More of the H5N8 story - should data be open?

In December 2014 I wanted to include the North American analysis of the origins of H5N8 when I was writing the paper about the European and Asian outbreaks of H5N8 having a single source. I had heard of the US H5N8 sequences but they were not yet public and so I contacted the US influenza researchers sending a draft of my single origin paper that I had submitted to Science to them. I have already blogged about what happened to the Science paper.

From: Andrew Dalby [mailto:A.Dalby@westminster.ac.uk]
Sent: Wednesday, December 17, 2014 4:54 PM
To: APHIS-NVSL Concerns
Subject: H5N8 sequences

Dear Sir/Madam,

I recently read the report about H5N8 in a gyrfalcon in Whatcom County. I see that you have identified it as being related to the Eurasian outbreaks of H5N8. I recently submitted a paper to Science showing that the Japanese and European outbreaks come from a common source and that this has diverged from the Korean sequences during the migration to summer breeding grounds before being spread along the long range migratory pathways. 

I have attached the submitted paper. 

Would it be possible for you to let me know as soon as the nucleotide sequences are available as I would like to add them to my analysis and also add the American migratory pathways to my maps. I have already updated the map to include the Washington case.

Thanks

Andy

Dr Andrew Dalby

University of Westminster

I received the following response.

From: , Mia Kim - APHIS <mia.kim.torchetti@aphis.usda.gov>Date: Friday, 19 December 2014 14:31To: Andrew Dalby <A.Dalby@westminster.ac.uk>Subject: FW: H5N8 sequences (UK)

Dear Dr. Dalby, 

Thank you for sharing your draft - indeed the H5N8 appears to be a hearty virus. Current information suggests the introduction into North America may represent a separate event from introductions in Europe. The sequences should be available in Genbank by next week and will keep you advised.All the best, Mia Kim Torchetti, DVM MS PhDAvian Viruses Section HeadDiagnostic Virology LaboratoryNational Veterinary Services LaboratoriesAmes, Iowa,  50010515-337-7590 (phone)515-337-7348 (fax)

Mia.Kim.Torchetti@aphis.usda.gov 

My final e-mail was to Mia

Friday, 19 December 2014 at 14:52 

Dear Mia, 

Thanks for the e-mail. Looking at the past US cases of H5N8 they are very different in the internal gene sequences to the Eurasian ones. It seems that there was a convergence to a H5N8 serotype via different segment rearrangements. It will be interesting to add the new sequence to the analysis.
Best wishes

Andy 

There were no more emails and I waited a considerable time for the release of the North American sequences, more than a few weeks and when they were released there was a large deletion in the original H5 gene which meant I never performed the analysis as it looked like a sequencing error.

Then they produced the paper about the H5N8 phylogenetic analysis in May 2015. That is less than one month after I got the single origin paper published in PeerJ. An anonymous referee delayed the PeerJ paper by asking me to carry out a complete analysis of all of the H5 and N8 genes to show that there was not a reassortment that produced the different outbreaks. The editor Claus Wilke correctly insisted that this was done despite me arguing that this was not common practice, I now think that it should be common practice but it still isn't. Claus did give invaluable advice by pointing out that this is easy to do using FastTree which has helped my subsequent research. This actually directed me to thinking about reassortment and the fact that analysis of single subtypes might be flawed.

What concerns me is whether the national laboratories should be publishing before they have time to analyse so that "research parasites" like myself can use the data. I was e-mailing in the hope of collaboration as the analysis was already done and was trivial for me to do again. I already blogged about the Taiwanese outbreak of H5N8 and the difficulties in getting the sequence data in a timely manner. While national laboratories need the publications to justify their funding I realise that they need to protect their data but on the other hand are they then providing a data service?

I am not sure that the national laboratories do not do more harm than good by hoarding and not openly sharing data. I think that they should be co-authors and collaborators with those who carry out the analysis as there biological work is often the most significant part of the process in terms of time and funds. But I do not think that they should try to do all of the steps of analysis when this is not their function or area of expertise. We are wasting skills and time and not making constructive use of the data.