Tuesday, June 27, 2017

HK CHP Avian Flu Report Week 25 & CIDRAP's BioRxiv Summary

H7N9 Epidemic Waves - June 14th - Credit FAO


In years past, by early May - or early June at the lastest - China's winter epidemic of H7N9 had run its course, and at most, we might see a dozen widely scattered cases over the summer (June through September). 
But this 5th epidemic wave - apparently driven by multiple genetic changes in the H7N9 virus - has been anything but ordinary.  In week 25, Hong Kong reports what would be a summer's worth of H7N9 cases (n=10) in any other year.
The virus's evolutionary changes are far from fully understood - and continue down several evolutionary pathways. But last night CIDRAP News published a summary by Lisa Schnirring of a new study in BioRxiv that describes several recent genetic changes in the virus.

A couple of excerpts, but follow the link to read it in its entirety.

Genetic analysis of H7N9 finds adaptations, clade patterns

Lisa Schnirring | News Editor | CIDRAP News
Jun 26, 2017

In the latest genetic analysis of H7N9 avian influenza samples from China, researchers said viruses circulating in the current fifth wave fall into two geographically separate clades of Yangtze River Delta lineages that have undergone substantial adaptation

Researchers have known that H7N9 forms two lineages, the Pearl River Delta (PRD) and the Yangtze River Delta (YRD). Most human cases in the current wave are from the YRD lineage, which aren't as reactive to existing candidate vaccine viruses. The YRD viruses have formed two subsets, YRD-1 and YRD-2.

Within the YRD-2 subset, the team observed two clades, one (YRD-2a) circulating in central and eastern China and the other (YRD-2b) mainly found in eastern Guangdong province, its likely origin. They said the YRD-2b clade also includes the recently identified highly pathogenic H7N9 viruses.


Call for close monitoring for spread

Analysis shows a higher rate of adaptation for YRD-2b, which the researchers said is concerning, given the emergence of highly pathogenic H7N9 within the clade. The investigators added that the highly pathogenic avian flu in domestic poultry can pose a serious risk, similar to what happened when H5N1 spilled back into wild birds, triggering the longest global outbreak to date.

(Continue . . . )

As we've seen in other studies this spring (see here, here, and here), the pace of H7N9's evolution and adaptation appears to be picking up. The recent spread - particularly of the newly emerged HPAI version (see OIE Confirms HPAI H7N9 In Heilongjiang Province), has raised new concerns that H7N9 may not remain just China's problem for much longer.

After dipping to just 5 new cases reported from the mainland two weeks ago, in week 25 China's NHFPC reported 10 cases, which Hong Kong's CHP summarizes below.

Avian Influenza Report
Avian Influenza Report is a weekly report produced by the Respiratory Disease Office, Centre for Health Protection of the Department of Health. This report highlights global avian influenza activity in humans and birds.

Reporting period: June 18, 2017 – June 24, 2017 (Week 25)
(Published on June 27, 2017)


  1. Since the previous issue of Avian Influenza Report (AIR), there were 10 new human cases of avian influenza A(H7N9) reported by the National Health and Family Planning Commission (NHFPC) from Beijing (2 cases), Sichuan (2 cases), Anhui (1 case), Guizhou (1 case), Hebei (1 case), Inner Mongolia (1 case), Jiangsu (1 case) and Tianjin (1 case). Since March 2013 (as of June 24, 2017), there were a total of 1548 human cases of avian influenza A(H7N9) reported globally. Since October 2016 (as of June 24, 2017), 742 cases have been recorded in Mainland China.
  2. Since the previous issue of AIR, there were no new human cases of avian influenza A(H5N6). Since 2014 (as of June 24, 2017), 16 human cases of avian influenza A(H5N6) were reported globally and all occurred in Mainland China. The latest case was reported on December 1, 2016.
  3. Since the previous issue of AIR, there were no new human cases of avian influenza A(H5N1). From 2011 to 2016, 10 to 145 confirmed human cases of avian influenza A(H5N1) were reported to the World Health Organization (WHO) annually (according to onset date). In 2017, there have been so far three cases in Egypt.*
 (Continue . . . )

As usual, we see the skewing towards older males, and mild cases are almost never reported. Between Mainland, Hong Kong, Macao and Taiwan - 750 cases have been reported since October - although it isn't known how many mild or asymptomatic cases go undetected.
For now, clusters are few, and human-to-human transmission has only rarely been reported. The virus, for all of its evolutionary strides, still hasn't adapted well enough to human physiology to spread effeciently.

How long that will hold true remains the $64 question.

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