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Biotech / Medical : SARS and Avian Flu -- Ignore unavailable to you. Want to Upgrade?

To: Biomaven who wrote (957)	8/25/2003 10:27:41 AM
From: Henry Niman	Respond to of 4232

Peter, There is homology (I think around 50% depending on which gene you look at - the most conserved would be the polymerase gene), but no long stretches anywhere of exact matches (I would guess that 20-30 is the longest stretch). Winnipeg found 750/750 matches in 7 patients and 749/750 in another). A recombinant would be eliminated if the same region was sequenced and both sequences were found. Until the same region is sequenced, the possibility of a recombinant remains.

To: Biomaven who wrote (957)	8/25/2003 11:11:58 AM
From: Henry Niman	Respond to of 4232

Peter, The only place you are going to get 750/750 matches is from SARS CoV. I could be mutated elsewhere or recombined elsewhere, but it didn't come from OC43. It could also be contaminating material from a positive control or a SARS patient, but to find in in 8 patients means the work is pretty sloppy. 3 of 5 antibody tests were positive and you could theoretically get cross reactivity there. However, OC43 is well known and quite prevalent, so virtually any antibody test would be designed to distinguish SARS CoV form its two common cousins OC43 and 229E.

To: Biomaven who wrote (957)	8/26/2003 8:41:58 PM
From: Henry Niman	Respond to of 4232

The article below suggests that the number of patients positive for SARS CoV sequences is now 12 and includes patients from both nursing homes (Kinsmen Lodge Place and a 101 bed facility, which is almost certainly Kinsmen Retirement Centre in Delta). 750/750 matches means the sequences are from SARS CoV. The question is whether the sequences are from patients of the nursing homes, or repeated contamination by the Winnipeg lab. After reporting 8 positives, its hard to believe that contamination would be involved in 4 more. The Winnipeg lab knows that there is worldwide interest in their results and have to be aware of the consequences of continuing to generate false positives because of contamination. It certainly looks like some require more than a finding of OC43 coronavirus in some samples. Some samples were also positive for meta-pneumovirus. Nether OC43 nor meta-pneumovirus detection explains the SARS CoV sequences. Its contamination or its SARS (or SARS recombinant or mutant). The sequence data are not due to cross reactivity with OC-43 or any other closely related cold coronavirus. >===== Original Message From "Henry L Niman, PhD" <henry_niman@hms.harvard.edu> ===== straitstimes.asia1.com.sg Vancouver Sars denial a cause for concern By Andy Ho

To: Biomaven who wrote (957)	8/27/2003 5:00:13 PM
From: Henry Niman	Read Replies (1) \| Respond to of 4232

The jig is up. The smoking gun has definitely been found in Surrey, BC. Details on the N gene sequence have come out and all exact matches were the same as Tor2. The one exception had a mutation which was an exact match for Frankfurt 1/FRA. The mutation also links back to the index case at Singapore who was infected at the Metropole Hotel. Some have said its all lab artifact, but coming up with a mutation which just happens to match Frankfurt 1/FRA is a pretty good trick. The gun is definitely smoking in Surrey, BC and it gets back to the Metropole Hotel via Frankfurt and Singapore.