Path: ...!2.eu.feeder.erje.net!feeder.erje.net!feeds.news.ox.ac.uk!news.ox.ac.uk!nntp-feed.chiark.greenend.org.uk!ewrotcd!news.eyrie.org!beagle.ediacara.org!.POSTED.beagle.ediacara.org!not-for-mail
From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: H5N1 genotype D1.1
Date: Sat, 28 Dec 2024 11:28:03 -0600
Organization: A noiseless patient Spider
Lines: 251
Sender: to%beagle.ediacara.org
Approved: moderator@beagle.ediacara.org
Message-ID: <vkpcf1$eam1$1@dont-email.me>
References: <vkn6ja$3qt4b$1@dont-email.me>
 <U6OdnRXCV-Eb3fL6nZ2dnZfqnPednZ2d@giganews.com> <vkp0th$bndj$1@dont-email.me>
Reply-To: rokimoto557@gmail.com
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8; format=flowed
Content-Transfer-Encoding: 8bit
Injection-Info: beagle.ediacara.org; posting-host="beagle.ediacara.org:3.132.105.89";
	logging-data="82439"; mail-complaints-to="usenet@beagle.ediacara.org"
User-Agent: Mozilla Thunderbird
To: talk-origins@moderators.isc.org
Cancel-Lock: sha1:i3sKNZKMCD8AFHsRXF/y2UOt+RE=
Content-Language: en-US
In-Reply-To: <vkp0th$bndj$1@dont-email.me>
Bytes: 17434

On 12/28/2024 8:10 AM, RonO wrote:
> On 12/27/2024 6:04 PM, *Hemidactylus* wrote:
>> RonO <rokimoto557@gmail.com> wrote:
>>> https://www.cidrap.umn.edu/avian-influenza-bird-flu/cdc-h5n1- 
>>> mutations-severely-ill-patient-could-boost-spread-risk-remains
>>>
>>> There has been a second severe case of H5N1 infection involving the D1.1
>>> genotype thousands of miles from each other.  In British Columbia a
>>> teenager was in critical condition with an H5N1 D1.1 infection.  The
>>> virus had two mutations that made it more infective in humans and it was
>>> a respiratory infection in that case.  The claim was that the two
>>> mutations occurred in the infected individual and the mutant took over
>>> to cause the severe infection.
>>>
>>> Another H5N1 D1.1 infection has occurred in Louisiana, and that patient
>>> also has mutations that account for the severity of the infection, that
>>> are not found among local wild birds, and they claim that they likely
>>> occurred within that individual.  Two such cases likely means that there
>>> is either a human adapted variant already existing, or that these
>>> mutations commonly occur, and the genotype D1.1 may already be a
>>> respiratory infection, so the two mutations would already be replicating
>>> in the tissue that they would better adapt the virus to infect.
>>>
>>> The Dairy virus is genotype B3.13.  Half it's genome comes from two
>>> other strains of influenza (one high path and one low path).  D1.1 is
>>> also a reassorted virus, but I can't find where the genotype is defined.
>>>   Both virus still retain the H5 and N1 genes of the Asian avian
>>> influenza virus that had 50% mortality in infected humans, but some of
>>> their genomes come from other virus strains.  The dairy virus human
>>> infections are mostly limited to eye infections, so the virus may not be
>>> replicating in respiratory tissue. B3.13 is only one mutation away from
>>> becoming more infective in humans, but somehow that mutation hasn't yet
>>> occurred in any infected human.  It may be that the mutation would not
>>> have an advantage replicating in mammary glands and tear ducts.
>>>
>>> The D1.1 genotype is likely replicating in tissue where the mutations
>>> would be selected for and would take over the infection of the host.
>>>
>>> The CDC is currently not differentiating the dairy infection from the
>>> D1.1 infections, but they should track them separately.  Both D1.1
>>> infected individuals are seriously ill, but the B3.13 infected
>>> individuals only have mild symptoms, mostly eye irritation.
>>>
>>> https://www.cdc.gov/bird-flu/situation-summary/index.html
>>>
>> You should post this stuff to Bluesky or elsewhere with a greater reach
>> than here.
>>
> Everything that I put up is already out on the web.  I do make my own 
> comments about it.
> 
> What is sad about this current fiasco is the suppression of the data, 
> and interpretations are suppressed of what is put out.  I haven't seen 
> an epidemiological analysis of the viral sequences since the first one 
> put out early in the infection when only around 8 states had been 
> identified to be infected.  They have all the sequences and should be 
> updating the phylogeny and determining how the virus is spreading at 
> least weekly, but that doesn't seem to be done.  That first study pretty 
> clearly indicated that dairy workers were likely spreading the virus. 
> New Mexico, Kansas, and South Dakota had not gotten cattle from Texas, 
> but they had somehow been infected by Texas strains.  Kansas and South 
> Dakota seemed to have been infected by the same viral lineage.  The CDC 
> and USDA refused to establish worker testing and contact tracing.  As 
> stupid as it may be contact tracing was only started in California and 
> resulted in the identification of a large number of infected dairies 
> indicating that all the other states had under estimated the infected 
> dairies in their states because they refused to look for them.  The USDA 
> finally started to assist California in contact tracing, and found so 
> many infected herds that they claimed that they were going to start bulk 
> milk tank testing in all infected states, but that never happened.  A 
> month later the USDA claimed that they were going to start bulk milk 
> tank testing in half a dozen states, and the list included some states 
> that had not admitted to have infected herds, but it left out the states 
> that should have been tested like Washington, Florida and Missouri that 
> were known to have the dairy virus in their states, but had not admitted 
> to having infected herds.
> 
> The press seems to just parrot what the USDA and CDC put out.  I still 
> can't understand why the October CDC article claiming that the virus 
> could survive the most common form of pasteurization has not gotten more 
> press coverage.  The CDC article recommended that the milk supply should 
> be reevaluated (the FDA claim was that pasteurization killed the virus). 
>   The FDA did respond immediately, but published a bogus protocol that 
> was asking for volunteer processing plants.  Nothing has come out of the 
> FDA in the last 2 months.  In order to test the milk supply adequately 
> the FDA needed to go to processing plants that were accepting infected 
> milk, evaluate the milk as it came in and after pasteurization.  They 
> needed to evaluate the entire process to see if there were any weak 
> points like start up, maintenence, and shift changes.  It only takes a 
> few gallons of milk to not be processed correctly to account for the 
> sick child in California and the Missouri patients that did not have 
> contact with cattle, but did drink milk, and if the CDC was correct and 
> viable infective virus is surviving the 72 degree C pasteurization, the 
> method needs to be modified so that it does kill all the virus 
> routinely.  99% effective is probably not effective enough.
> 
> https://wwwnc.cdc.gov/eid/article/30/11/24-0772_article
> 
> QUOTE:
> Abstract
> Highly pathogenic avian influenza A(H5N1) detected in dairy cows raises 
> concerns about milk safety. The effects of pasteurization-like 
> temperatures on influenza viruses in retail and unpasteurized milk 
> revealed virus resilience under certain conditions. Although 
> pasteurization contributes to viral inactivation, influenza A virus, 
> regardless of strain, displayed remarkable stability in pasteurized milk.
> END QUOTE:
> 
> They found that infective virus survived 72 degree for 15 to 20 seconds, 
> and survived as infective virus in refrigerated milk for 4 days (the 
> extent of the trial, the virus likely survives for more than 4 days).
> 
> I do not understand why this study is not cited in the cases of the 
> California child and the two Missouri cases.  The FDA is still silent 
> about their reevaluation of the milk supply that they claimed that they 
> were starting in early Nov..  The FDA claimed to be responding, but the 
> press never did.
> 
> https://www.fda.gov/food/alerts-advisories-safety-information/ 
> investigation-avian-influenza-h5n1-virus-dairy-cattle
> 
> QUOTE:
> 10/3/2024 - Silo Study
> Since the onset of the Highly Pathogenic Avian Influenza A H5N1 (H5N1) 
> outbreak in dairy cattle earlier this year, researchers across the 
> federal and state governments have been working to understand the 
> prevalence of H5N1 in the U.S. milk supply. This week, states were 
> invited to participate in a new study that will generate data to aid in 
> the understanding of the prevalence of H5N1 in bulk raw cow’s milk 
> received by dairy processing facilities across the nation. Dubbed “the 
> silo study,” the information garnered from this research can help inform 
> the national strategy to control the spread of the virus to other dairy 
> cattle and avian flocks, and to identify any viral transformations.
> END QUOTE:
> 
> The FDA claims to have initiated the Silo study the day that the CDC 
> released their Nov. newsletter (Oct. 3rd) containing the research 
> article.  The CDC and FDA had obviously been in contact before the 
> release of the CDC research article.  In early Nov. the FDA claimed that 
> they were starting it, but it is now the end of December and nothing has 
> come out of this effort.  If you read the research protocol you should 
> understand that the study was designed to fail to adequately test the 
> milk supply.  The processing plants that do not volunteer that likely do 
> not have their plants up to specifications, and are more likely to have 
> other issues like training and quality control, are the plants that you 
> want to evaluate.  You do not want volunteer dairies, but you want the 
> dairies sending in infected milk.  Dairies are supposed to take sick 
> cows out of the milk supply.  You want the dairies that are not doing a 
> good job of identifying sick cows, not the dairies that say it is OK to 
> test their milk.
> 
> Ron Okimoto
========== REMAINDER OF ARTICLE TRUNCATED ==========