Henry Niman's discussions
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6 votes
Emergence and Fixing of Antiviral Resistance in Influenza A Via Recombination and Hitch Hiking
- Document Type:
- Manuscript (Preprint)
- Date:
- Received 29 January 2009 21:07 UTC; Posted 10 February 2009
- Tags:
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4 votes
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
- Document Type:
- Manuscript (Preprint)
- Date:
- Received 07 May 2008 22:53 UTC; Posted 08 May 2008
- Tags:
Most recent comment by Henry Niman on 26 Mar 2009 05:29
HA and NA sequences from the H5N1 outbreak in Assam, India in November, 2008 have been released at Genbank (A/chicken/Assam/140187/2008 and A/chicken/Assam/140203/2008). The sequences are the Uvs Lake version of clade 2.2.3 which spread throughout Europe between the summer of 2007 and early 2008. All published NA sequences from those outbreaks had G743A. In contrast, the 2008 sequences from India do not.
However, G743A was not on the initial sequences which came from a massive wild bird outbreak at Uvs Lake in Mongolia (as well as adjacent areas in southern Russia) in the summer of 2006. The strain was subsequently associated with outbreaks in South Korea and Japan in late 2006 / early 2007. Those sequences also did not have G743A. It was acquired by Uvs Lake sequences that were associated with the poultry outbreak in Kuwait in early 2007. At the same time G743A was also acquired by multiple clade 2.2 backgrounds in Egypt, as well as distinct clade 2.2.3 isolates in Russia and clade 2.2 isolates in Ghana and Nigeria.
Thus, the absence of G743A in the Uvs Lake sequences in India suggests that birds carrying those sequences had not traveled west into Europe, the Middle East, and Africa, but remained in the South Asia flyway that connects India with Mongolia and southern Russia.
0 new comments have been made since Henry Niman's last post
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11 votes
Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
- Document Type:
- Manuscript (Preprint)
- Date:
- Received 10 September 2007 09:26 UTC; Posted 12 September 2007
- Tags:
Most recent comment by Henry Niman on 15 Jan 2008 11:03
Sequences twelve 2007 chicken isolates from Nigeria were just made public. These sequences fully support the aggregation of single nucleotide polymorphisms previously described in the human influenza HA sequence, A/Nigeria/6/07. Four of the chicken isolates were virtually identical to the human influenza HA sequence (see list below), while six more were closely related. Two of the isolates were closely related to a subset of 2006 isolates from Nigeria.
The “Aggregation” paper described 14 polymorphisms that were shared with other clade 2.2 isolates. All 14 of these polymorphisms were present in the newly released chicken influenza sequences from Nigeria. Thirteen of the fourteen were in the four sequences virtually identical to the human influenza sequence. The only polymorphism, C1480T, not in the four closely related sequences was present in the two isolates related to the subset of 2006 isolates. In addition, seven of the fourteen polymorphisms (G295A, A433G, G643A, G781A, C981T, G1685A, A1708G) were present in the ten most closely related sequences.
These data support the previously described aggregation of single nucleotide polymorphisms from diverse clade 2.2 sub-clades.
This aggregation is most easily explained by homologous recombination in H5N1 influenza A.
Virtually identical HA sequences
EU148428 A/chicken/Nigeria/1071-23/2007
EU148372 A/chicken/Nigeria/1071-4/2007
EU148380 A/chicken/Nigeria/1071-5/2007
EU148396 A/chicken/Nigeria/1071-9/2007Closely related HA sequences
EU148356 A/chicken/Nigeria/1071-1/2007
EU148404 A/chicken/Nigeria/1071-10/2007
EU148412 A/chicken/Nigeria/1071-15/2007
EU148420 A/chicken/Nigeria/1071-22/2007
EU148436 A/chicken/Nigeria/1071-29/2007
EU148444 A/chicken/Nigeria/1071-30/2007More distantly related HA sequences
EU148364 A/chicken/Nigeria/1071-3/2007
EU148388 A/chicken/Nigeria/1071-7/20070 new comments have been made since Henry Niman's last post
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10 votes
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
- Document Type:
- Manuscript (Preprint)
- Date:
- Received 10 September 2007 12:42 UTC; Posted 12 September 2007
- Tags:
Most recent comment by Henry Niman on 15 Jan 2008 09:08
Full sequences for H5N1 from twelve 2007 chicken isolates from Nigeria have just been released (listed below). Ten of the NA sequences are closely related to the human influenza NA sequence previously released (A/Nigeria/6/07). Like 2006 isolates from Nigeria, the human 2007 sequence did not have G743A. However, two of the four closely related sequences (A/chicken/Nigeria/1071-10/2007 and A/chicken/Nigeria/1071-22/2007) did have G743A. These sequences represent the eleventh H5N1 clade 2.2 genetic background that acquired G743A in 2007.
The initial Nature Precedings report describes six genetic backgrounds that appended G743A in early 2007. More recently, there have been multiple H5N1 outbreaks in Europe, including the recent outbreak in mute swans in England. As noted by DEFRA today, these sequences are closely related to recent sequences from Czech Republic and Poland. These comments indicate all reported H5N1 in Europe since the summer of 2007 have been related to the Uva Lake strain of clade 2.2.3.
The Uva Lake sequences did not have G743A, nor did the recent sequences from the outbreak in South Korea at they end of 2006. Those sequences were also closely related to the Uva Lake isolates. However, there have now been four NA sequences released from 2007 outbreak in Germany and Krasnodar, representing distinct Uva Lake clade 2.2.3 genetic backgrounds. All four have G743A.
The appending of the same synonymous polymorphism, G743A, onto eleven distinct clade 2.2 genetic backgrounds in Russia (Moscow and Krasnodar), Egypt (four genetic backgrounds), Ghana, Germany (Bavaria, Saxony, and Thuringen), and Nigeria, is not easily explained by selection of de novo copy errors.
These acquisitions are more consistent with a mechanism involving homologous recombination with a common donor sequence.
Most closely related to A/Nigeria/6/07
EU148414 A/chicken/Nigeria/1071-15/2007
EU148446 A/chicken/Nigeria/1071-30/2007
EU148406 A/chicken/Nigeria/1071-10/2007
EU148422 A/chicken/Nigeria/1071-22/2007Closely related to A/Nigeria/6/07
EU148358 A/chicken/Nigeria/1071-1/2007
EU148430 A/chicken/Nigeria/1071-23/2007
EU148438 A/chicken/Nigeria/1071-29/2007
EU148374 A/chicken/Nigeria/1071-4/2007
EU148382 A/chicken/Nigeria/1071-5/2007
EU148398 A/chicken/Nigeria/1071-9/2007Distantly related to A/Nigeria/6/07
EU148366 A/chicken/Nigeria/1071-3/2007
EU148390 A/chicken/Nigeria/1071-7/20070 new comments have been made since Henry Niman's last post
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19 votes
Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
- Document Type:
- Manuscript (Preprint)
- Date:
- Received 16 August 2007 16:24 UTC; Posted 16 August 2007
- Tags:
Most recent comment by Henry Niman on 05 Oct 2007 07:56
The recent publication
Hatta M, Hatta Y, Kim JH, Watanabe S, Shinya K, et al. (2007) Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice. PLoS Pathog 3(10): e133 doi:10.1371/journal.ppat.0030133
provides additional positive data for the spread of clade 2.2 (Qinghai) H5N1 by migratory birds in Europe, the Middle East, and Africa. The paper reinforces earlier observations on the role of PB2 E627K and temperature on the replication of clade 2.2 H5N1 in avian and mammalian hosts.
E627K is present in virtually all human isolates of seasonal flu. This change allows seasonal flu to replicate most efficiently at lower (33 C) temperatures, which are found in mammalian noses and throats. This property may contribute to the seasonal aspects of human influenza in northern and southern locations.
However, this also leads to a lowering of the H5N1 level in birds, which have a body temperature of 41 C. Consequently, clade 2.2 circulates undetected in surveillance program that focus on detection in live healthy birds. In contrast, birds that have trouble maintaining body temperature allow the levels to rise, leading to detection of clade 2.2 in dead or dying wild birds, which has been reported in Europe, the Middle East, and Africa. All of the “Asian” H5N1 reported in those regions has been clade 2.2 and almost all isolates have PB2 E627K, one of the markers of clade 2.2 in birds.
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1 vote
Visualization of and Access to CloudSat Vertical Data through Google Earth
- Document Type:
- Manuscript
- Date:
- Received 03 August 2007 04:17 UTC; Posted 03 August 2007
- DOI:
- doi:10.1038/npre.2007.595.1
- Tags:
Most recent comment by Henry Niman on 05 Aug 2007 02:14
Congratulations on bridging the gap between scientific data and access by the general public. Tools such as Google Earth are becoming increasingly popular, and use of GPS devices to generate precise map coordinates is also on the rise.
The devices have come into play in the public health arena. Government reports on disease outbreaks are now using map coordinates which have up to six decimal places, allowing for precise mapping.
These reports are public, and I have used such reports on avian influenza
http://www.oie.int/downld/AVIAN%20INFLUENZA/A_AI-Asia.htm
to map new outbreaks. The map coordinates have come into wide use in the past year, and are now included in almost all reports. Public access to Google Earth, with user friendly mapping using the map coordinates and point and click zooming, generates interactions with real disease outbreak data, such as H5N1 outbreaks in Europe, by the general public
http://maps.google.com/maps/ms?ie=UTF8&hl=en&t=h&msa=0&msid=106484775090296685271.000434e9d3e9066b4203c&ll=50.190968,11.689453&spn=6.485709,13.205566&z=6&om=0
More detailed tools, such as the ones you describe, will increase involvement of the general public with scientific data, which is a major plus.
0 new comments have been made since Henry Niman's last post
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21 votes
H5N1 Clade 2.2 Polymorphism Tracing Identifies Influenza Recombination and Potential Vaccine Targets
- Document Type:
- Manuscript
- Date:
- Received 27 July 2007 11:41 UTC; Posted 27 July 2007
- DOI:
- doi:10.1038/npre.2007.553.1
- Tags:
Most recent comment by Henry Niman on 02 Aug 2007 03:51
There are additional indications of frequent dual infections. NIAID has an influenza sequencing program and details of isolates are posted. Samples submitted by Ohio State University list the serotype of the sample as well as the serotype of the sequenced plaque purified clones. Frequently, the serotypes do not match, indicating the birds are infected by at least two distinct serotypes. This is in addition to co-infections by closely related viruses of the same serotype.
Dual infections in birds are quite common.
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35 votes
Swine Influenza A Evolution via Recombination – Genetic Drift Reservoir
- Document Type:
- Manuscript (Preprint)
- Date:
- Received 07 July 2007 03:02 UTC; Posted 10 July 2007
- Tags:
Most recent comment by Henry Niman on 05 Feb 2009 02:02
HA sequences from Kenya have been released through the US Air Force surveillance program. These sequences identified high levels of oseltamivir resistance H1N1 in Kenya, and provided additional support for recombination and the role of A193T in the fixing of H274Y.
Most of the sequences fell into two groups. One matched the sequences released from isolates collected last season in Kenya. These sequences had G189N (H3 numbering), which was encoded by two adjacent non-synonymous changes, G604A and G605A. However, a second group matched the oseltamivir resistant isolates identified in South Africa over the summer. These isolates also had G189N, but were flanked by two additional changes S187N and A193T. S187N was found in clade 2C in Hong Kong, while A193T had also been in clade 2C prior to acquisition by the clade 2B sub-clade that emerged worldwide this season. There were six isolates (see list below) that had the three receptor binding changes, S187N, G189N, and A193T, which was the dominant sub-clade in South Africa and also was in an isolate from Washington State. Moreover, phylogenetic analysis of the NA sequences suggests an isolate from Chiba, Japan also matches this group. The isolates in Kenya were collected in October and November, but support an earlier Kenya origin for G189N.
In addition to the series that matches the isolates from South Africa, another isolate, A/Mbagathi/7586/2008, has G189A and A193T, which matches another isolate from the US that emerged this season, A/Hawaii/19/2008. This combination also matches another series from Japan this season, based on phylogenetc analysis of NA.
Another Kenya isolate from the summer, A/Kisumu/6543/2008, has G189N plus H196R. H196R is in the dominant H1N1 sub-clade reported to date in the United States, as well as multiple locations in Japan this season.
Yet another isolate, A/Kisii/7577/2008, has G189N plus A193T.
Thus, the isolates from Kenya contain a number of combinations of receptor binding domain polymorphisms which match H1N1 isolates with H274Y on NA, as well as A193T on HA.
S187N, G189N, A193T
Kisii/7541/2008
Kisii/7547/2008
Kisii/7559/2008
Kisii/7562/2008
Kisii/7570/2008
Kisii/7576/2008
Johannesburg/10/2008
Johannesburg/25/2008
Johannesburg/34/2008
Johannesburg/35/2008
Johannesburg/46/2008
Washington/05/2008
Chiba/86/2008G189A, A193T
Mbagathi/7586/2008
Hawaii/19/2008
Miyagi/35/08
Yamaguchi/26/08
Yamaguchi/27/08
Yamaguchi/28/08H196R (G189V, A193T also in all but Kisumu)
Kisumu/6543/2008
Hawaii/21/2008
Pennsylvania/08/2008
Pennsylvania/092008
Texas/15/2008
Texas/16/2008
Texas/17/2008
Texas/18/2008
Sendai/103/08
Sendai-H/2103/08
Sendai/104/08
Sendai/105/08
Yokohama/95/08
Yokohama/96/080 new comments have been made since Henry Niman's last post
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26 votes
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
- Document Type:
- Manuscript (Preprint)
- Date:
- Received 14 July 2007 11:45 UTC; Posted 16 July 2007
- Tags:
Most recent comment by Henry Niman on 26 Nov 2007 08:22
The paper, “Phylogenetic analyses of highly pathogenic avian influenza virus isolates from Germany in 2006 and 2007 suggest at least three separate introductions of H5N1 virus” by Starik, et al, doi:10.1016/j.vetmic.2007.10.012 includes detail on three isolates collected in Germany during the summer of 2007. A/Cygnus olor/Germany/R1349/07 is from the south, A/Cygnus olor/Germany/R1359/07 is from central Germany, as is A/Podiceps nigricollis/Germany/R1393/07. The paper includes a phylogenetic tree which shows all three sequences clustering together. However each sequence is distinct, supporting independent introductions by wild birds. The sequences are most closely related to A/grebe/Tyva/Tyv06-02/2006, which was isolated from the massive wild bird outbreak in and around Uva Lake in Mongolia in 2006.
The location on the tree is virtually identical to A/chicken/Krasnodar/300/2007 isolated September 5, 2007. Based on comments by DEFRA, all of these sequences will be closely related to H5N1 in the Czech Republic, France, and England. They will likely have NA G743A, which was appended onto at least seven genetic backgrounds in 2007, including the Krasnodar isolate.
0 new comments have been made since Henry Niman's last post
Most recent comment by Henry Niman on 25 Mar 2009 09:53
The Japan NIH has released a new NA phylogenetic tree of H1N1 this season. Included are nine isolates from 2009, which all map with the major sub-clade in Japan. The tree also includes isolates from South Korea which map to the same dominant branch. HA sequences from these isolates have A193T and the flanking polymorphism of G189A. These sequences are also in a small number of isolates from the US and match the first five H1N1 isolates from Italy, as well as isolates from Taiwan.
Also included are isolates from Japan that were associated with an elementary school in the fall, which matches the dominant H1N1 sub-clade in the US. HA sequences from these isolates have A1893T with G189V and H196R.
Japan NIH also released titers of 18 isolates against ferret reference anti-sera. These data clearly demonstrate significant drift of the recent isolates from last year’s H1N1 vaccine target, A/Solomon Islands/3/2006 (clade 2A). However, last season there was little clade 2A in circulation, raising concerns that the drift was accelerated by a poorly matched vaccine. Although the 18 test antigens represented multiple recent sub-clades, with HA sequences with A193T plus one or two additional changes at flanking positions 187, 189, and 196, all had reductions in titers when tested with the clade 2A reference anti-sera. Two were reduced four fold, but the remainder had reductions ranging from eight to thirty-two fold.
Similar results were generated for clade 2C, which was represented by recent anti-sera against A/Shiga/8/2008. One isolate was reduced four fold while the rest were reduced eight to thirty-two fold. These lower titers help explain the spread of clade 2B in Asia, where clade 2C was widespread last season.
However, reduced titers were also seen for A/Brisbane/59/2007 (clade 2B), although results were more complex. Two reference sera were used. One was directed against Brisbane/59 grown in eggs and like last season, the anti-sera had significant cross reactivity with the reference sera as well as the recent isolates. The mammalian cell isolate however discriminated between the reference sera, especially for clade 2C, where the titer was reduced eight fold. This level of reduction was also seen for four of the test isolates. Three were the dominant sub-clade in Japan, while the other was the dominant sub-clade in the US. These titer reductions support reports of vaccine failures in Asia and North America.
The recent announcement that the H1N1 target for the 2009/2010 will remain unchanged, raise concerns of more vaccine failures next season.
0 new comments have been made since Henry Niman's last post
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