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

Thogotovirus

e.g., Thogoto virus, Dhori virus

Isavirus

e.g., Infectious salmon anemia virus

Conserved terminal sequences of genomic RNAs

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¯¯¯¯¯