Rhiza Labs FluTracker Forum

A number of HA and NA sequences from Italy have been released at Genbank, including one from 2010 and another from Dec 31, 2009.
13 of 16 full HA sequences have D225E and 11/13 have C940T (which was previously seen primarily in sequences from the US and Japan). The sequences with D225E were largely from the summer (Aug/Sept) and a few of the July collections were from travelers from the UK.
There are also 10 partial HA sequences from late fall (Nov) which do not have RBD changes.

The large number of D225E isolates was expected because Italy had released NA sequences earlier (without HA) and a large number had markers found exclusively in D225E HA sequences at Genbank.

Dr.Niman, I am still learning sequences and wondered what the effect of 225E/206T/HA syn314k actually means for us in the UK. Am I correct in saying that travellers from the UK went to Italy with a combination of these sequences?

The virus moves around pretty easily and the sequences only represent a subset of what is out there. However, the sequences have an associated characterization page and a few of the recent sequences from Italy have notes that the virus was isolated from a traveler returning for UK (and these sequences have D225E). The two versions of position 206 are quite widespread (each makes up about half of the sequences, so I don't put a lot of weight into that change).
Most of the D225E sequences in Italy had C940T, which has the following sequences with the same change (the recent Italian sequences will appear shortly)

gb|CY054979.1| Influenza A virus (A/California/VRDL55/2009(H1... 32.2 12
gb|CY054939.1| Influenza A virus (A/California/VRDL48/2009(H1... 32.2 12
gb|CY054931.1| Influenza A virus (A/California/VRDL45/2009(H1... 32.2 12
gb|CY054899.1| Influenza A virus (A/California/VRDL39/2009(H1... 32.2 12
gb|CY054891.1| Influenza A virus (A/California/VRDL38/2009(H1... 32.2 12
gb|CY054851.1| Influenza A virus (A/California/VRDL32/2009(H1... 32.2 12
gb|CY054715.1| Influenza A virus (A/California/VRDL5/2009(H1N... 32.2 12
gb|GU369672.1| Influenza A virus (A/Ankara/28/2009(H1N1)) seg... 32.2 12
gb|CY052951.1| Influenza A virus (A/Texas/45061755/2009(H1N1)... 32.2 12
gb|CY052631.1| Influenza A virus (A/Texas/45061670/2009(H1N1)... 32.2 12
gb|CY052607.1| Influenza A virus (A/Texas/45034157/2009(H1N1)... 32.2 12
dbj|AB535745.1| Influenza A virus (A/Nagasaki/HA-53/2009(H1N1... 32.2 12
dbj|AB535744.1| Influenza A virus (A/Nagasaki/HA-52/2009(H1N1... 32.2 12
dbj|AB530488.1| Influenza A virus (A/Nagasaki/HA-44/2009(H1N1... 32.2 12
gb|GQ457514.1| Influenza A virus (A/California/25/2009(H1N1))... 32.2 12
gb|GQ422381.1| Influenza A virus (A/Milan/83/2009(H1N1)) segm... 32.2 12
gb|GQ387430.1| Influenza A virus (A/Catalonia/378/2009(H1N1))... 32.2 12
gb|GQ387382.1| Influenza A virus (A/Italy/172/2009(H1N1)) hem... 32.2 12
gb|GQ351314.1| Influenza A virus (A/Hong Kong/2369/2009(H1N1)... 32.2 12

Dr. Niman

Thank you for all you do and thank you for keeping us informed

Yes, many thanks!

Here is te NA travel log of isolates that likely have D225E in HA sequence from pandemic H1N1

gb|CY054981.1| Influenza A virus (A/California/VRDL55/2009(H1... 32.2 12
gb|CY054941.1| Influenza A virus (A/California/VRDL48/2009(H1... 32.2 12
gb|CY054933.1| Influenza A virus (A/California/VRDL45/2009(H1... 32.2 12
gb|CY054901.1| Influenza A virus (A/California/VRDL39/2009(H1... 32.2 12
gb|CY054893.1| Influenza A virus (A/California/VRDL38/2009(H1... 32.2 12
gb|CY054861.1| Influenza A virus (A/California/VRDL33/2009(H1... 32.2 12
gb|CY054853.1| Influenza A virus (A/California/VRDL32/2009(H1... 32.2 12
gb|CY054717.1| Influenza A virus (A/California/VRDL5/2009(H1N... 32.2 12
gb|CY054063.1| Influenza A virus (A/Hong Kong/CUHK-72146/2008... 32.2 12
gb|CY054579.1| Influenza A virus (A/Catalonia/S2143/2009(H1N1... 32.2 12
gb|CY054559.1| Influenza A virus (A/Catalonia/S2099/2009(H1N1... 32.2 12
gb|FJ865271.1| Influenza A virus (A/Cambodia/R105/2007(H1N1))... 32.2 12
gb|GU367326.1| Influenza A virus (A/Novgorod/01/2009(H1N1)) s... 32.2 12
gb|GU361110.1| Influenza A virus (A/Stockholm/091120-2/2009(H... 32.2 12
gb|GU332632.1| Influenza A virus (A/cat/IA/26991/2009(H1N1)) ... 32.2 12
gb|CY052092.1| Influenza A virus (A/Italy/233/2009(H1N1)) seg... 32.2 12
gb|CY053402.1| Influenza A virus (A/Catalonia/S2010/2009(H1N1... 32.2 12
gb|CY053392.1| Influenza A virus (A/Catalonia/S1947/2009(H1N1... 32.2 12
gb|CY053386.1| Influenza A virus (A/Catalonia/S1944/2009(H1N1... 32.2 12
gb|CY052953.1| Influenza A virus (A/Texas/45061755/2009(H1N1)... 32.2 12
gb|CY052633.1| Influenza A virus (A/Texas/45061670/2009(H1N1)... 32.2 12
gb|CY052609.1| Influenza A virus (A/Texas/45034157/2009(H1N1)... 32.2 12
gb|CY052362.1| Influenza A virus (A/UAE/G01/2009(H1N1)) segme... 32.2 12
gb|CY052069.1| Influenza A virus (A/Belarus/42/2009(H1N1)) se... 32.2 12
gb|CY052067.1| Influenza A virus (A/Belarus/4/2009(H1N1)) seg... 32.2 12
gb|CY052061.1| Influenza A virus (A/Belarus/25/2009(H1N1)) se... 32.2 12
gb|CY052059.1| Influenza A virus (A/Belarus/24/2009(H1N1)) se... 32.2 12
gb|CY052057.1| Influenza A virus (A/Belarus/23/2009(H1N1)) se... 32.2 12
gb|CY052043.1| Influenza A virus (A/Catalonia/S1835/2009(H1N1... 32.2 12
gb|CY052041.1| Influenza A virus (A/Catalonia/S1834/2009(H1N1... 32.2 12
gb|CY052037.1| Influenza A virus (A/Catalonia/S1830/2009(H1N1... 32.2 12
gb|CY052035.1| Influenza A virus (A/Catalonia/S1829/2009(H1N1... 32.2 12
gb|CY052033.1| Influenza A virus (A/Catalonia/S1828/2009(H1N1... 32.2 12
gb|CY052021.1| Influenza A virus (A/Norway/3206-3/2009(H1N1))... 32.2 12
gb|GU186779.1| Influenza A virus (A/chicken/Brescia/1902(H7N7... 32.2 12
gb|CY051977.1| Influenza A virus (A/Catalonia/S1758/2009(H1N1... 32.2 12
gb|CY051956.1| Influenza A virus (A/Catalonia/S1698/2009(H1N1... 32.2 12
gb|CY051941.1| Influenza A virus (A/Catalonia/S1674/2009(H1N1... 32.2 12
gb|CY051938.1| Influenza A virus (A/Catalonia/S1672/2009(H1N1... 32.2 12
gb|CY051928.1| Influenza A virus (A/Catalonia/NS5408/2009(H1N... 32.2 12
gb|CY050320.1| Influenza A virus (A/Catalonia/S1641/2009(H1N1... 32.2 12
gb|CY050317.1| Influenza A virus (A/Catalonia/S1637/2009(H1N1... 32.2 12
gb|CY050314.1| Influenza A virus (A/Catalonia/S1632/2009(H1N1... 32.2 12
gb|CY050308.1| Influenza A virus (A/Catalonia/S1606/2009(H1N1... 32.2 12
gb|CY050305.1| Influenza A virus (A/Catalonia/S1605/2009(H1N1... 32.2 12
dbj|AB530994.1| Influenza A virus (A/mallard/Hokkaido/24/2009... 32.2 12
gb|CY049743.1| Influenza A virus (A/Catalonia/S1592/2009(H1N1... 32.2 12
gb|CY049737.1| Influenza A virus (A/Catalonia/S1587/2009(H1N1... 32.2 12
gb|CY049729.1| Influenza A virus (A/Catalonia/S1545/2009(H1N1... 32.2 12
gb|CY049711.1| Influenza A virus (A/Catalonia/S1490/2009(H1N1... 32.2 12
gb|CY049708.1| Influenza A virus (A/Catalonia/S1479/2009(H1N1... 32.2 12
gb|CY049705.1| Influenza A virus (A/Catalonia/S1478/2009(H1N1... 32.2 12
gb|CY049055.1| Influenza A virus (A/Catalonia/S1453/2009(H1N1... 32.2 12
gb|CY049052.1| Influenza A virus (A/Catalonia/S1436/2009(H1N1... 32.2 12
gb|CY049028.1| Influenza A virus (A/Catalonia/S1379/2009(H1N1... 32.2 12
gb|CY049025.1| Influenza A virus (A/Catalonia/S1369/2009(H1N1... 32.2 12
gb|CY049019.1| Influenza A virus (A/Catalonia/S1350/2009(H1N1... 32.2 12
gb|CY049016.1| Influenza A virus (A/Catalonia/S1333/2009(H1N1... 32.2 12
gb|CY049013.1| Influenza A virus (A/Catalonia/S1331/2009(H1N1... 32.2 12
gb|CY049004.1| Influenza A virus (A/Catalonia/S1304/2009(H1N1... 32.2 12
gb|CY049001.1| Influenza A virus (A/Catalonia/S1300/2009(H1N1... 32.2 12
gb|GU134732.1| Influenza A virus (A/Italy/179/2009(H1N1)) seg... 32.2 12
gb|GU134731.1| Influenza A virus (A/Italy/178/2009(H1N1)) seg... 32.2 12
gb|GU134730.1| Influenza A virus (A/Italy/177/2009(H1N1)) seg... 32.2 12
gb|GU134729.1| Influenza A virus (A/Italy/176/2009(H1N1)) seg... 32.2 12
gb|GU134727.1| Influenza A virus (A/Italy/174/2009(H1N1)) seg... 32.2 12
gb|GU134726.1| Influenza A virus (A/Italy/173/2009(H1N1)) seg... 32.2 12
gb|GU134724.1| Influenza A virus (A/Italy/171/2009(H1N1)) seg... 32.2 12
gb|GU134723.1| Influenza A virus (A/Italy/170/2009(H1N1)) seg... 32.2 12
gb|GU134721.1| Influenza A virus (A/Italy/168/2009(H1N1)) seg... 32.2 12
gb|GU134718.1| Influenza A virus (A/Italy/165/2009(H1N1)) seg... 32.2 12
gb|GU123921.1| Influenza A virus (A/Italy/154/2009(H1N1)) seg... 32.2 12
gb|GU123920.1| Influenza A virus (A/Italy/153/2009(H1N1)) seg... 32.2 12
gb|GU123918.1| Influenza A virus (A/Italy/151/2009(H1N1)) seg... 32.2 12
gb|GU123917.1| Influenza A virus (A/Italy/150/2009(H1N1)) seg... 32.2 12
gb|GU123914.1| Influenza A virus (A/Italy/147/2009(H1N1)) seg... 32.2 12
gb|GU123913.1| Influenza A virus (A/Italy/146/2009(H1N1)) seg... 32.2 12
gb|GU123912.1| Influenza A virus (A/Italy/158/2009(H1N1)) seg... 32.2 12
gb|GU123909.1| Influenza A virus (A/Italy/142/2009(H1N1)) seg... 32.2 12
gb|GU123907.1| Influenza A virus (A/Italy/140/2009(H1N1)) seg... 32.2 12
gb|GU123906.1| Influenza A virus (A/Italy/139/2009(H1N1)) seg... 32.2 12
gb|GU123905.1| Influenza A virus (A/Italy/138/2009(H1N1)) seg... 32.2 12
gb|GU123904.1| Influenza A virus (A/Italy/137/2009(H1N1)) seg... 32.2 12
gb|GU123903.1| Influenza A virus (A/Italy/136/2009(H1N1)) seg... 32.2 12
gb|GU065292.1| Influenza A virus (A/Poland/266/2009(H1N1)) se... 32.2 12
gb|GU065291.1| Influenza A virus (A/Poland/253/2009(H1N1)) se... 32.2 12
gb|GU065290.1| Influenza A virus (A/Poland/304/2009(H1N1)) se... 32.2 12
gb|CY047308.1| Influenza A virus (A/Catalonia/S1286/2009(H1N1... 32.2 12
gb|CY047291.1| Influenza A virus (A/Catalonia/S1273/2009(H1N1... 32.2 12
gb|CY047288.1| Influenza A virus (A/Catalonia/S1272/2009(H1N1... 32.2 12
gb|CY047279.1| Influenza A virus (A/Catalonia/S1269/2009(H1N1... 32.2 12
gb|CY047270.1| Influenza A virus (A/Catalonia/S1265/2009(H1N1... 32.2 12
gb|CY047267.1| Influenza A virus (A/Catalonia/S1260/2009(H1N1... 32.2 12
gb|CY047264.1| Influenza A virus (A/Catalonia/S1254/2009(H1N1... 32.2 12
gb|CY047258.1| Influenza A virus (A/Catalonia/S1249/2009(H1N1... 32.2 12
gb|CY047255.1| Influenza A virus (A/Catalonia/S1248/2009(H1N1... 32.2 12
gb|CY047246.1| Influenza A virus (A/Catalonia/S1242/2009(H1N1... 32.2 12
gb|CY047244.1| Influenza A virus (A/Catalonia/S1237/2009(H1N1... 32.2 12
gb|GQ160533.1| Influenza A virus (A/New Jersey/01/2009(H1N1))... 32.2 12

Large number (about 80) HA partial sequences from Italy (and a few Germany) at GISAID. Many have D225E.

The numbers for Italy are something like 45/77 have D225E.

To clarify further, the sequences from Italy were collected between July and Noverber at two locations (Pavia and Milan). Although there are 45 examples of D225E, there are ZERO examples of D225G or D225N, making it pretty clear that "random mutations" are utter nonsense.