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Media Myth On Jeddah Camel MERS Sequence
For one thing, there are other known camel coronaviruses, which at least in theory might have generated a positive hit on the MERS test.
“I would want to know for sure that the MERS corona[virus] PCR assay does not pick up those viruses,” said Koopmans, chief of virology at the National Institute of Public Health for the Netherlands.
“PCR positive, that tells that there is most likely a coronavirus. But the sequencing will tell whether it is MERS corona. But it’s of course a strong signal if they used the MERS coronavirus assays.”
The above comments suggest that the PCR positive on the Jeddah camel may be due to a related beta2c coronavirus that is not >99% identical to the consensus sequence for the published human cases. However, comments by Ziad Memish and Gregory Hartl strongly suggest that the MERS PCR test was used to declare the camel positive.
The MERS PCR test is very different than the PCR test used to identify coronavirus sequences in bats, which date back to questions raised by the SARS outbreak in 2003. In that outbreak SARS-CoV sequences were identified in multiple species found in Hong Kong markets (such as civet cats and raccoon dogs). These sequences were almost identical to human sequences suggesting the interspecies jumps were linked to the proximity of the market animals and humans and did not represent the natural reservoir for SARS-CoV.
Consequently, a universal coronavirus probe was created to detect all know coronavirus sequences. This probe was directed against a conserved region of the RNA dependent RNA polymerase and therefore positives samples required sequencing to determine if the coronavirus was alpha, beta, or gamma, as well further divisions. This approach showed that many different types of coronavirus viruses were in bats, including a SARS-related series. The bat testing led to the dividion of betacornaviruses into four groups, including 2a for sequences similar to the human cold virus, OC43, and 2b for sequences closely related to SARS-CoV. Additional bat beta coronaviruses were classified as 2c and 2d.
The first confirmed MERS-CoV case (60M) had symptoms similar to SARS-CoV, but tested negative for all know human coronaviruses. However, PCR testing using the universal probe generated a positive, and sequencing identified a novel betacornavirus that was most closely related to bat coronavirus 2c sequences. The universal probe was also used to PCR confirm the second case (49M from Qatar who was diagnosed in England). Sequencing showed that it was 99.5% identical to the first case, confirming the discovery of a new human coronavirus. The full sequences were only 82% identical to bat beta 2c sequences from China. More closely related bat beta 2c sequences were subsequently identified in Europe and Africa, but the most closely related sequence had a 92.5% identity until the Bisha bat sequence was released, which was an exact match with the EMC/12 sequence from the Bisha case. However, only 203 BP were generated for the bat sequence (full sequences are over 30,000 BP).
The sequences from the first two human cases were used to create a new set of primers that are specific for MERS. PCR confirmation requires a positive result for two regions, and all MERS PCR positive human cases have yielded sequences that were >99.5 identical to the consensus sequence.
Thus, the comments by Ziad Memish and Gregory Hartl indicate the camel was MERS PCR positive, which was based on the same probes used to identify human cases and therefore signal MERS-CoV. The sequences from the camel and case will determine if the sequences are more than 99.9% identical, signaling interspecies transmission, but the use of the human MERS CoV test insures that the camel sample has MERS-CoV sequences.