Mike Coston at Avian Flu Diary has a very useful survey of recent flu news: Bird Flu: Confusing Reports Out Of Indonesia. Go read it.
Archive for March, 2011
[Avian Flu Diary] Bird Flu: Confusing Reports Out Of Indonesia
On March - 1 - 2011
(Tue, 01 Mar 2011 12:05:00 +0000)
# 5346
While confusing bird flu reports out of Indonesia are not exactly unusual, most of the time ambiguities arise from the use of machine-translation software to convert Indonesian (Bahasan) to something resembling English.
These translations can usually deliver the gist of a story, but are far less reliable when it comes to details. Which is why I often prefer to wait until we can get an English language report from the Jakarta Post, or Antara News before posting.
But today, as you’ll see, even those sources are capable of generating confusion.
A sampling of English language reports follows, along with a bit of discussion about why the virus remains rife in Indonesia.
First, from the Jakarta Post we get a report that alludes to there having been 41 human cases of bird flu since the start of the year.
A remarkable number, unless (as I suspect) they simply omitted the word `suspected’ from the story.
Given the media attention that a cluster of 7 cases in 2006 evoked, pending further information, I’m not quick to assume that all of these cases have been laboratory confirmed.
Here is the lede from the story:
New bird flu cases strike 11 regencies in West Java
Yuli Tri Suwarni, The Jakarta Post, Bandung | Tue, 03/01/2011
New bird flu cases have been detected in 11 of West Java’s 26 cities and regencies. Experts are blaming a lack of public awareness about the importance of cleanliness when handling poultry coupled with the effects of climate change.
Since Jan. 4, 2011, there have been 41 reported avian flu infections in humans in Indonesia, with nearly 33,929 chickens dead from the virus.
From Ida at BFIC - a joint project of Kobe University in Japan and the Institute of Tropical Disease, Airlangga University, Indonesia – we get some excellent analysis of the above story, and a nicely done graphic showing 11 regencies in West Java currently combating bird flu outbreaks.
West Java ::: H5N1 spreads in 11 regencies
Posted by Ida on March 1, 2011
The Jakarta Post is covering current bird flu situation in West Java province. It mentioned about H5N1 spreading in 11 regencies: Bekasi, West Bandung, Purwakarta, Majalengka, Sukabumi, Kuningan, Indramayu, Garut, Depok, Bogor and Sumedang.
Again, unpredictable weather and lack of public awareness are the main causes of disease-spreading. The article also mentioned about 41 reported avian influenza infection in human since January 2011. This is rather vague, is the article talking about “suspect” patients or actually confirmed (and reported) cases?
To date, household chicken farming, which is done with very low biosecurity practice, is common Indonesia. Chickens are raised free-ranged and cage-less, and many news articles mentioned about H5N1-infected chickens dropped dead from the tree branches, where chickens were sleeping on at night.
This is one of the factors of continuous H5N1 outbreak in Indonesia birds.
-adm-
In another English report from West Java, provided this time by Antara News, we learn that vaccine shortages in the Cirebon District leave more than 90% of the domestic poultry unprotected against the H5N1 virus.
But, as you’ll see, the numbers don’t add up.
Bird flu continuing to menace Cirebon district
Tue, March 1 2011 14:44 | 194 Views
Sumber, W Java (ANTARA News) - Cirebon district in West Java remains vulnerable to bird flu infection because of the local government`s limited capability to vaccinate chickens, an official said.
The district`s related authorities need to keep monitoring the threat of bird flu in a sustainable way partly due to the area`s big chicken population, Enjuswatiningsih said.
Speaking to newsmen here Tuesday, Enjuswatiningsih, head of Cirebon district`s agriculture, plantation, livestocks, and forestry office, said the district had 2.2 million ducks and chickens.
However, the related authorities could only vaccinate 20,000 chickens and ducks or just about seven percent of the total population annually, she said.
Three numbers: 2.2 million birds, 20,000 vaccinations, and 7% coverage.
One or more must be wrong.
Vaccinating 7% of 2.2 million birds would require 154,000 doses, not 20,000. And if you could only vaccinate 20,000 birds, you’d have a coverage of less than 1% . . . not 7%.
But mangled math aside, as a practical matter it probably makes little difference whether the district has 1% or 7% vaccine coverage. In either scenario it would leave in excess of 2 million chickens and ducks unvaccinated in Cirebon.
While China, Egypt, Vietnam, and Indonesia all rely heavily on bird flu vaccinations to protect their massive poultry operations, most countries have embraced culling as the preferred method of control.
Vaccines can allow low-grade, asymptomatic infections to go undetected in flocks, and spread to other birds. And over time, the virus can drift enough to evade the vaccines in use.
Dr. C.A. Nidom, whose name has appeared often in this blog, was quoted two years ago in Poultry Indonesia as saying:
Poultry Indonesia Printing Edition, March 2009
(excerpts)
Chairul Anwar Nidom, a virologist with the Tropical Disease Centre at Airlangga University in Surabaya, said a common policy on bird flu was lacking among government agencies, making controlling the disease more difficult.
Nidom criticized the government’s policy of vaccinating poultry rather than culling, believing that it masks the virus, and ultimately contributes to its mutation.
In 2009 the OIE (World Organization For Animal Health) reaffirmed their long-standing position that vaccination of poultry cannot be considered a long-term solution to combating the avian flu virus.
In Avian influenza and vaccination: what is the scientific recommendation?, the OIE reiterates their strong recommendation that humane culling be employed to control avian influenza, and advising that vaccines should only be used as a temporary measure.
But for countries where poultry represents a large part of their food security, and where small holdings and backyard chickens are common, culling can be politically and economically a difficult policy to maintain.
As far as the current situation on the ground in Indonesia is concerned, we’ll simply have to wait for better information.
Stay tuned.
[Avian Flu Diary] PNAS: Reassortment Of H1N1 And H9N2 Avian viruses
On March - 1 - 2011
(Tue, 01 Mar 2011 01:36:00 +0000)
# 5345
We’ve a study published today in PNAS that is shedding new light on the possibility of seeing a biologically `fit’ and virulent novel virus emerge from a reassortment between the H9N2 avian flu and the (former) pandemic H1N1 swine flu.
Researchers in China – using reverse genetics – created 127 hybrid viruses in the laboratory and tested them on mice for compatibility, replication ability, and virulence.
They found that half of the hybrid viruses were biologically `fit’ as far as replication goes, and 8 hybrids were significantly more pathogenic than either of their parental viruses.
A link to the study, followed by excerpt from the abstract, and then I’ll return with more.
High genetic compatibility and increased pathogenicity of reassortants derived from avian H9N2 and pandemic H1N1/2009 influenza viruses
Yipeng Sun,Kun Qin, Jingjing Wang, Juan Pu, Qingdong Tang, Yanxin Hu, Yuhai Bi,Xueli Zhao, Hanchun Yang, Yuelong Shu, and Jinhua Liu
Abstract
H9N2 influenza viruses have been circulating worldwide in multiple avian species and repeatedly infecting mammals, including pigs and humans, posing a significant threat to public health. The coexistence of H9N2 and pandemic influenza H1N1/2009 viruses in pigs and humans provides an opportunity for these viruses to reassort.
<SNIP>
Our results indicate that some avian H9-pandemic reassortants could emerge with a potentially higher threat for humans and also highlight the importance of monitoring the H9-pandemic reassortant viruses that may arise, especially those that possess the PA gene of H1N1/2009 origin.
When it comes to pathogenicity of flu viruses, mice are reasonably good test subjects . . . but are not necessarily the best physiological surrogates for humans.
The authors of this study are quoted in the media as saying their next step is to repeat these experiments with ferrets and guinea pigs, lab animals that have more human-like respiratory systems.
We’ve discussed reassortment many times before, so those familiar with the concept may wish to skip ahead.
Shift, or reassortment, happens when two different influenza viruses co-infect the same host swap genetic material.
Influenza A viruses have 8 gene segments (PB2, PB1, PA, HA, NP, NA, M1, M2, NS1, NS2).
Which means that any two compatible influenza viruses could conceivably – and under the right conditions – generate more than 250 different combinations by swapping one or more of their 8 (potentially) interchangeable gene segments.
The key words being “under the right conditions”.
If it were easy, or a common occurrence, we’d be up to our hip boots in new, reassorted viruses all the time.
But it happens often enough that we recognize it as a real threat. Shift is how new pandemic strains are born, and it was precisely the mechanism that created the 2009 `swine’ flu strain.
While the novel H1N1 `swine flu’ virus needs no introduction, the H9N2 avian virus is less well known. It is endemic in poultry across Asia, and while rare, we have seen a handful human infections.
How often humans are really infected is unknown, since surveillance and testing among poultry farmers in China is practically non-existent.
A few notable H9N2 stories from the past include:
- In December 2008 I ran a blog featuring an interview in which world famous Hong Kong virologist Malik Peiris cautioned that the H9N2 virus may be circulating far more commonly than we believe. Revisiting A Malik Peiris Interview On H9N2
- A little over a year ago, in H9N2: The Other Bird Flu Threat, I wrote about the World Health Organization recommending the creation of a candidate vaccine virus for H9N2. According to the latest vaccine update from the WHO, work continues on that candidate vaccine virus.
- And just this past November, in Study: The Continuing Evolution Of Avian H9N2, we looked at computer modeling that suggested that the H9N2 virus moving towards becoming more `human-adapted’.
Today’s PNAS study, like many others before it . . .
EID Journal: H1N1 Reassortment Possibilities
. . . point out the potential for nature’s laboratory to come up with new, and potentially devastating, flu strains through genetic reassortment. Granted, less virulent hybrid flu strains are also a possibility.
While we may not be able to stop the next pandemic from happening - knowing which dangerous hybrids to look for, and conducting aggressive global surveillance - may help us detect the next outbreak at the earliest possible moment.
And a few extra week’s warning could make all the difference between having a vaccine in time to mitigate the pandemic’s peak, or having it arrive after the worst had passed.
[Crof's H5N1] H1N1 and bird flu virus produce dangerous hybrids: Chinese researchers
On March - 1 - 2011
Via Reuters, a report from one of Asia’s best medical reporters, Tan Ee Lyn: H1N1 and bird flu virus produce dangerous hybrids. Note that the bird flu virus in question is H9N2, not H5N1. Excerpt:
The H1N1 swine flu virus is compatible with a bird flu virus that is endemic in poultry in Asia and they can produce hybrid viruses packed with greater killing power, Chinese researchers warned on Monday.
The scientists made 127 hybrid viruses by mixing genes of the H1N1 and the avian H9N2 virus in a laboratory, and eight of the hybrids turned out to be more virulent than either parents when tested in mice.
The H1N1 pandemic of 2009 turned out to be milder than feared and human infections of H9N2 in China in the past are not known to have caused severe disease.
But the experts said their hybrid offspring - or “reassortants” - cannot be casually dismissed.
“The main message is that the H1N1 can combine in certain ways with the H9N2 to create reassortants and some of the viruses had an increased pathogenicity comparing with the parent viruses in mice,” lead author Jinhua Liu, of the College of Veterinary Medicine at the China Agricultural University in Beijing, wrote in an email to Reuters.
Liu and his colleagues, who published their findings in the Proceedings of the National Academy of Science, warned in their paper: “The possibility of novel pandemic strains being generated from reassortment between avian H9N2 and H1N1/2009 influenza viruses exists.”
[Crof's H5N1] Indonesia: B2B H5N1 in 11 West Java regencies
On March - 1 - 2011
Via The Jakarta Post, some worrying news: New bird flu cases strike 11 regencies in West Java. Excerpt:
New bird flu cases have been detected in 11 of West Java’s 26 cities and regencies. Experts are blaming a lack of public awareness about the importance of cleanliness when handling poultry coupled with the effects of climate change.
Since Jan. 4, 2011, there have been 41 reported avian flu infections in humans in Indonesia, with nearly 33,929 chickens dead from the virus.
West Java Animal Husbandry Office head Kusmayadi said Monday that the virus was spreading because of the unpredictable weather.
The public’s awareness of the importance of cleanliness in poultry sheds has also dropped significantly.
The largest number of chicken deaths was found in a poultry shed in Sukabumi, where 30,000 chickens had died.
“Raining, dry, raining, dry. The weather has strengthened the attacking power of the virus at a time when public awareness is diminishing,” Kusmayadi said.
The 11 cities and regencies struck by the new bird flu outbreaks were Bekasi, West Bandung, Purwakarta, Majalengka, Sukabumi, Kuningan, Indramayu, Garut, Depok, Bogor and Sumedang.
The latest case was in Garut, where 1,000 chickens raised in residents’ yards were reported to have died since Jan. 12, 2011, because of the virus.
“They were late to report [the deaths] and the chicken carcasses were thrown randomly in open fields,” Garut Animal Husbandry Office head Dida K. Endang said.
Garut General Hospital has also been treating two patients since last week suspected of having bird flu. The two patients were a 49-year-old and a nine-month-old infant.
The two had high fevers reaching 38 degrees Celsius and were suffering from breathing problems. The results of blood tests were not yet available, Garut Health Office head Dede Rohmansyah said.
“There have been 163 patients suffering from influenza-like illnesses in the areas where dead chickens were found. But, hopefully, they are not infected with bird flu,” Dede said.
I should hope not! Scores of human H5N1 cases suddenly breaking out in one area would be really alarming.