The world is getting a clearer picture of the extent and shape of the recent flu outbreak as testing for the new virus ramps up. The results reveal that the virus has made it to a wide variety of locations globally, but it doesn't appear to be spreading rapidly within the population that has been exposed to infected individuals outside of Mexico. The results of some of these tests suggest that a vaccine should be a viable option, and the CDC is actively considering this prospect.
The World Health Organization released its latest update this morning which pegs the number of confirmed cases at 985 globally; the group has produced a nice map showing the details. The US, Mexico, and Canada continue to dominate the diagnoses, accounting for over 900 of the total cases. Still, more than 10 countries in Europe now have confirmed cases, as do a few of the nations south of Mexico and three countries around the Pacific rim. Outside of North America, however, it appears that the majority of these infections were picked up during travel to Mexico, rather than as a result of internal spread.
The same seems to be true in the US, where the majority of spread within the country occurred in a single school in New York City, despite confirmed cases appearing in over 30 states; shutting that school seems to have limited further spread. Still, the authorities at the Centers for Disease Control seem to think that the spread observed so far is not atypical for a flu virus. Lethality outside of Mexico appears to be very low, with only a single death in the US resulting from a case with Mexican origin.
One of the initial holdups when it comes to testing for the newly described virus is the complexity of the process. Because of the large genetic diversity of the flu virus (which we described earlier), the only thing that can be said using a simple antibody test is whether a given virus is influenza A. To learn more than that, you have to dive into the genetic material itself. But, as we noted, the flu virus uses RNA for its genetic material, which is much more difficult to work with than DNA.
According to CDC guidance, the accepted standard for testing of the new virus is a standard laboratory technique for working with RNA, one termed "Real Time RT-PCR." Basically, the virus' RNA is first converted to DNA using an enzyme reaction catalyzed by an enzyme called reverse transcriptase—the RT in the technique's name.
Once DNA is obtained, it becomes possible to do PCR, or polymerase chain reaction. That technique uses repeated cycles of a copying reaction to produce an exponential amplification of specific DNA sequences. The specificity, in this case, is provided by short pieces of DNA called "primers" that allow only sequences specific to a given virus to be amplified.
The real-time aspect takes place during the PCR reactions. Each reaction is spiked with a fluorescent dye that has properties that depend on the presence of a double-helical DNA molecule. There are more of these DNA molecules present as the PCR reaction proceeds, so it's possible to measure changes in fluorescence to track the progress of the reaction and extrapolate back to an estimate of how much DNA was present at the start. Real Time RT-PCR can, at least roughly, provide a measure of how much of a specific virus' RNA was present in a given sample.
The problem with all of this is that, although it's easy to buy a Real Time RT-PCR kit that provides all the needed enzymes and chemicals, actually using it requires lots of custom materials. These range from the equipment that controls the PCR reactions, which must have the lights and sensors to monitor small changes in fluorescence, down to the primers that are specific to a given flu virus. Not every health authority necessarily has a Real Time RT-PCR machine and, up until the sequence of this specific flu strain was determined, nobody had the primers.
According to the CDC, it has managed to use its public health emergency declaration to expedite getting the necessary reagents to public health authorities in various states, allowing testing to go on in local labs instead of requiring samples be sent to the CDC headquarters in Atlanta. That should help clear the testing backlog, especially as the spread of the virus appears to be reasonably limited at this point.
There's a general assumption that the flu outbreak—if it isn't already cresting—is likely to decline in the near future, as outbreaks of this sort tend to be prevalent during winter in the northern hemisphere. The big question is what we can expect from this strain of flu when winter rolls around. Nobody really knows for sure. Flu strains have been identified with various degrees of virulence and drug resistance, and it's distinctly possible that the virus could further adapt to human hosts over the next few months, so public health authorities are taking reasonable precautions.
The CDC has already restocked the doses of antiviral medication it distributed to the states last week, and it's putting the groundwork in place to develop a vaccine should one be deemed necessary. Complete sequencing of the viral DNA, which is now a small and inexpensive step beyond the RT-PCR testing described above, has been done with a variety of samples worldwide, and these indicate that all the circulating viruses are 99-100 percent identical. This should make producing a specific vaccine less of a challenge than it might otherwise be.
Continued isolation and sequencing will be key to getting a sense of the virus' evolution in the coming months, revealing things like its mutation rate and the accumulation of changes that might help it adapt to human hosts. In the meantime, the worries over the current outbreak have at least allowed public health authorities to reiterate some basic messages that will be useful whatever develops: wash your hands often, cover your mouth when sneezing and coughing, and stay at home when you're sick.