Dr Niman Comments from Recombinomics (Oct 2006)
Posted in: darrelrussell.com edit
08 Jan 2009
| H5N1 Outbreaks in Ningxia Hui and Inner Mongolia Recombinomics Commentary October 4, 2006 A new outbreak of bird flu has killed about 1,000 poultry in northern China in the second such case in a week, state media reported on Wednesday. Some 72,930 domestic poultry have been slaughtered and the outbreak is now under control, Xinhua news agency said. Laboratory tests had confirmed the H5N1 strain of the virus, which can be deadly to humans, it added. The outbreak, in Henan New Village in Yinchuan, regional capital of the desert-like Ningxia Hui region, follows a similar occurrence in neighbouring Inner Mongolia. The two H5N1 bird flu outbreaks in northern China is not a suprise. Over the summer there was a massive die-off of waterfowl in Tuva (http://www.recombinomics.com/News/06270601/H5N1_Tuva.html) in southern Siberia and northern Mongolia. The Qinghai strain was isolated and the H5N1 was rapidly evolving. The later samples could be distinguished from the earlier sequences (http://www.recombinomics.com/News/07260601/H5N1_Tuva_Mongolia.html), signaling significant recombination. New sequences create new problems. Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11278) Phylogenetic Trees (http://www.recombinomics.com/phylo.html) http://www.recombinomics.com/News/10040603/H5N1_Northern_China.html | |||||||||
Recombinomics Commentary
October 20, 2006
There is a state of panic among citizens Governorate Western fear of the spread of the bird flu pandemic. The Directorate of Health called the detention of sick Ula Abdel Razek, 28 years housewives and evaluates Enberoh city of Dakahlia Governorate in hospital.
Pathogenesis of Mahala under suspicion بانفلونزا infected birds. Been sent a sample of blood for examination by central labs in Cairo. As has been sampling from all Almkhalten them. This is the third case that emerged in the province within days.
The above translation provides detail for a second suspect H5N1 bird flu victim in Egypt, and mentions a third case. The first case has been confirmed (http://www.recombinomics.com/News/10100601/H5N1_Egypt_Confirmed.html) by WHO on October 11 (http://www.who.int/csr/don/2006_10_11/en/index.html), and several outbreaks have been reported in Egypt (http://www.recombinomics.com/News/09040602/H5N1_Egypt_2.html), as well as neighboring Sudan (http://www.recombinomics.com/News/09120601/H5N1_Sudan_2.html).
These cases coincide with migratory birds head south for the fall and winter and raise questions about the lack of H5N1 reports in Turkey and other countries in the Middle East. H5N1 was confirmed in Turkey and Romania in October, 2005 and H5N1 in Siberia over the summer indicates a new wave of H5N1 infections would be expected at this time in the same regions as reported in 2005. The only country reporting H5N1 this season is the Ukraine (http://www.recombinomics.com/News/09040603/H5N1_Ukraine_2.html). Last season, many countries failed to report H5N1 until after fatalities were reported in humans in Turkey in early January, 2006.
Reporting failures in these areas this season highlights major questions about surveillance and transparency in these countries again this season.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11473)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10200601/H5N1_Egypt_3.html
Recombinomics Commentary
October 30, 2006
A suspected case of human bird flu has been reported in the northern Egyptian governorate of Gharbiyah, raising the number of possible infected humans in the area to five, al-Ghomhuria reported, citing a local
hospital.
A 23-year-old woman in the city of Tanta was suspected of having symptoms of avian flu and was transported to a local hospital
The above translation indicates that the number of suspect bird flu cases in the Gharbiyah governorate continue to rise. The only confirmed (http://www.who.int/csr/don/2006_10_11/en/index.html) case (39F (http://www.recombinomics.com/News/10100601/H5N1_Egypt_Confirmed.html)) from Samanoud has died today (http://today.reuters.com/News/CrisesArticle.aspx?storyId=L3068642), one month after developing symptoms. The H5N1 HA sequence from this patient has been released, and it has a polymorphisim, M230I (http://www.recombinomics.com/News/10220603/H5N1_M230I.html), which is adjacent to the receptor binding domain.
Although reports on the latest fatality cite negative tests on relatives, the increasing number of hospitalized patients (http://www.recombinomics.com/News/10200601/H5N1_Egypt_3.html) in the area is cause concern.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=12251)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10300601/H5N1_Egypt_Increase.html
Recombinomics Commentary
October 26, 2006
Researchers from Beijing Genome Institute have released approximately 300 H5N1 sequences this month. The sequences are from poultry, wild birds, and swine (http://www.recombinomics.com/News/10190601/H5N1_China_Swine_Evolution.html) and define the evolution of H5N1 in China. A series of sequences was deposited February 28, 2005 at Genbank under the title “A cohort of AIV H5N1 subtypes isolated from wild aquatic birds and domestic poultry revealed rapid transmission, frequent reassortment, and identifiable recombination events“. The recent sequences confirm (http://www.recombinomics.com/News/10050603/H5N1_Recombination_Confirmation.html) the earlier clear cut examples of recombination (http://www.recombinomics.com/News/03090602/H5N1_Recombination_Guangdong_NA.html), and extend and expand the earlier observations back to 1997 through isolates from 2004.
One striking example of recombination can be seen in A/chicken/Jilin/hl (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=Search&dopt=DocSum&term=txid404167%5BOrganism:noexp%5D)/2004(H5N1). Although the isolate has an H5 that has origin tarcing back to the first H5 in the 1996 Guangdong goose, and the N1 is similar to NA in in genotype G+, as seen in human isolates from 2003 from patients in Hong Kong who had visited Fujian Province, the remaining six gene segments have extensive regions of identity with H9N2 isolates from China the mid and late 1990’s (see deatils here (http://www.flutrackers.com/forum/showthread.php?t=12082)). The large stretches of identity were similar to the identities found between Canadian swine 2004 PB2 (http://www.recombinomics.com/phylo/Canadian_Swine_PB2.html) and PA (http://www.recombinomics.com/phylo/Canadian_Swine_PA.html) isolates and 1977 swine sequences from Tennessee. The sequence fidelity for over 25 years in Canada or 10 years in China, raises serious questions about the importance of random mutations in seasonal variation of seasonal and pandemic flu.
Similarly, the extensive regions of identity with H9N2 were not due to reassortment, which shuffles who gene segments but does not change the gene sequence. Each of the 6 gene segments had regions of identity with H5N1 isolates in addition to regions from H9N2 isolates, indicating that each of the six gene segments was generated by homologous recombination.
Although clear cut examples of recombination in H5N1 fro Hong Kong had been reported previously (see slides linked here (http://www.recombinomics.com/presentations.html)), the sequences from China show that the frequency is markedly higher than indicated by the sequences in the databases at GenBank or Los Alamos. Most of the sequences from Hong Kong or China are partial sequences, which can generate strong bias in the database, especially if the withheld regions represent “unexpected” results based on the submitted sequences. These partial sequences would then under represent the frequency or importance of recombination in the evolution of H5N1 and would also impact the development of vaccine based on the recombination in H5N1 isolates.
Similarly, the withholding of new sequences such as the Qinghai sequences generated by Weybridge from European samples collected in 2005 or early 2006, also limits analysis.
To date, most analysis by WHO and consultants have focused on what was thought to be random mutations. These new data from China support the view that the polymorphisms in H5N1 are not due to recent mutations and are far from random. These polymorphisms can be readily found in the expanding database and are present in earlier isolates in subtypes and locations which would be likely to donate new polymorphisms via homologous recombination and there are predictable.
The new sequences from China with identifiable recombination, including recombination between H5N1 and H9N2, highlight the need for a robust database of full sequences. Recently full H5N1 Qinghai sequences have been generated through the NIAID influenza sequencing project. This project has also been used to generate full sequences from avian serotypes other than H5N1. the failure to generate full sequences of H5N1 in Asia generated by St Jude and Hong Kong University and release of H5N1 sequences hoarded by Weybridge remain a cause for concern and impeded the development of vaccines targeting immerging pandemic H5N1 strains.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=12082)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10260601/H5N1_H9N2_N_China.html
Recombinomics Commentary
October 10, 2006
The woman, 39-year-old Hanan Aboul Magd of the Nile Delta province of Gharbiya, has been in hospital since October 4 and has been treated with the drug Tamiflu, state news agency MENA said.
The woman was on a respirator but her condition was stable
MENA reported that the newly infected woman had raised a flock of 11 ducks from her home north of the Egyptian capital. Two became sick and died, and she then slaughtered the rest before she was hospitalized.
Chickens on rooftops may be particularly susceptible to catching the virus from infected migrant birds, which fly along the densely populated Nile valley during migration, experts have suggested.
The above confirmation of the first human H5N1 bird flu case this season in Africa is not unexpected. Recently Egypt reported new H5N1 infections in birds in several locations (http://www.recombinomics.com/News/09040602/H5N1_Egypt_2.html), and birds should be migrating into the area. The Ukraine has also reported (http://www.recombinomics.com/News/09040603/H5N1_Ukraine_2.html) recent H5N1 outbreaks as has Sudan. (http://www.recombinomics.com/News/09120601/H5N1_Sudan_2.html).
Last season H5N1 infections were reported in Romania and Turkey in October. Although H5N1 had migrated into Europe, the Middle East, and Africa, most countries, including Egypt, did not report H5N1 until human fatalities were confirmed in Turkey in January of this year. Those reports were followed by acknowledgement of H5N1 in many countries in the region.
This year, most countries are again failing to detect or report H5N1 migration into the area. This lack of transparency is cause for concern.
Similarly, the sequences from most of the H5N1 in Europe have been withheld by Weybridge, who presented in May 2006 a phylogenetic tree (http://www.recombinomics.com/phylo/Brown_Italy_2.html) of approximately 80 isolates from Europe in early 2006. They have only released one bird sequence, from a turkey isolated in October, 2005 as well as five human sequences (4 from Turkey and 1 from Azerbaijan). Although Weybridge has indicated they will release the sequences, they have hoarded the data for 8-12 months.
The sequences are critical for identification of the evolution of tehse isolates via recombination. Full sequences from the Capua lab are being released through the NIAID Influenza Sequencing program. It facilities like Weybridge do not have the resources for timely sequencing and release of the data, turning the samples over to NIAID would be appropriate. NIAID generates sequences at no charge, but sequences are made public instead of placing the data into the private WHO database.
Bejing Genomics Institute is releasing full sequences of H5N1 (http://www.recombinomics.com/News/10050603/H5N1_Recombination_Confirmation.html) isolates China. These sequences (http://www.flutrackers.com/forum/showthread.php?t=11309) clearly demonstrate the evolution of H5N1 via recombination, which is also seen in the recent Qinghai sequences. In the past examples of recombination has been hampered because most of the H5N1 sequences from Hong Kong and China generated by Hong Kong University and St Jude have been partial sequences. These sequences should also be completed or turned over to NIAID so a full data set can be generated to map out a more complete picture of the H5N1 evolution by recombination.
The scandalous lack of full sequences in H5N1 isolates should be corrected.
Resources are now available to rectify these sequencing shortfalls.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11473)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10100601/H5N1_Egypt_Confirmed.html
Recombinomics Commentary
October 5, 2006
New H5N1 bird flu sequences have been deposited at Genbank and Los Alamos (see list here (http://www.flutrackers.com/forum/showthread.php?t=11309) and here (http://www.flutrackers.com/forum/showthread.php?t=11204)). These sequences were deposited by the Beijing Genome Institute and represent complete sequences of all eight gene segments of H5N1 isolates from poultry and wild birds in China from 1997 to 2004. Some of these sequences are updated versions of a series of sequences released earlier this year under the title “A cohort of AIV H5N1 subtypes isolated from wild aquatic birds and domestic poultry revealed rapid transmission, frequent reassortment, and identifiable recombination events.” The sequence contained a number of examples of clear-cut recombination (http://www.recombinomics.com/News/03090602/H5N1_Recombination_Guangdong_NA.html).
Recently additional sequences from the 1970’s were released and these sequences from Hong Kong are well conserved in the above 2004 sequences, which again raise questions about the central dogma of influenza genetics which maintains that season variation is due to random mutations. In addition to the sequences from the 1970’s, the new sequences from 1997 also show a high level of sequence conservation. In the PB2 gene the 2004 tree sparrow sequence, A/tree sparrow/Henan/2 (http://flu.lanl.gov/search/view_record.html?accession=DQ073400&database=fluA)/2004(H5N1) between positions 685 and 2146 has only three differences with the 1997 chicken sequence, A/chicken/Hubei/wi (http://flu.lanl.gov/search/view_record.html?accession=DQ997107&database=fluA)/1997(H5N1). This sequence conservation is inconsistent with an error prone polymerase lacking a proof reader function as the source of seasonal variation in human flu, or rapid evolution in pandemic flu.
Instead, the data clearly shows that both season flu and pandemic flu evolve via homologous recombination. The confirmation of the earlier data demonstrates that the clear examples of recombination are not due to lab error, but reflects the primary mechanism of influenza evolution.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11309)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10050603/H5N1_Recombination_Confirmation.html
| Asymptomatic H5N1 Infected Chickens in Indonesia Recombinomics Commentary October 5, 2006 Head of the West Java Animal Husbandry Office, Rachmat Setiadi, said the warning was made following the discovery of healthy chickens that tested positive with H5N1 virus from a serology test conducted on 20 chickens around the house of two dead flu victims -- 23-year-old IJ and his 20-year-old brother -- in Kebonwaru area, Batunggal The above comments indicate asymptomatic chickens can carry H5N1 bird flu. Although many H5N1 sequences from birds and people in Indonesia have been published, the link between H5N1 in dead poultry, and H5N1 in dead patients has not been established. All reported sequences from human cases in 2006 on the island of Java have has a novel HA cleavage site. The novel cleavage site has only been detected in one duck (http://www.recombinomics.com/News/08310601/H5N1_Indo_Duck_Cleavage.html) on Java in Indramayu, and that sequence was similar to a few human sequences from late 2005 / early 2006 (in upper twig of lower branch of HA tree (http://www.recombinomics.com/phylo/Indo_Karo_HA1.html)). The vast majority of human cases are on a separate twig of the lower branch, and these do not match (http://www.recombinomics.com/News/08120601/H5N1_Match_Unlikely.html) any reported poultry isolates on Java. Matching sequences have been found in two chickens in central Sumatra (http://www.recombinomics.com/News/09140601/H5N1_Sumatra_Chickens.html), isolated in 2005. The H5N1 asymptomatic chickens on Java are positive for antibodies. It is not clear if H5N1 sequences have been detected in the asymptomatic birds. These infections could represent a separate reservoir. There have also been repots on the recovery of suspect bird flu victims. However, these patients have been H5N1 negative, so it remains unclear if they are infected with H5N1, or if the H5N1 sequence from these recovered is different than the H5N1 fatal cases. Almost all H5N1 human sequences in Indonesia are from fatal cases. Asymptomatic chickens in Vietnam (http://www.recombinomics.com/News/04230502/H5N1_Asymptomatic_Chickens.html) have also been reported previously. Clearly more surveillance and sequences from H5N1 infected people, birds, and other mammals are indicated. Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11288) Phylogenetic Trees (http://www.recombinomics.com/phylo.html) http://www.recombinomics.com/News/10050601/H5N1_Asymptomatic_Chickens_Java.html | ||||||||
Recombinomics Commentary
October 22, 2006
On October 11 the WHO update (http://www.who.int/entity/csr/don/2006_10_11/en/index.html) confirmed an H5N1 infection in a patient (39F) in the Gharbiya governorate (http://www.recombinomics.com/News/10100601/H5N1_Egypt_Confirmed.html) in the Nile Delta. Today the sequence of the HA gene from that patient was released, A/Egypt/12374-NAMRU3 (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=407369)/2006(H5N1). The rapid release of this sequence by the US Naval Medical Research Unit in Cairo is to be commended. It was deposited at GenBank on October 13, 2006 and released shortly thereafter.
This Qinghai sequence has the common HA cleavage site, GERRRKKR, and has many polymorphisms found in isolates from birds and human cases from Egypt and Djibouti reported earlier this year. However, the sequence also has an alteration, M230I, near the receptor binding domain.
Changes in the receptor binding domain are cause for concern because they can alter the ease of transmission. Last year another change in the receptor binding domain, S227N, was predicted (http://www.recombinomics.com/News/10220501/H5N1_H9N2_Recombination.html) based on donor sequences in H9N2 in birds in the Middle East. That change was found (http://www.recombinomics.com/News/01120602/H5N1_Turkey_S227N_Recombinant.html) in the index case in Turkey, which was linked to a very large cluster (http://www.recombinomics.com/News/01220601/H5N1_Kocyigit_Ozcan_Timeline.html). Two of the four human sequences made public contained this change (http://www.recombinomics.com/News/06230603/H5N1_S227N_Turkey_Cases.html).
Changes in the receptor binding domain in the Qinghai strain are of additional concern because the Qinghai strain has already acquired a mammalian polymorphism, PB2 E627K. This change increases polymerase activity at lower temperatures. It offers strong selective advantage, and therefore is all in human H1, H2, and H3 isolates. The acquisition by H5N1 was first reported in isolates from Qinghai Lake in China. Subsequent isolates in Russia, Mongolia, Afghanistan, Turkey, Azerbaijan, Germany, Sudan, Italy, Croatia Slovenia, Niger, Nigeria, and the Ivory Coast in 2005 and 2006 has shown that this change has become fixed in the Qinghai strain.
Thus, additional changes in or near the receptor binding domain of Qinghai isolates are cause for concern. Results of testing of additional suspect H5N1 patients in Egypt (http://www.recombinomics.com/News/10200601/H5N1_Egypt_3.html) have not been announced. However, H5N1 in Egypt may be further spread by migratory birds.
The change in the cleavage site has been reported in H5N2 birds from Mexico, as well as H5N1 from Vietnam. Recombination between Clade 1 H5N1 in Vietnam and Clade 2 Qinghai H5N1 provides a mechanism for further genetic diversity in the Qinghai strain. The Egypt isolates also have polymorphisms found in human H5N1 isolates in in Indonesia. These acquisitions via recombination demonstrate additional genetic diversity.
The geographic expansion of H5N1 by wild birds in China as well as the Qinghai strain in Europe, the Middle East, and Africa, creates additional opportunities for recombination and added genetic diversity.
This added geographical reach, coupled with increased genetic diversity, are cause for concern.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11964)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10220603/H5N1_M230I.html
| H5N1 Isolation Failures at USDA Raise Pandemic Concerns Recombinomics Commentary October 18, 2006 The USDA National Veterinary Services Laboratories (NVSL) confirmed the presence of H6N2 through virus isolation in a pool of five samples of the 11 samples collected from wild Green-winged Teals in the Rice Lake Conservation Area of Fulton County, Illinois. Initial screening results announced on Sept. 29 indicated that H5 and N1 subtypes might be present in the collected samples, but further testing was necessary to confirm the H and N subtypes as well as pathogenicity. The failure to isolate the H5N1 in the Green-winged Teal samples from Illinois is cause for concern. This failure may be due in part to pooling of samples, which can lead to an isolation failure because of overgrowth by a serotype not detected in the testing of the pooled samples. A similar failure was reported for Northern pintail samples (http://www.recombinomics.com/News/09210602/H5N1_Montana.html) from Montana. One sample was positive for H5N1, but H5N3 was detected even though sixteen samples were H5 positive. It remains unclear if the H5N3 serotype was from samples that were H5 positive but N1 negative, or was from the H5N1 positive sample. In any even, no isolation of H5N1 in Montana was reported. The number of isolation failures remains unclear. H5N1 has been isolated in Maryland (http://www.recombinomics.com/News/09010602/H5N1_Maryland_Sequences.html), Michigan (http://www.recombinomics.com/News/08140604/H5N1_Michigan_Sequence.html), and Pennsylvania (http://www.recombinomics.com/News/09020601/H5N1_Pennsylvania.html). H5 was detected in a live market in New Jersey, but no mandatory OIE report was filed. Media reports suggested it was not H5N1, but all H5 infected poultry, regardless of N serotype, requires an OIE report. Similarly, media reports indicate H5 has been found in California (http://www.recombinomics.com/News/09300601/H5_Lakeport_CA.html), Washington State (http://www.recombinomics.com/News/10040602/H5_Washington.html), and possibility Alaska, but addition detail from the USDA have not been announced. Similarly, serotypes other than H5N1 are announced only for H5N1 positive samples. It is unclear what, if anything is isolated from the H5 positive samples. These isolation failures raise concerns that low levels of HPAI H5N1 could be missed due to pooling of samples, low sensitivity in the isolation procedure, or other technical issues including collection / transport / degradation issues (http://www.recombinomics.com/News/06210601/H5_Winnipeg_Failure.html). Isolation of HPAI H5N1 from health wild birds is rare. Although such isolations have been reported in Russia (http://www.recombinomics.com/News/10160502/H5N1_Species_Russia.html), the vast majority of H5N1 isolates have come from dead birds or live poultry on farms that have fatal H5N1 infections. Thus, although isolation of HPAI H5N1 from live wild birds is rare, the above protocol involves pooling samples, lowering the sensitivity of the isolation procedure. Repeated failures to isolate any H5N1 from H5N1 positive samples raise concerns about assurances on the detection of low path H5N1. The USDA testing cannot exclude mixtures of low path and high path H5N1 in samples that are H5N1 positive. H5 was detected in a dead gosling on Prince Edward Island (http://www.recombinomics.com/News/06210603/H5_PCR_PEI.html). Only one dead goose was tested, but four died suddenly after displaying bird flu symptoms. Low path H5 rarely causes sudden death in waterfowl, although the Qinghai strain of H5N1 is known to kill waterfowl, including thousands of bar headed geese at Qinghai Lake in May, 2005. This strain has been transported and transmitted by long range migratory birds into Europe, the Middle East, and Africa. The H5N1 has been found in flyways that connect to northwestern and northeastern North America. Sequence data from North American H5 isolates have polymorphisms that are predominantly found in Asia. Similarly, North American polymorphisms (http://www.recombinomics.com/News/02220601/H5N1_Astrakhan_NA.html) have been found in the Qinghai stain in Asia. Recent sequence data from China, shows that recombination is extensive (http://www.recombinomics.com/News/10120601/H5N1_China_Evolution.html) in H5N1 infect poultry (http://www.recombinomics.com/News/10060601/H5N1_H7N1_PB1_Recombination.html) and wild birds (http://www.recombinomics.com/News/03060605/H5N1_Recombination_Henan_PB2.html). These recombination events have moved sequences into Indonesia and have generated swine H5N1 sequences with polymorphisms found in the Qinghai strain of H5N1 as well as H5N1 found in human isolates on Java as well as isolates from the Karo cluster. Thus far, only four genes of an H5N2 isolate from British Columbia in August, 2005 (http://www.recombinomics.com/News/11190504/H5_LPAI_Quebec_British_Columbia.html) has been released. This isolate has acquired North American (http://www.recombinomics.com/News/03180602/H1_Recombination_Swine_PB2_More.html) swine sequences (http://www.recombinomics.com/News/07190601/H5_BC_Mallard_Swine.html), as well as HPAI H5N1 sequences from Asia. These acquisitions indicate dual infections and associated recombination is common in H5 in North America. No other H5 sequences from 2005 isolates in Canada or any 2006 H5 isolates from the United States or Canada have been released. The explosion in the detection of H5 in Canada last year, as well as Canada and the United State this year raises concerns about the evolution of H5 in North America as well as the repeated isolation failures at the USDA. Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11788) Phylogenetic Trees (http://www.recombinomics.com/phylo.html) | |||||||||
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Recombinomics Commentary
October 26, 2006
There is a state of panic among citizens enough after the seizure of the child Basma Essam seven months yesterday on suspicion Bismnod بانفلونزا infected birds. The bodies of the Ministry of Health had seized two cases in the last few hours and another case a few days ago have been transferred to the Abbasiya Hospital of the gravity of their situation.
The above translation describes additional suspect H5N1 bird flu cases (http://www.recombinomics.com/News/10200601/H5N1_Egypt_3.html) in Egypt. The status of cases hospitalized last week have not been reported.
The HA sequence of case confirmed (http://www.recombinomics.com/News/10100601/H5N1_Egypt_Confirmed.html) earlier this month has been published. It has a M230I change (http://www.recombinomics.com/News/10220603/H5N1_M230I.html) near the receptor binding domain, which could affect transmissibility. A change two positions upstream, S227N, was associated (http://www.recombinomics.com/News/01120602/H5N1_Turkey_S227N_Recombinant.html) with large fatal clusters (http://www.recombinomics.com/News/01220601/H5N1_Kocyigit_Ozcan_Timeline.html) in Turkey earlier this year.
More information on these new and earlier admissions in Egypt would be useful
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11473)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10270601/H5N1_Egypt_Grow_2.html
| H5N1 Recombination Evidence Excluded from Genbank Recombinomics Commentary October 26, 2006 H5N1 bird flu sequences were released (http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/shipment.cgi) this month via the NIAID Influenza sequencing project (http://www.niaid.nih.gov/dmid/genomes/mscs/influenza.htm) (see list here (http://www.flutrackers.com/forum/showthread.php?t=11338)). The samples were submitted by the Capua lab in Italy. Although HA sequences from several of the isolates had been reported previously, many were partial sequences and in most cases the sequences from the other seven gene segments were not released. The NIAID program generates full sequences on all eight gene segments, which provide powerful profiles that can be used to trace origins or newly emerging genes, which can be used. These origins can be used to predict (http://www.recombinomics.com/News/10220501/H5N1_H9N2_Recombination.html) new sequences, as was done (http://www.recombinomics.com/News/01120602/H5N1_Turkey_S227N_Recombinant.html) for S227N in Turkey (http://www.recombinomics.com/News/01120601/H5N1_Turkey_Polymorphism_HA.html) at the beginning of this year. Recent data from northern China has included compelling evidence (http://www.recombinomics.com/News/10050603/H5N1_Recombination_Confirmation.html) that H5N1 in China is evolving via recombination (http://www.recombinomics.com/News/10120601/H5N1_China_Evolution.html). These sequences are transmitted and transported by migratory birds, which has led to widespread detection (http://www.recombinomics.com/News/04050601/H5N1_Fujian_Spread_China.html) of the Fujian strain, which was present in all human cases in China, and subsequently detected in wild birds in Hong Kong (http://www.recombinomics.com/News/08170601/H5N1_Fujian_Wild_Birds.html), as well as Laos and Malaysia earlier this year. Moreover, these sequences are also appearing in human Indonesian isolates, which do not match (http://www.recombinomics.com/News/10050602/H5N1_Indo_Match_Failures.html) the poultry isolates. Thus, a full sequences of all eight gene segments are essential for predicting new sequences generated by recombination. The full sequence of the HA gene of a Qinghai isolate from Afghanistan demonstrates how recombined regions are excluded in partial sequences, and raises questions on why the H5N1 sequences generated by St Jude and Hong Kong University are largely partial sequences. The partial sequences are from H5N1 isolates in Hong Kong, China, and Vietnam and are important (http://www.recombinomics.com/PR/031006.html) in mapping the interactions in dual infections involving H5N1 in Asia. The original HA sequence from a chicken A/chicken/Afghanistan/1207 (http://flu.lanl.gov/search/view_record.html?accession=DQ661910&database=fluA)/2006 was 1602 BP and was missing the 5’ portion of the gene, the sequence from the NIAID program was a full sequence (http://flu.lanl.gov/search/view_record.html?accession=CY016787&database=fluA)of 1734 BP and the region missing from the initial submission included a string of four polymorphisms between positions 42 and 62. These polymorphisms are defined by Qinghai H5N1 HA sequences, and clustering of such polymorphism is a strong signal for recombination. The first polymorphism (T42C) was also found in a 2003 duck isolate from China (see detail here (http://www.flutrackers.com/forum/showthread.php?t=12063)). The second polymorphism was found in two 2004 duck H5N2 isolates from Malaysia (A/duck broiler/Malaysia/F118/08 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=73695581)/04 and A/duck broiler/Malaysia/F189/07 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=73621253)/04). The third polymorphism, C53, was found in a large number of low and high path H5 including all three isolates above (C53T is found in Qinghai isolates from Nigeria). The fourth polymorphism, G62A, has a much more limited distribution, which includes high path H5N1 in Mongolia and China as well as the two low path ducks from Malaysia. The matching of 3 of the 4 continuous polymorphisms (http://www.flutrackers.com/forum/showpost.php?p=42572&postcount=10) strongly suggests that these three polymorphism were acquired from a sequence similar to the low path duck sequences in Malaysia. These acquisitions are further supported by two additional polymorphisms downstream from the cluster of three. G175A is present in the full sequence from NIAID. The wild type sequence is in the early isolate. G175A also has a limited distribution among H5 isolates, including the two ducks from Malaysia. Similarly, C268T also has a limited distribution in H5N1 isolates from Asia (Russia, Mongolia, and Indonesia) as well as the two low path ducks from Malaysia. C268T is in both Afghan sequences. The same type of distribution is found for T868C, which is in high and low path H5 isolates from Asia and Europe, including the two low path ducks from Malaysia. Thus, of the six polymorphisms shared by the Malaysian ducks and the chicken from Afghanistan, only two were present in the original partial sequence. The first three were missing because only a partial sequence was submitted, and the fourth polymorphism difference in the two submitted sequences. The presence of the two low path duck sequences in the origin Afghan sequence suggested recombination. However, the presence of six polymorphisms in the full sequences strongly suggests that these sequences were present in the high path Qinghai sequence because of recombination with a low path H5 sequence similar to the two sequences from Malaysia. Confirmation via additional sharing in the other 7 gene segments was limited because the N in the low path was N2 instead of N1 in the Qinghai strain, and the other six gene segments from the Malaysian isolates have not been submitted. This example highlights the limitations created by partial sequences and the absence of information for all eight gene segments. This missing data, limits the tracing of the polymorphisms, which identifies parental strains as well as prior dual infections. It remains unclear why the majority of H5N1 sequences from Hong Kong, China, and Vietnam submitted by St Jude and Hong Kong University are partial sequences, particularly for the four genes most likely to show recombination (PB2, PB1, PA, and NP), but full sequences should be generated and placed in the database to provide a clearer picture of recombination and dual infections involving the various versions of H5N1 in Asia. Media Sources (http://www.flutrackers.com/forum/showthread.php?t=12063) Phylogenetic Trees (http://www.recombinomics.com/phylo.html) http://www.recombinomics.com/News/10270602/H5N1_Recombination_Excluded.html | |||||||||
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Recombinomics Commentary
October 22, 2006
A scientist, who conducted researched at Ulaanbaatar agricultural university veterinary clinic, has become infected with bird flu. On October 23, the Onoodor periodical informs that Mongolian emergency ministry refuses to release any additional information; however, as it became known to the press, the scientist became infected a week ago.
The researcher was hospitalized with high temperature. As National Infectious Disease Center director Mendbayar Altanhuu stressed, preliminary analysis confirmed that the man had the avian flu virus.
The above translation suggests that the first human H5N1 case in Mongolia has been detected. It is not clear if the infection was linked to a lab procedure by the veterinarian/scientist, or was acquired through proximity to infected birds. Earlier media reports described a massive outbreak of H5N1 (http://www.recombinomics.com/News/06270601/H5N1_Tuva.html) in Tuva and adjacent areas in Mongolia. Several Qinghai sequences from isolates in Tuva (http://www.recombinomics.com/News/07260601/H5N1_Tuva_Mongolia.html) and Mongolia (http://www.recombinomics.com/News/07060602/H5N1_Qinghai_Mongolia.html) have been released.
However, reported human cases of the Qinghai H5N1 infections have been limited to Turkey, Iraq, Azerbaijan, Egypt, and Djibouti.
If confirmed, this would be the first human H5N1 case in Mongolia.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11965)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10220601/H5N1_Mongolia_Vet.html
Recombinomics Commentary
October 6, 2006
New H5N1 sequences have been released (http://www.recombinomics.com/News/10050603/H5N1_Recombination_Confirmation.html) from northern China. In several instances these are sequences from earlier isolates which were originally submitted to GenBank by the Beijing Genome Institute on February 28, 2005 under the title, “A cohort of AIV H5N1 subtypes isolated from wild aquatic birds and domestic poultry revealed rapid transmission, frequent reassortment, and identifiable recombination events.” One of the sequences with clear cut homologous recombination (http://www.recombinomics.com/News/03080601/H5N1_Recombination_Henan_PB1_More.html) was A/chicken/Henan/210 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=61698125)/2004(H5N1). The re-sequenced sample, A/chicken/Henan/wu (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=115382769&dopt=genbank)/2004(H5N1) is identical in 7 of the 8 gene segments. The sole difference was in PB2 and the new sequences which removed the premature termination codon. The new sequence confirms the previously identified recombination.
However, the recombination in northern China was not limited to sequences generated by the Beijing Genome Institute. A recent paper (http://www.flutrackers.com/forum/showpost.php?p=36913&postcount=1) by Harbin Veterinary Research Institute and St Jude described the relationship between an H7N2 isolate from a chicken in Hubei in 2002, A/chicken/Hubei/1 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=51340292&dopt=genbank)/2002(H7N2), and a 1979 H7N1 isolate from an African starling, from a quarantined bird in England, A/African starling/England-Q/983 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=51340279&dopt=genbank)/1979(H7N1). Those sequences however had a region of identity with a 2001 H5N1 chicken sequence, A/chicken/Hubei/718 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=85692716&dopt=genbank)/2001(H5N1) generated by the China Agricultural University in Beijing. The sequence between positions 1729 and 2182 of the 1979 and 2001 isolates were identical, even though the two PB1 sequences were only 93% homologous.
The region of identity between the two PB1 sequences strongly supports acquisition via homologous recombination, and the identity between the sequences that were 22 years apart shows that the sequence could be faithfully copied over an extended time period. These data were similar to Canadian swine (http://www.recombinomics.com/News/03200601/H1_Recombination_Swine_PA.html) data which also had examples of clear cut (http://www.recombinomics.com/News/03180602/H1_Recombination_Swine_PB2_More.html) recombination as well as long stretches of identity in sequences that were isolated over 25 years apart (see identities in PB2 (http://www.recombinomics.com/phylo/Canadian_Swine_PB2.html) and PA (http://www.recombinomics.com/phylo/Canadian_Swine_PA.html)).
The examples of frequent and clear cut homologous recombination involving sequences faithfully copied for several decades seriously challenges the dogma of influenza genetic which maintains that seasonal variations are due to genetic drift cause by random mutations generated by a polymerase lacking a proof reading function and pandemic shifts are due to reassortment.
The latest examples of recombination show that the random muations can easily be generated by homologous recombination between closely related sequences, and genetic shifts can be generated by recombination between distantly related genes. The acquisition of single nucleotide changes (SNPs) by homologous recombination is also supported by polymorphism tracing through an expanding sequence database. The “new: polymorphisms are easily found in earlier sequences which are frequently found in closely related sequences which are transported and transmitted by wild birds.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11322)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10060601/H5N1_H7N1_PB1_Recombination.html
Recombinomics Commentary
October 11, 2006
H5N1 sequences from northern China are being released by the Beijing Genome Institute. Some of these sequences are repeats of earlier sequences released under the title, “A cohort of AIV H5N1 subtypes isolated from wild aquatic birds and domestic poultry revealed rapid transmission, frequent reassortment, and identifiable recombination events” and these sequenced confirm (http://www.recombinomics.com/News/10050603/H5N1_Recombination_Confirmation.html) the clear cut examples (http://www.recombinomics.com/News/03090602/H5N1_Recombination_Guangdong_NA.html) of homologous recombination.
The new sequences are generally full sequences of all eight gene segments and provide valuable information of the evolution and transmission of H5N1 in China. Many of the sequences are from poultry from various Northern provinces in China in 1997. H5N1 was first detected in 1996 in a goose from Guangdong. The following year, the first human H5N1 were reported in Hong Kong. The human isolates had the characteristic HA polybasic cleavage site, RERRRKKR, found in most of the HPAI throughout Asia. However, the human NA sequences have a 19 amino acid deletion in the stalk portion of the protein, which was not in the Guangdong goose. The human H5N1 also had internal genes (PB2, PB1, PA, NP) which matched sequences from H9N2 And H6N1. This constellation of genes was also found in bird isolates.
This constellation disappeared after Hong Kong culled over 1.5 million birds in 1997. However, the same constellation was recently found in smuggled eggs from Vietnam, indicating the genes continued to circulate in a reservoir outside of Hong Kong.
Reported human H5N1 re-appeared in Hong Kong in a family that visited Fujian province in 2003. The constellation of these genes was designated as the Z+ genotype. The following year the Z genotype emerged in H5N1 exploding out of China, including human cases in Vietnam and Thailand.
However, the NA of the Z genotype had a 20 amino acid deletion in the stalk region that overlapped the earlier 19 amino acid deletion. Many of the 1997 sequences that were just released have this 20 amino acid deletion, and therefore provide an early history of the NA from the Z genotype.
Analysis of these sequences indicates that they have moved into wild birds in eastern Asia. These sequences are distinct from the Qinghai sequences that were first detected at Qinghai Lake in 2005 and subsequently migrated to Russia, Mongolia, Kazakhstan, Europe, the Middle East, and Africa.
The sequences recently released link isolates in northern China and Japan to sequences in southeast Asia, including Indonesia. This linkage is largely via a number of polymorphisms acquired via recombination.
The new sequences also have large regions of identity in sequences isolated years apart. The first 1141 positions of NA from the 1997 Hubei isolate, A/chicken/Hubei/wj (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=115382791&dopt=GenBank)/1997(H5N1), are identical to the 2003 Hubei isolate, A/chicken/Hubei/wo (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=115502942&dopt=GenBank)/2003(H5N1). Similarly, positions 43-709 of the 2004 blackbird isolate, A/blackbird/Hunan/1 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=56672764&dopt=GenBank)/2004(H5N1), are also identical.
The conservation of these sequences raise serious questions about the role of random mutations in the seasonal changes of pandemic H5N1. As` noted earlier, strong conservation is also seen in Hong Kong isolates from the late 70’s, indicating copy errors are not a major source of the seasonal changes.
The same type of evolution was seen in Canadian swine isolates from 2003-2004 which had large portions of exact copies of 1977 PA (http://www.recombinomics.com/phylo/Canadian_Swine_PA.html) and PB2 (http://www.recombinomics.com/phylo/Canadian_Swine_PB2.html) genes. Similarly, the positions 593 and 2033 the PB1 of the 1997 isolate, A/chicken/Hubei/wj (http://flu.lanl.gov/search/view_record.html?accession=DQ997120&database=fluA)/1997 is IDENTICAL to the 2004 isolate,
A/chicken/Henan/wu (http://flu.lanl.gov/search/view_record.html?accession=DQ997224&database=fluA)/2004, even though the sequences are 7 years apart.
Thus, the current data shows that H5N1 sequences can be faithfully copied over long time periods, and the portions of genes can be exchanged by homologous recombination (http://www.recombinomics.com/News/10060601/H5N1_H7N1_PB1_Recombination.html).
These examples are most easily found in multiple isolates collected over a limited time frame. The sequences show identity and then abruptly diverge. These regions of conservation are spread across the gene and do not represent immutable regions or regions that consistently evolve at different rates.
The detection of such recombination in H5N1 in Asia has been hampered by the release of partial sequences or the release of a limited number of genes. NIAID has a program (http://www.niaid.nih.gov/dmid/genomes/mscs/influenza.htm) that will generate complete sequences of all eight gene segments. Filling in the database holes created by the partial sequences would be useful.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11465)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10120601/H5N1_China_Evolution.html
Recombinomics Commentary
October 22, 2006
The sequence of H5N1 isolated from a chicken in Romania last year, A/chicken/Romania/4793 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=116230145)/05(H5N1), has been released. The partial HA sequence has a novel HA cleavage site, GDRRKKR. This is the first public sequence of H5N1 from Romania, which reported one of the first confirmed H5N1 cases in the region in October, 2005. Although the sequences generated by Weybridge have been withheld, a phylogenetic tree (http://www.recombinomics.com/phylo/Brown_Italy_2_Bottom.html) of HA H5N1 sequences in Europe has been published. There are several distinct groupings on the tree that include isolates from Romania. However, the full presentation (http://www.fao.org/ag/againfo/subjects/en/health/diseases-cards/conference/documents/I.Brown.pdf) included a discussion of the isolates from Europe describe several novel cleavage sites, but no contained the E to D change seen above, suggesting that the published sequence represents yet another version of the Qinghai strain of H5n1 circulating in Europe.
The cleavage sit above has not been reported previously, but the E to D change has been found in geese in Malaysia. That cleavage site is generated by taking the common HA cleavage site in H5n1 in Asia, RERRRKKR and changing the E to generate RDRRRKKR. Similarly, the common Qinghai change has changed he first position of the common sequence to a G, resulting in GERRRKKR. Thus, the novel cleavage site in Romania can be generated by recombining the Malaysian duck sequence with the common Qinghai sequence.
The partial HA sequence has additional polymorphisms shared by a subset of the Qinghai isolates. A1099G is shared with Qinghai isolates from the area, but the polymorphism is also found in many H5N1 isolates from Indonesia. The sharing of polymorphsism between a subset of Qinghai isolates and a subset of Indonesian isolates signal additional recombination between these two groups.
Recent sequences from China define the evolution of H5N1 (http://www.recombinomics.com/News/10120601/H5N1_China_Evolution.html), including isolates from 1997, with the 20 amino acid NA deletion found in the Z Genotype, which exploded out of China in 2004. These sequences have many clear-cut examples of recombination, (http://www.recombinomics.com/News/10050603/H5N1_Recombination_Confirmation.html) and can also be found in wild birds. These isolates also share regions of identity with Indonesian isolates, including human isolates from the Karo cluster as well as the Indonesia sub-clade chosen as a vaccine target.
Recently, WHO expanded the number of H5N1 vaccine targets (http://www.recombinomics.com/phylo/HA_Vaccine.html) to four, because of four distinct clades or sub-clades linked to fatal infections in humans. These expanded targets highlight the rapid evolution of H5N1 due to extensive recombination in a population of increased genetic complexity. The sharing of polymorphisms between these distinct groups helps define additional recombination events that define future vaccine targets.
The HA sequence released today from a patient infected this month has additional examples of regions of H5N1 shared between Qinghai and Indonesian isolates.
Media Sources (http://www.flutrackers.com/forum/showthread.php?t=11939)
Phylogenetic Trees (http://www.recombinomics.com/phylo.html)
http://www.recombinomics.com/News/10220602/H5N1_Romania_Novel.html
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