The H7N9 Reassortment – Credit Eurosurveillance
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Like crime scene investigators looking to identify a killer, scientists are using modern laboratory tests on collected evidence to profile, identify, and hopefully halt the outbreak of H7N9 that has suddenly erupted in Eastern China.
One of the most sophisticated tools in their arsenal is genetic sequencing, which can often tell scientists where a virus has been, and just importantly, where it might be going.
Virologists know that viruses tend to produce single nucleotide substitutions as they replicate, and the longer that a virus circulates, the more of these point mutations it will accrue.
Some types of point mutations are more likely to occur when a virus replicates in an avian host, while others are more apt to show up when infecting a human or other mammalian host.
By looking at these specific genetic markers, they can often make intelligent guesses as to where the virus has been.
By the same token, some amino acid substitutions are known to increase a virus’s affinity for certain types of hosts, which can give us a clue as to where a virus might be heading.
Which brings us to a report, published today in the journal Eurosurveillance, that examines 7 H7N9 virus samples collected early in China’s outbreak and calculates the genetic distance between them.
The researchers then compared that genetic distance to samples collected from two other H7 outbreaks of the past (Italy H7N1 and Netherlands H7N7), in order to estimate how long this H7N9 virus may have been circulating.
First the link, abstract, and some excerpts (slightly reparagraphed for readability).
Rapid communications
Guiding outbreak management by the use of influenza A(H7Nx) virus sequence analysis
M Jonges , A Meijer, R A Fouchier, G Koch, J Li, J C Pan, H Chen, Y L Shu, M P Koopmans
The recently identified human infections with avian influenza A(H7N9) viruses in China raise important questions regarding possible source and risk to humans.
Sequence comparison with an influenza A(H7N7) outbreak in the Netherlands in 2003 and an A(H7N1) epidemic in Italy in 1999–2000 suggests that widespread circulation of A(H7N9) viruses must have occurred in China.
The emergence of human adaptation marker PB2 E627K in human A(H7N9) cases parallels that of the fatal A(H7N7) human case in the Netherlands.
<SNIP>In the current study, we compared the sequence diversity observed during the Dutch A(H7N7) outbreak and Italian A(H7N1) epidemic with the initial A(H7N9) virus sequences from the current outbreak in China.
The maximum genetic distance generated during the three months of the Dutch HPAI A(H7N7) outbreak in concatenated HA, NA and PB2 segments of A(H7N7) viruses was 25 nucleotide substitutions.
For the Italian LPAI A(H7N1) epidemic, the distance generated during a nine-month period was 66 nucleotide substitutions.
For the A(H7N9) outbreak strains, this genetic distance is 35 substitutions, or 21 substitutions when the outlier strain A/Shanghai/1/2013 is ignored (Figure).
<SNIP>
Conclusion
Comparative analysis of the first virological findings from the current outbreak of influenza A(H7N9) virus infection in China with those from other influenza A(H7Nx) outbreaks suggests that widespread circulation must have occurred, resulting in major genetic diversification.
Such diversification is of concern, given that several markers associated with increased risk for public health are already present. Enhanced monitoring of avian and mammalian animal reservoirs is of utmost importance as the public health risk of these A(H7N9) viruses may change following limited additional modification.
The genetic distance between samples collected in China suggest that this virus may have been circulating for months before it was finally detected, but in what host remains a subject of debate.
Also of concern to these researchers was the finding of the PB2 E627K mutation in the human isolates, but not in those collected from birds.
This substitution - the swapping out of the amino acid Glutamic acid (E) at position 627 for Lysine (K) – has been linked to increased influenza virulence in the past.
The authors write:
Remarkably, the PB2 segments of the four available human virus genome sequences from China all carry this E627K substitution, which is absent in the virus isolates obtained from birds and the environment [2]. In addition, three of the four infections with the virus with PB2 E627K were fatal. There are two plausible explanations for this observation:
- the mammalian adaptation markers are selected during replication in humans following exposure to viruses that do not have this mutation, which are circulating in animals;
- the mammalian adaptation markers result from virus replication in animals from which humans become infected.
The relatively protracted disease course in the current outbreak of A(H7N9) virus infection, with relatively mild symptoms at first, followed by exacerbation in the course of a week or longer, is suggestive of the first hypothesis, similar to the outbreak in the Netherlands.
In this scenario, an important difference in the A(H7N7) observations from the Netherlands is the frequency of finding the PB2 E627K mutation in humans (4/4 A(H7N9) sequenced patient strains compared with 1/61 sequenced A(H7N7) patient strains).
Therefore, an outstanding question is whether the A(H7N9) viruses are more readily mutating in humans or milder cases are being missed.
Contact investigations have found no mild cases and only one asymptomatic case), but in order to address this issue, more enhanced testing of persons exposed to a similar source is needed, using the most sensitive tests available on the optimal clinical specimen type obtained at the right time.
While this study adds substantially to our knowledge of this virus, we are still a long way from understanding where it came from, how it is circulating, and exactly how much of a public health threat it poses.
Still, it is absolutely remarkable that just a little over 2 weeks into this outbreak, we are seeing this type of in-depth research published online.
