Orthomyxoviridae

Single-stranded, minus-sense, segmented RNA genome: influenza A and B have 8 segments, influenza C has 7 segments

Sequences shown here are those of the genomic minus-strand RNA

Influenzavirus A

e.g., influenza A/PR/8/34(H1N1), influenza A/156/97(H5N1)

Influenzavirus B

e.g., influenza B/Lee/40, influenza B/Ann Arbor/1/66

Influenzavirus C

e.g., influenza C/California/78, influenza C/JJ/50

Isavirus

e.g., Infectious salmon anemia virus

Conserved terminal sequences of genomic RNAs

Recognized for replication, transcription or packaging: Terminal 5' 22 nt and 3' 26 nt of influenza A/PR/8/34 segment 8 are sufficient for vRNA, cRNA and mRNA synthesis, and nucleocapsid assembly [Luytjes, et al., 1989].
The 3' sequence requirement may be as little as 13-14 nt of the 3' terminus [Piccone, et al., 1993; Seong and Brownlee, 1992; Yamanaka, et al., 1991].
Reconstituted cores of the tick-borne Thogoto virus are able to transcribe an influenza A virus vRNA-like promoter and hybrid Thogoto-influenza A promoters [Leahy, et al., 1997].
Utilization of the cis-acting sequences are similar but different for Influenza A and B [Lee, et al., 1998].

Conserved across all genera: Comparison using as prototype PB2 of Influenza A/PR/8/34 (Cambridge)

Influenza A
PR/8/34 (Cambridge) H1N1
Segment 5' end viral RNA 3' end : | : | : | : | : PB2 1 AGUAGAAA CAAGGUCGUUUUUA.....UUGAAUAUAAUUGACCUGCUUUCGCU PB1 2 -----G-- -----CAU-----C.....A-UC-A--GG--UG------------ PA 3 -------- ------AC-----U.....A-UUUGGAUCAGU------------- HA 4 -------- -----GU------C.....-GUUU-UAUU--CC--------U--- NP 5 -------- -----GUA-----C.....GA-UGAU--UC-AC--------U--- NA 6 -------- -----AGU-----G.....A-UC--U-U-AACC------------ M1, M2 7 -------- ------A------U.....-CUUUC-AU--CU------------- NS1 NS2 8 -------- -----GU------U.....-AUGUCU-UG-CAC--------U---

INFLX1 V00603 FLAP1M0X J02151 ORINF9 V01106 ORIN14 V01088 FLANPM0X J02147 FLANAMK J02146 ORINF2 V01099 FLANSMCB J02150

Influenza A
Hong Kong/156/97
H5N1
NS1 NS2 8 -------- -----GU------U.....-AUGUCU-UG-CAC--------U---

AF036360 AF036360

Influenza A
duck/Australia/341/83 H15N8
HA 4 -------- -----GU------C.....--C-U-U-GUA-CC--------U---

FLAHEMAC L43916

Influenza B
Ann Arbor/1/66
(segments 4 and 6 from Lee/40)
PB1 1 -------- --C-AG-C-----U.....--C-UCU---AG-CU-C----CU--- PB2 2 -UG----- --C-AG-A-----C.....CAUCU-GA--AC-CU-C----CU--- PA 3 -------- --C-UG-A------.....GGC--AUC--AC-CA-C----CU--- HA 4 -----U-- ----AG-A-----C.....A-AUUAGA--A--CAAC----CU--- NP 5 -------- ---CAG-A-----U.....-GAG-AGA--A--CUG-----CU--- NB NA 6 -----U-- ----AG-A-----C.....--CU-AGA-UA--CU------CU--- M1 7 -------- ---C-CAC-----C.....A-UUUA-G--AGUG-G-----CU--- NS1 NS2 8 -----U-- ----AGGA------.....GACU-A-C--A--CU------CU---

FLBPB1WT M20170 FLBPB2WT M20168 FLBPAWT M20172 FLBHAZ0 K00423 FLBNPWT M20174 FLBNA0 J02095 FLBM1WT M20176 FLBNSWT M20225

Influenza C JJ/50
(segment 4 from Johannesburg/66; segments 5, 7 from California/78)
1 --C--U-G ----AGGA------.....GAC-U-UCC-A-CC-------CU--- 2 --C--U-G -----GGA-----U.....GAUUUCCAU-A-CC-------CU--- 3 --C--U-G -----GGA-----U.....GAC-U-UCGGA-CC-------CU--- 4 --C--U-G -----GGA-----G.....AAC-U---U-ACCC-------CU--- 5 --C--U-G -----AG------G..... 6 --C--U-G -----GGA-----U.....---UU--G--A-CC-------CU--- 7 --C--G-G -----GGA------.....--UGGA-A-G-ACC-------CU---

FLCPB2A M28061 FLCPB1A M28060 FLCP3A M28062 FLCHAJ0 M17868 FLCNPCA M17700 FLCJJM M22038 FLC5NS0 M10087

Thogoto
SiAr 126
Segment 2 strain not reported
PB2 1 -- -----U-----CGA-----C.....--CUC-G-CCA-CG-U--U---U--- PB1 2 -- -----U-----CGC-----U.....---UG-U-GGAGCG----U---U--- PA 3 -- -----U---A-CAC-----U.....-GUC--G-C-AGUG-U--U---U--- gp75 4 N- ---U-U---A-CA------U.....-GA-GG-AC--CUG-U--U---U--- NP 5 -- -----U-----CA------U.....AGCC--U-UGACUG----U---U---

TVI17873 Y17873 AF004985 AF004985 THORNA3 D00540 THOGP75A M77280 TVRNAS5 X96872

Dhori
Indian/1313/61
2 -- ---U-U---A-CA------U.....-GACUGUC--C-- -U--U---U--- 4 .....ACC-UCG---C-- -U--U---U--- NP 5 ------C-U---A-CAA-----U.....A-UUUCGA--C-- -U--U-A-U--- M1 7 -- -----U---A-CAG-----U.....-G-UC--GU-C-- -U--U-A-U---

DHVPB1 M65866 TBVSEG4 M34002 DHVNPA M17435 DHVM1PRO M95567

ISAV
Sotra 92/93
PB1 2 .....-G-UUAU---AGAG-G-U---- ---

ISAVPB1P AJ002475

ISAV
Glesvaer
7 ----A--- AUG CAC----CU.....AAUU--GA-UCGUG--AU---- ---

AF220607 AF220607

5' and 3' ends are invert repeats that can potentially form panhandle structures

e.g., segment 1 of Influenza A/PR/8/34

                  5' end AGUAGAAACAAGGUCGUU_____
                         ||:|:||||||| : :||     )
                  3' end UCGCUUUCGUCCAGUUAA¯¯¯¯¯

Influenza A PR/8/34 (Cambridge) H1N1	Segment 5' end viral RNA 3' end : \| : \| : \| : \| : PB2 1 AGUAGAAA CAAGGUCGUUUUUA.....UUGAAUAUAAUUGACCUGCUUUCGCU PB1 2 -----G-- -----CAU-----C.....A-UC-A--GG--UG------------ PA 3 -------- ------AC-----U.....A-UUUGGAUCAGU------------- HA 4 -------- -----GU------C.....-GUUU-UAUU--CC--------U--- NP 5 -------- -----GUA-----C.....GA-UGAU--UC-AC--------U--- NA 6 -------- -----AGU-----G.....A-UC--U-U-AACC------------ M1, M2 7 -------- ------A------U.....-CUUUC-AU--CU------------- NS1 NS2 8 -------- -----GU------U.....-AUGUCU-UG-CAC--------U---	INFLX1 V00603 FLAP1M0X J02151 ORINF9 V01106 ORIN14 V01088 FLANPM0X J02147 FLANAMK J02146 ORINF2 V01099 FLANSMCB J02150
Influenza A Hong Kong/156/97 H5N1	NS1 NS2 8 -------- -----GU------U.....-AUGUCU-UG-CAC--------U---	AF036360 AF036360
Influenza A duck/Australia/341/83 H15N8	HA 4 -------- -----GU------C.....--C-U-U-GUA-CC--------U---	FLAHEMAC L43916
Influenza B Ann Arbor/1/66 (segments 4 and 6 from Lee/40)	PB1 1 -------- --C-AG-C-----U.....--C-UCU---AG-CU-C----CU--- PB2 2 -UG----- --C-AG-A-----C.....CAUCU-GA--AC-CU-C----CU--- PA 3 -------- --C-UG-A------.....GGC--AUC--AC-CA-C----CU--- HA 4 -----U-- ----AG-A-----C.....A-AUUAGA--A--CAAC----CU--- NP 5 -------- ---CAG-A-----U.....-GAG-AGA--A--CUG-----CU--- NB NA 6 -----U-- ----AG-A-----C.....--CU-AGA-UA--CU------CU--- M1 7 -------- ---C-CAC-----C.....A-UUUA-G--AGUG-G-----CU--- NS1 NS2 8 -----U-- ----AGGA------.....GACU-A-C--A--CU------CU---	FLBPB1WT M20170 FLBPB2WT M20168 FLBPAWT M20172 FLBHAZ0 K00423 FLBNPWT M20174 FLBNA0 J02095 FLBM1WT M20176 FLBNSWT M20225
Influenza C JJ/50 (segment 4 from Johannesburg/66; segments 5, 7 from California/78)	1 --C--U-G ----AGGA------.....GAC-U-UCC-A-CC-------CU--- 2 --C--U-G -----GGA-----U.....GAUUUCCAU-A-CC-------CU--- 3 --C--U-G -----GGA-----U.....GAC-U-UCGGA-CC-------CU--- 4 --C--U-G -----GGA-----G.....AAC-U---U-ACCC-------CU--- 5 --C--U-G -----AG------G..... 6 --C--U-G -----GGA-----U.....---UU--G--A-CC-------CU--- 7 --C--G-G -----GGA------.....--UGGA-A-G-ACC-------CU---	FLCPB2A M28061 FLCPB1A M28060 FLCP3A M28062 FLCHAJ0 M17868 FLCNPCA M17700 FLCJJM M22038 FLC5NS0 M10087
Thogoto SiAr 126 Segment 2 strain not reported	PB2 1 -- -----U-----CGA-----C.....--CUC-G-CCA-CG-U--U---U--- PB1 2 -- -----U-----CGC-----U.....---UG-U-GGAGCG----U---U--- PA 3 -- -----U---A-CAC-----U.....-GUC--G-C-AGUG-U--U---U--- gp75 4 N- ---U-U---A-CA------U.....-GA-GG-AC--CUG-U--U---U--- NP 5 -- -----U-----CA------U.....AGCC--U-UGACUG----U---U---	TVI17873 Y17873 AF004985 AF004985 THORNA3 D00540 THOGP75A M77280 TVRNAS5 X96872
Dhori Indian/1313/61	2 -- ---U-U---A-CA------U.....-GACUGUC--C-- -U--U---U--- 4 .....ACC-UCG---C-- -U--U---U--- NP 5 ------C-U---A-CAA-----U.....A-UUUCGA--C-- -U--U-A-U--- M1 7 -- -----U---A-CAG-----U.....-G-UC--GU-C-- -U--U-A-U---	DHVPB1 M65866 TBVSEG4 M34002 DHVNPA M17435 DHVM1PRO M95567
ISAV Sotra 92/93	PB1 2 .....-G-UUAU---AGAG-G-U---- ---	ISAVPB1P AJ002475
ISAV Glesvaer	7 ----A--- AUG CAC----CU.....AAUU--GA-UCGUG--AU---- ---	AF220607 AF220607