Sa)(+CHO) + S164T (Sa) + I216T + I295V	n = 0
6B.1A1^a= 6B.1A + S183P	n = 0
6B.1A5 = 6B.1A + S183P + N260D	n = 1
6B.1A5A = 6B.1A5 + N129D + T185I (Sb)	n = 245
+ D187A (Sb)(RBS) + Q189E (Sb)	99
+ D187A (Sb)(RBS) + Q189E (Sb) + A73E (Cb) + T120I	16
+ K130N + N156K (Sa) + L161I (Sa) + V250A + HA2: T147A	108
6B.1A5B = 6B.1A5 + E235D (Ca1) + HA2: V193A	n = 39
+ K160M (Sa) + T216K	2
+ K160M (Sa) + T216K + K130N + H296N	15
+ K160M (Sa) + T216K + K130N + H296N + P137S (Ca2) + V272I	22
6B.1A7 = 6B.1A + K302T + HA2: I77M + N169S + E179D	n = 2
+ E68D + S121N + L161I (Sa) + T120A	1
Influenza A(H3N2)	N = 80
3C.2a1b = 3C.2a^b + N171K (D) + N121K (D) + K92R (E) + H311Q (C) + HA2: I77V + G155E	n = 0
3C.2a1b/T131K = 3C.2a1b + E62G (E) + R142G (A) + T131K (A) + HA2:V200I	n = 44
+ K83E (E) + Y94N (E)	4
+ Q197R (B) + S219F (D) + HA2: V18M	3
+ Q197R (B) + S219F (D) + HA2: V18M + K207R (D)	32
+ Q197R (B) + S219F (D) + HA2: V18M + K207R (D) + S144R (A)	4
3C.2a1b/T135K = 3C.2a1b + E62G (E) + R142G (A) + T135K (A)(RBS)(−CHO) + T128A (B)(−CHO)	n = 31
+ S137F (A)(RBS) + A138S (A)(RBS) + F193S (B)	2
+ S137F (A)(RBS) + A138S (A)(RBS) + F193S (B) + E50K (C)	8
+ A138S (A)(RBS) + G186D (B) + D190N (B)(RBS) + F193S (B) + S198P (B)	19
3C.3a^a = 3C.3^c + L3I + S91N (E) + A138S (A)(RBS) + N144K (A)(−CHO) + F159S (B) + F193S (B) + N225D (RBS) + K326R + HA2: D160N	n = 5
Influenza B/Victoria lineage	N = 260
V1A.1 (Δ2)^a = V1A + Δ162–163 (160-loop) + D129G (120-loop) + I180V + HA2: R151K	n = 1
V1A.3A (Δ3) = V1A + Δ162–164 (160-loop) + I180T + K209N	n = 0
V1A.3B (Δ3) = V1A + Δ162–164 (160-loop) + K136E (120-loop)	n = 259
+ G133R (120-loop) + E128K (120-loop)	117
+ R133K (120-loop) + E128K (120-loop)	79
+ N150K (150-loop) + G184E + N197D (190-helix)(−CHO) + R279K	1
Influenza B/Yamagata lineage	N = 1
Clade 3^d	n = 1
+ R48K + L172Q + D232N (230-region)( + CHO) + M251V	1
HA: haemagglutinin; (+/ − CHO) signifies gain/loss of potential N-linked glyscosylation; (RBS) signifies substitution affecting the receptor binding site. The number of viruses belonging to the specified influenza A subtype or B lineage are shown in bolded font as N=number. The number of viruses belonging to a parent genetic group are also shown in bold as n=number. The number of viruses within that parent group bearing the additional substitutions specified are shown in normal font. Specified substitutions are for HA1 unless specified as for HA2. ^a Indicates 2019/20 trivalent influenza vaccine strain. ^b Clade 3C.2a defined by 3C + L3I + N144S (A) + N145S (A) + F159Y (B) + K160T (B) (+ CHO) + N225D (RBS) + Q311H (C) + HA2: D160N. ^c Clade 3C.3 defined by 3C + T128A(B)(−CHO) + R142G (A) + N145S(A). ^d Indicates 2019/20 quadrivalent influenza vaccine strain. SPSN virus bears additional substitutions in relation to the vaccine strain as shown.