Norway Provides Distinct 225G Coding from Lung in September Male Fatality

[sharon sanders]

2009-11-30

Norway Provides Distinct 225G Coding from Lung in September Male Fatality

A/Norway/3206-3 HA and NA, sampled on 2009-09-01 from the post-mortem lung of a male fatality imports a new 225G to Norway.

Only CatNS2001 and CatNS2008 from early August carry this variant Glycine coding at amino acid 225 that is seen as T717A, GGt->GGa. Neither of the cross segment pair, HA syn413K or NA syn407V, appears in this sample. Norway3206 carries a second HA polymorphism at 140S, a change found only 3 times within the reservoir, but found elsewhere in 1918 specimens, H5N1 Avian, Seasonal 2007, 2008, 2009 and the red-winged tinamou from 2008.

The Norway NA shows one residue of interest at syn291V, a change that is found in 102 sequences including TamiFlu Resistant HK2369, Almati01, Tomsk01, Poland and with deep penetration through Italy and Catalonia.

Two different codings for Glycine at residue 225 at this early stage of the pandemic demonstrates an ability within ΣPF11 for an individual strain to adapt quickly.

[Celvin11]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

The man was elderly, in his 70's. He had several severe chronical diseases and was in respirator several days until death occured

He died 16 September as the only male in Norway that month

[Sally Furniss]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

collection date is "01-Sep-2009"

[Celvin11]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

If stated collection date is is correct (1 Sep), he could not be the September Male Fatality

The only one who died in Norway prior to that date was the Danish trucker (lorry driver), aged 58, who died on 25 August. He was never hospitalized, and he died when sleeping. He likely catched infection in Denmark

On 23 July a Spaniard died on a cruise ship between Poland and Norway.

[sharon sanders]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

Thanks Celvin11.

[Sally Furniss]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

country="Norway: Oslo" . Is that where the patient was hospitalised or where sample was processed?

[Celvin11]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

Post-mortem autopsy of Dansh lorry driver was performed at Ullevål University Hospital in Oslo

25 Aug is pretty close to 1 Sep. Could this be the case ?

[Celvin11]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

Is it possible to get a confirmation that date of sampling - 1 Sep - is stated correctly, from source that provided the info ?

Its a bit surprising if it turns out to be the Danish lorry driver, since he was never hospitalized

[Hogweed]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

Is it possible to get a confirmation that date of sampling - 1 Sep - is stated correctly, from source that provided the info ?

Its a bit surprising if it turns out to be the Danish lorry driver, since he was never hospitalized

Why is that surprising if the sample is from post-mortem tissue? Date of sampling (whatever the definition of "sampling") is not likely to be date of death and can not be earlier.

[sharon sanders]

Re: Norway Provides Distinct 225G Coding from Lung in September Male Fatality

reply from NS1 -

While it is noble to attempt correlation of clinical data to sequence data, no amount of detective work will be conclusive due to lack of cooperation on both sides of the puzzle and privacy laws. Please do not expect to collaborate and corroborate. You may find less participation than you expect from those involved with the actual ultimate origin of the data. Try, but do not be surprised if no information is forthcoming. You will notice that the more recent deposits at GenBank have shown significant improvement in annotation. Researchers around the world applaud those labs that have taken the extra time to provide those very important pieces of data.

--

The polymorphisms that we were able to study are noted in the post. You will see that Norway3206-3 was not fully reviewed due to time and funding constraints, so please do not take the polymorphism list as exhaustive. If I recall properly, this sequence did not display mixed peaks (admixture) on the sequencing trace at 225, so no Nucleotide Ambiguity Codes (R, W, et al) exist in that section of the RBD. Norway3206-3 did display a variant coding, GGt=>GGa, for the 225G but did not fall onto the cross-linked background from the Ukraine.