H7N9 – Discussion, April 1, 2013 to June 3, 2013 (Closed)

[JJackson]

Re: H7N9 ?Discussion

Regarding the negative test results on undefined respiratory disease, or H7N9 contacts, etc.: If the primer is not set to look for H7N9 (assuming RT-PCR) or H7Nx, doesn't that mean they can acually miss it? But if a new primer can be developed quickly, I assume they can retest samples.

.

I briefly covered this in a link in the first post but this is in a little more detail. My understanding, which might be wrong, is that it depends on the labs equipment and staff. Simpler regional labs will have RT-PCR and staff trained to run a supplied primer against samples looking for matches. The 'supplied primers' are likely to sort out Type B, Type A and then differentiate the Type As into the seasonal flu sero-types H3N2 and H1N1. Our new flu would pass the Type A test but fail on both sero-types giving a 'Type A - un-subtyped' result. It was the increasing number of these returning from the Mexico boarder States of the USA at the start of the 2009 H1N1 pandemic that lead to its sequencing by the CDC in Atlanta. Note here that there was already an H1N1 test in these primers but the new strain was sufficiently different to not be a match. I recall reading at the time that prior to sequences being available - based solely on antigenic testing - the HA from H1N1(2009) would probably have been classified as an new sero-type and, presumably, been designated H17.
Samples of the 'Type A - unsubtyped' would then be forwarded to a lab with real time RT-PCR and primer generating capacity. They can then generate and test primers until they have a match, grow product to sequence and send out the new primer to the client labs which will then be able to correctly identify the new strain in their samples.
This link is to a beginners guide to RT-PCR produced by a company which sells kits for producing primers. They have a list of their kits at the end of the .pdf with a brief description of what each is capable of doing.

[JJackson]

Re: H7N9 ?Discussion

I have a sidescroll in this thread, probably due to the big picture in post #3.

Had the same problem but resolved it by shrinking my text font until it all fitted in one screen width. A better solution might be to use one of those natty scroll bars you use on some of your longer sequence list but I am not sure how you generate them. Just shrinking the graphic might lead to the sequence font becoming unresolvable, being bit-mapped rather than vectored.

[Giuseppe]

Re: H7N9 ?Discussion

HK SFH said that H7N9 virus gene sequences demonstrated that the virus has a 'signature' that indicates its ability to infect human. See main forum post... It remains sensitive to NAI drugs.

[sharon sanders]

Re: H7N9 ?Discussion

I have a sidescroll in this thread, probably due to the big picture in post #3.

I had these sidescrolls before, but I never read whether other
readers experience the same thing.
It also seems that they may be gone when I reboot but appear
again on the next reboot, unpredictable.

The lines are very long and you have to shift on the bottom bar
to read each line and then back for the next line.

And when you post the "edit","quote",save","go advanced" icons may be
far right, only visible after scrolling

that's why I usually use short lines, so the text is still readable
when someone adds big pictures

I moved that post to the archives where I am going to try to fix the side scroll. I will move the post back onto this thread afterwards.

[gsgs]

Re: H7N9 ?Discussion

well, we all know where to find the info, even if links are not allowed.

signature= E627K(PB2),Q226L(HA),new 5aa deletion in N9

quails have both receptors, quail/G1/1997 is one of the
H9-strains, see e.g. the Peiris paper.
But the new H7N9 is not from that strain

[Pathfinder]

Re: H7N9 ?Discussion

Hat tip: Diane Morin

Opinion

Is This a Pandemic Being Born?

China's mysterious pig, duck, and people deaths could be connected. And that should worry us.

BY LAURIE GARRETT |APRIL 1, 2013
...

On March 25, Chinese authorities seized manufactured pork buns that were found to be made from Zhejiang pigs that had died of the mysterious ailment. The possibly contaminated pork was in the Chinese food supply. By the end of March, at least 20,000 pig carcasses and tens of thousands of ducks and swans had washed upon riverbanks that stretch from the Lake Qinghai area all the way to the East China Sea -- a distance roughly equivalent to the span between Miami and Boston. Nobody knows how many more thousands of birds and pigs have died, but gone uncounted as farmers buried or burned the carcasses to avoid reprimands from authorities.

While environmental clean-up and agricultural authorities scrambled to remove the unsightly corpses and provide the anxious public with less-than-believable explanations for their demise, a seemingly separate human drama was unfolding. On Feb. 19, a man identified by Xinhua, China's state news agency, only as Li, an 87-year old retiree, was hospitalized in Shanghai with severe respiratory distress and pneumonia. On March 4, Li went into severe cardio-respiratory failure and succumbed.
...
According to Chinese authorities, some of the dead pigs tested antibody-positive for circoviruses, or PCV-2, and samples of the virus were isolated from Huangpu River. The implication was that the Shanghai pigs died of PCV-2, a type of virus that is harmless to human beings, as well as birds. Photographs of the carcasses reveal that the animals were large adult hogs, but PCV-2 does not kill adult pigs -- it is lethal to fetuses and newborn piglets.
...
The Chinese health authorities have to date offered no cause of death for the ducks and swans, failed to describe any unusual genetic features that might have turned the PCV-2 into an adult pig-killer virus, and insisted there is no connection between the pigs, people, and birds. Though the surviving woman, Han, had some contact with live chickens, according to Xinhua, neither Li nor Wu had any known contact with birds. Wu has been identified variously as a butcher, meat processor, and employee of a meat plant -- all of which might imply he had contact with pigs.
...
One very plausible explanation for this chain of Chinese events is that the H7N9 virus has undergone a mutation -- perhaps among spring migrating birds around Lake Qinghai. The mutation rendered the virus lethal for domestic ducks and swans. Because many Chinese farmers raise both pigs and ducks, the animals can share water supplies and be in fighting proximity over food -- the spread of flu from ducks to pigs, transforming avian flu into swine flu, has occurred many times. Once influenza adapts to pig cells, it is often possible for the virus to take human-transmissible form. That's precisely what happened in 2009 with the H1N1 swine flu, which spread around the world in a massive, but thankfully not terribly virulent, pandemic.

If the pigs, people, and birds have died in China from H7N9, it is imperative and urgent that the biological connection be made, and extensive research be done to determine how widespread human infection may be...
...
Full text:

http://www.foreignpolicy.com/articles/2013/04/01/is_this_a_pandemic_being_born_china_pigs_virus?page=0,3

[Emily]

Re: H7N9 ?Discussion

According to Chinese authorities, some of the dead pigs tested antibody-positive for circoviruses, or PCV-2, and samples of the virus were isolated from Huangpu River. The implication was that the Shanghai pigs died of PCV-2, a type of virus that is harmless to human beings, as well as birds. Photographs of the carcasses reveal that the animals were large adult hogs, but PCV-2 does not kill adult pigs -- it is lethal to fetuses and newborn piglets.

That doesn't seem to be true currently. PCV-2 can kill adult pigs.

http://www.flutrackers.com/forum/sho...0&postcount=23

Seems to be evolving more virulence per a couple of 2012 references:

Spread like a wildfire--the omnipresence of porcine circovirus type 2 (PCV2) and its ever-expanding association with diseases in pigs

Identification of an emerging recombinant cluster in porcine circovirus type 2

A duck circovirus has been identified in China, too.
Detection of duck circovirus in China: A proposal on genotype classification

Possible cross-species transmission of circoviruses and cycloviruses among farm animals

[Pathfinder]

Re: H7N9 ?Discussion

Opinion

Bird flu a reminder of things we dare not forget

SCMP Editorial
Wednesday, 03 April, 2013 [Updated: 03:29

...
Mainland authorities say there is no evidence of human-to-human infection, but the virus seems to have mutated and the circumstances are worrying. Two sons of one of the dead men contracted pneumonia and one died, although H7N9 was not found in either of them. The World Health Organisation says it is too early to rule out a link with dead pigs found floating in the Huangpu river, even if tests have not found it.

Hong Kong's secretary for food and health, Dr Ko Wing-man, says it remains important to find out if there has been human-to-human transmission. Tests showing the three did not infect each other raise the possibility of more than one infection source and he says it is also important to look out for epidemics among animals.
...
It took a month and three weeks before we learned of the deaths of the two men with H7N9. In light of the lack of information which left Hong Kong unprepared for Sars, this has prompted questions about the notification system set up to avoid a similar situation.
...

http://www.scmp.com/comment/insight-opinion/article/1205755/bird-flu-reminder-things-we-dare-not-forget

[Pathfinder]

Re: H7N9 ?Discussion

Hattip Giuseppe Michieli

World Health Organization
Frequently Asked Questions on human infection with A(H7N9) avian influenza virus, China

Updated 2 April 2013
...
3. Is this infection related to more than 16,000 pig carcasses recently found dumped in rivers around Shanghai?

While the dead pigs were part of the overall investigation, there was no evidence of any connection.
...

http://www.flutrackers.com/forum/showthread.php?t=202771

[JimO]

Re: H7N9 ?Discussion

Based on the timelines I've seen, the first two cases of H7N9 were contracted in mid- to late-February, but the dead pigs were not reported in the river until a couple of weeks later.

Hattip Giuseppe Michieli

World Health Organization
Frequently Asked Questions on human infection with A(H7N9) avian influenza virus, China

Updated 2 April 2013
...
3. Is this infection related to more than 16,000 pig carcasses recently found dumped in rivers around Shanghai?

While the dead pigs were part of the overall investigation, there was no evidence of any connection.
...
http://www.flutrackers.com/forum/sho...d.php?t=202771

[Catbird]

Re: H7N9 ?Discussion

Hattip Giuseppe Michieli

World Health Organization
Frequently Asked Questions on human infection with A(H7N9) avian influenza virus, China

Updated 2 April 2013
...
3. Is this infection related to more than 16,000 pig carcasses recently found dumped in rivers around Shanghai?

While the dead pigs were part of the overall investigation, there was no evidence of any connection.
...
http://www.flutrackers.com/forum/sho...d.php?t=202771

From an article I posted last night: http://www.flutrackers.com/forum/sho...0&postcount=56

Shanghai to strengthen the prevention and control of H7N9 avian influenza, the Shanghai Animal CDC today salvaged Huangpu River upstream float the dead pigs sampling Thirty-four retained samples for universal primers detection of avian influenza, avian influenza virus is not found."

Our thread about the dead pigs included reports that there were an estimated 15,000 dead pigs. I'm no statistician but 34 out of 15,000 seems to be an insufficient sample rate. I am curious if the WHO knows what, if any, additional testing was done.

The geographical dispersion of the cases makes it seem unlikely that the dead pigs in the river are the source - unless the virus has also become widespread in swine throughout the region. But, I think that more than 34 samples need to be tested before they can be ruled out.

[gsgs]

Re: H7N9 ?Discussion

they need to check the chickens, not pigs.
Mexico has to check the pigs.

[gsgs]

Re: H7N9 ?Discussion

you could as well argue that the virus having human markers is a good sign.
It doesn't transmit human to human seapite these markers.
So we needn't worry that it acquires the markers to imoprove
on that as with H5N1.

In poultry it probably circulates since quite some months
but isn't gone HP yet as we saw earlier in several outbreaks.
So it has some potential to go more virulent.

There could be lots of mild human cases without the virulence markers

[sharon sanders]

Re: H7N9 ?Discussion

Speaking of poultry....

Where is all the culling?

I have not seen one report that mentions any mass cullings.

Case #3 routinely went to a farm to shop for food and is where she possibly selected a chicken ill with H7N9. Where is the quarantine? The cleanup? The mass poultry cullings that are typical in a human outbreak of any avian influenza?

Am I missing something?

[gsgs]

Re: H7N9 ?Discussion

it's assumed to be LP in chickens
it also has the short cleavage site

we've seen in the past that this often converted to HP after some months, though.

asymptomatic chickens means, it's hard to find