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Commentary
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Betacornavirus Nomenclature
Recombinomics
Commentary 16:30
November 24, 2012
The above comment on nomenclature for the novel betacornavirus is incorrect. The name list above was assignede by the Health Protection Agency (HPA) to the short sequence from the first Qatar case (49M). The HPA has now released the full sequence for this isolate and changed London1 to England1. However, that name only refers to the sample from the Qatar case and is unrelated to the sample from the first confirmed fatal case from Saudi Arabia (60M) which was designated “human betacornavirus 2c EMC/2012”.
The naming of the isolates loosely follows name rules for influenza isolates, which is faithfully followed. Coronavirus isolate names, especially those for the novel cornaviruses in group 2c, are still in a bit of flux. SARS isolates mapped to group 2b and other human coronavirus like OC43 map to a group 2a. The mapping is generated by phylogenetic analysis of the sequences from the various isolates.
For influenza, the naming is quite straight forward. The first field lists the viral type (A, B , or C). The second field lists the species of origin (but left blank if the species is human). The third field lists the location of the isolate (location of the lab collecting the sample). The fourth field is the sample number (which may include letters defining multiple isolates from the same host or information linked to the lab of origin). The fifth field is the year of isolation. The name can also be followed by the serotype of the isolate.
However, samples from traveling hosts can have confusing locations. There are several recent examples for H3N2v isolates. In the fall of 2010 WHO issued a pager alert because two H3N2v cases had been identified. The alert cited cases from Illinois and Pennsylvania. The Illinois case gave a sample at Evanston Hospital (located in northern suburb of Chicago, Illinois). However, the sequence was designated A/Wisconsin/12/2010 (possibly because the case was a Wisconsin resident, attended an agricultural fair in Wisconsin, or linkage of a novel influenza to a large metropolitan city was alarming).
Other examples are confusing because of travel. A recent case who attended an agricultural fair in southern Indiana was treated at a hospital in northern Kentucky, leading to an isolate name of A/Kentucky/11/2012, even though Kentucky denied any H3N2v cases. Similarly, West Virginia residents attended an agricultural fair in Gallia, Ohio, but samples were given a West Virginia location because samples were collected at hospitals in Mason County, West Virginia.
Although all six of the confirmed betacornavirus cases involved individuals from Saudi Arabia or Qatar, at least three of the isolates were from samples collected or tested at hospitals in Europe, which is reflected in the name.
The first case was from Saudi Arabia, but the location was designated EMC (for Erasmus Medical Center). However, the isolate was not given a sample number, so a second isolate this year would create a naming problem.
Similarly, the isolate for first Qatar case was generated at the HPA in London, leading to the name cited above. However, the HPA has now generated a full sequence from this case and designated the isolate “coronavirus genotype 2c strain England 1”, which was abbreviated England1CoV in its most recent phylogenetic trees (which also included sample number H123990006).
The second Qatar case was hispitalized in Germany, while the Riyadh cluster involves two confirmed and two suspect cases, and samples for these cases, as well as the third case, which was also hospitalized in Riyadh, presumably were collected in Saudia Arabia.
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