I guess someone's always trying to build a better mousetrap:
" The centre also said that before the patient fell ill, he had used chopsticks to try to catch a rat. Tests on rats caught in the man's apartment in the Panyu Lijiang Garden showed they had coronavirus.
Hong Kong medical experts say the Sars virus is close in form to the coronavirus found in rats."
Prior to the SARS outbreak, rat coronaviruses had been isolated and sequenced and these isolates were quite unlike the SARS CoV. The rat sequences were most like mouse hepatitis virus, another class II coronavirus.
SARS CoVs have very limited homology to the previously sequenced rat coronaviruses and the sequence from the Guangzhou patient is approximately 99% homologous to SARS CoV (at least in the S, M, and N genes, which are the three described in the recent press release).
The comment that the patient's sequence is close to the coronavirus sequence found in rats in the patient's apartment raises several new issues. The first brings back the potential for contamination. The patient's sequence is quite distinct from all SARS CoVs at GenBank, but a similar sequence in rat material from the apartment raises the possibility of that material contaminating the patient's sample. If sequence data was obtained from the patient before rat samples entered the lab, then of course such contamination would not be possible.
The sequence from the patient is clearly novel. The entire S gene has been sequenced and it is 98.8% to 99.4% homologous with SARS CoV sequences at GenBank. That means there are 22 nucleotide differences between the Guangzhou sequence and the closest sequence at GenBank and difference among all of the SARS CoV sequences is only an additional 22 nucleotides, so the recent sequence clearly is distinct from all of the other sequences. The sequence itself will provide more data, because some of the changes in the SARS CoV are related to the time of isolation last season while others are linked to geographical location.
The sequence homology with Guangzhou rat isolates also may relate to the 99% homology in the N gene. If the patients N gene really has 10-11 nucleotide changes, then linkage to SARS CoVs from an animal reservoir other than masked palm civets is likely. Most of the SARS CoVs have exact matches with the N gene from the masked palm civets, and 10-11 changes would again set the Guangzhou isolate(s) apart from the SARS CoVs at GenBank.
In any event, the novel SARS CoV described in yesterday's press release is clearly a virus that will undergo considerable scrutiny and a more extensive screening of Guangzhou rats should be a high priority.
straitstimes.asia1.com.sg
Is it Sars or not?
By Mary Kwang
CONFUSION over whether a suspected Sars patient in Guangzhou has the disease deepened yesterday when tests suggested he might have been infected by a new strain of the virus, the Chinese media reported.
Xinhua news agency, quoting a Chinese medical expert, Professor Zhong Nanshan, director of the Guangzhou Institute of Respiratory Diseases, said that test results showed a possibility that the Sars coronavirus had taken a new form. |
