Ron, Several SARS CoV sequences were released at GenBank today from Taiwan (last seasons outbreak) and papers will appear shortly in Lancet and NEJM supporting the following molecular analysis of SARS, which gives some insight into the re-emergence in Guangzhou and future problems in vaccine development:
The new SARS CoV sequences from Taiwan make it abundantly clear that most of the Taiwan infections trace back to the Amoy Gardens outbreak in Hong Kong. In the Amoy Gardens outbreak, the index case, CUHK-AG3, had three diagnostic mutations. One, T26477G, had been seen in isolate, CUHK-Su10, from the mother of the Prince of Wales index case. The other two, T3852C and C11493T, were detected in an isolate, CUHK-AG3, from a fatal Amoy Gardens case. Interestingly, this isolate did not have the mutation linked to the Prince of Wales index case, but instead had a mutation, A28102C, that had been previously found in a masked palm civet isolate, SZ3. This combination raised the possibility that this fatal case was in fact infected with a recombinant SARS CoV.
This likely recombinant raises the question of how often such recombinations happen and the recent release of another sequence, Shanghai QXC1, at GenBank this week, provided another clear example of recombination. The isolate had come from a Shanghai tourist who had visited Beijing, and analysis of the SARS CoV showed that the 5' end of the genome had indeed come from Beijing, including multiple markers found in Beijing and other early isolates from mainland China. However, the 3' portion of the genome, beginning with Spike gene clearly looked like it linked back to the Metropole Hotel. This 3' portion included T23220G, which had been previously seen in Tor2, isolated from the son of the Toronto index case, which of course came from the Metropole Hotel. However, the Shanghai isolate was from a patient who had developed symptoms in May, so much could have happened between May and the February outbreak at the Metropole Hotel.
However, the disappearing and reappearing of Metropole Hotel markers was evident much earlier. They entered the public domain with the publication of sequences of initial Singapore isolates. The Singapore outbreak was also linked to the Metropole Hotel via another super spreader event. The index case was one of three tourists who had visited the Metropole Hotel and she was linked directly to three of the other four published Singapore sequences. Her isolate, SIN2500, did not have markers in common with the other isolates from the hotel, but an isolate from her physician, Frankfurt1 and FRA, had a mutation, T26600C, that was also seen in HKU-39849, which came from the brother-in-law of the Metropole Hotel index case. Thus, the common mutation was missing from the common contact, the Singapore index case. This mutation skipping was seen in another mutation, C28268T, found in the physician's isolate. He had no contact with the Singapore index case's grandmother before he left for a scientific meeting in New York, yet this second mutation was in the isolate, SIN2774, from the grandmother, but it also was not seen in the common contact, the isolate from the Singapore index case.
This mutation skipping again comes back to the Metropole Hotel via the third international link, Hanoi. The Hanoi outbreak was also linked to a visitor to the Metropole Hotel and the isolate, Urbani, which was from the physician who first alerted WHO to the SARS outbreak. The Urbani isolate also had mutations that were rarely seen. However, one of the mutations, C7919T was found in one of the Taiwan isolates, TWC1, which had the 3 markers tied to the Amoy Gardens outbreak. Another Urbani mutation, A19064G, is also found in TWC1, as well as two more isolates from Taiwan, TWC2 and TWC3, which also have the three markers linked to Amoy Gardens.
Thus, it is becoming increasingly clear that the patients actually have multiple sequences which can be passed onto contacts, but may not appear in the one isolate from an index case. In fact a higher number of these multiple species may be the hallmark of super spreaders.
In any event, it is clear that the SARS CoV is capable of considerable mixing and matching of well conserved mutations within the same individual. More examples of quasi-species in Beijing, involving the Spike mutations seen in the BJ302 series will be published soon as will more examples of these "missing mutations" from the Metropole Hotel. This frequent shuffling of genetic information in SARS CoVs has serious implications for the design and efficacies of vaccines, and this molecular shuffling will probably be seen in "humanized" animal SARS CoVs, which may play a significant role in the current re-emerging outbreak in Guangzhou. |
