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This is the most recent in chronological order from Instiutut Pasteur in Cambodia by Buchy 2009, Sorn 2012 and Horm 2013..
Buchy et al. 2009 Molecular Epidemiology of Clade 1 Influenza A Viruses (H5N1), Southern Indochina Peninsula, 2004?2007 Volume 15, Number 10?October 2009 - Emerging Infectious Disease journal ? CDC-http://wwwnc.cdc.gov/eid/article/15/10/09-0115_article.htm
Sorn, S., et al. Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade. Infect. Genet. Evol. (2012), http://dx.doi.org/10.1016/j.meegid.2012.05.013 http://www.sciencedirect.com/science...67134812002158
and now
Horm et al.2013 Influenza A(H5N1) Virus Surveillance at Live Poultry Markets, Cambodia, 2011 - Vol. 19 No. 2 - February 2013 - Emerging Infectious Disease journal CDC
(Also in 2009 see Guti?rrez, Ramona A.; Naughtin, Monica J.; Horm, Srey V.; San, Sorn; Buchy, Philippe et al. 2009. "A(H5N1) Virus Evolution in South East Asia." Viruses 1, no. 3: 335-361. 6 October 2009
The following chronological articles of Cambodian isolates in HA clade1, 1.1 and proposed 1.1A by researchers with epidemiological evidence of proposed sublinaeges 1-6!
Notable strain designation A/Cambodian/W0329318/2012 is an HA 1.1 clade however is a new designation which I haven?t come across in GISAID or any other public database!
It's "W0" is similar to anther human case in January A/Cambodia/W0112303/2012 or CB19 in Influenza Virus Traceability Mechanism (IVTM)
----------------------------------------------------------------------
Summary of Diagnostic Results
Influenza type A (H5N1): 1 of 1 materials
Source IVTM-SRC363, Human, Cambodia
Source Type Human
Country/Area Cambodia
Notes CDC ID# 2012788593
CB19
Deceased
Created on 29-Aug-2012 15:38:03 | Last modified on 29-Aug-2012 15:38:03
Original Specimen IVTM-ORG703, Human, Cambodia
Date of
collection 10-Jan-2012
IVTM Parent IVTM-SRC363
Notes CDC ID# 2012788593
CB19
Deceased
Influenza type A (H5N1)
Specimen Type virus isolate cell culture
Place of collection Cambodia
Created on 29-Aug-2012 15:38:53 | Last modified on 29-Aug-2012 15:38:53
Influenza Virus Traceability Mechanism
Case CB19 background:
"Avian influenza ? situation in Cambodia
16 January 2012 - The Ministry of Health (MoH) of the Kingdom of Cambodia has announced a confirmed case of human infection with avian influenza A (H5N1) virus.
The case was a 2 year-old male from Banteay Meanchey Province. He developed symptoms on 3 January 2012 and was admitted to hospital on 9 January 2012. He is on Tamiflu and has been ventilated.
There have been reports that the boy was exposed to sick poultry in his village. He is the 19th person in Cambodia to become infected with the H5N1 virus; to date, 16 of these cases have died from complications of the disease.
The National and local Rapid Response Teams (RRT) are conducting outbreak investigation and response following the national protocol. Hospital staff who had contact with the case have been offered oseltamivir. To date, none of the human contacts have tested positive for A (H5N1)."
or see
Joint Statement by the Ministry of Health, Kingdom of Cambodia and World Health Organization (WHO). Nineteenth Human Case of Avian Influenza H5N1 in Cambodia.13 January 2012
-------------------------------------------------------------------------
The other cases are CB "case" 20 and CB "case" 21 in 2012
-----------------------------------------------------------------------
Influenza Virus Traceability Mechanism:WHO
Summary of Diagnostic Results
Influenza type A (H5N1): 1 of 1 materials
Source IVTM-SRC364, Human, Cambodia
Source Type Human
Country/Area Cambodia
Notes CDC ID# 2012788599
CB20
Deceased
Created on 29-Aug-2012 15:39:42 | Last modified on 29-Aug-2012 15:39:42
Original Specimen IVTM-ORG704, Human, Cambodia
Date of collection 28-Mar-2012
IVTM Parent IVTM-SRC364
Notes CDC ID# 2012788599
CB20
Deceased
Influenza type A (H5N1)
Specimen Type virus isolate cell culture
Place of collection Cambodia
Created on 29-Aug-2012 15:39:42 | Last modified on 29-Aug-2012 15:39:42
Influenza Virus Traceability Mechanism
Case CB20 background:
Avian influenza ? situation in Cambodia ? update
5 April 2012 - The Ministry of Health (MoH) of the Kingdom of Cambodia has announced a confirmed case of human infection with avian influenza A (H5N1) virus.
"The 6 year-old female from Kampong Chhnang Province developed symptoms on 22 March 2012. After initial treatment at the village, she was later admitted to hospital in Phnom Penh on 28 March. She died on 30 March. Infection with avian influenza A (H5N1) virus was confirmed by Institut Pasteur du Cambodge on 30 March.
It was reported that the patient had contact with sick or dead poultry prior to onset of illness.
The National and local Rapid Response Teams (RRT) are conducting outbreak investigation and response following the national protocol. In addition, a public health education campaign is being conducted to inform families on how to protect themselves from contracting avian influenza.
To date, of the 20 cases reported in Cambodia since 2005, 18 have been fatal."
or see
Joint Statement by the Ministry of Health, Kingdom of Cambodia and World Health Organization (WHO). Twentieth Human Case of Avian Influenza H5N1 in Cambodia.2 April 2012
-----------------------------------------------
Summary of Diagnostic Results
Influenza type A (H5N1): 1 of 1 materials
Source IVTM-SRC365, Human, Cambodia
Source Type Human
Country/Area Cambodia
Notes CDC ID# 2012788600
CB21
Deceased
Created on 29-Aug-2012 15:41:20 | Last modified on 29-Aug-2012 15:41:20
Original Specimen IVTM-ORG705, Human, Cambodia
Date of collection 25-May-2012
IVTM Parent IVTM-SRC365
Notes CDC ID# 2012788600
CB21
Deceased
Influenza type A (H5N1)
Specimen Type virus isolate cell culture
Place of collection Cambodia
Created on 29-Aug-2012 15:42:11 | Last modified on 29-Aug-2012 15:42:11
Influenza Virus Traceability Mechanism
Case CB21 background:
WHO | Avian influenza ? situation in Cambodia ? update
"Avian influenza ? situation in Cambodia ? update
29 May 2012 - The Ministry of Health (MoH) of the Kingdom of Cambodia has announced a confirmed case of human infection with avian influenza A (H5N1) virus.
The case was a 10 years old female from Kampong Speu Province. She developed symptoms on 20 May 2012 and after initial treatment at the village was eventually admitted to the hospital on 25 May with symptoms of fever and shortness of breath. Infection with avian influenza A(H5N1) virus was confirmed by Institute Pasteur du Cambodge on 26 May 2012, however, despite intensive medical care, she died on 27 May 2012.
There are reports of recent deaths among poultry in her village and the patient prepared sick chicken for food prior to becoming sick.
The girl is the twenty-first person in Cambodia to become infected with A(H5N1) virus and 19 have died from the disease.
The National and local Rapid Response Teams (RRT) are conducting outbreak investigation and response following the national protocol. In addition, a public health education campaign is being conducted in the village to inform families on how to protect themselves from contracting avian influenza."
or see
Joint Statement by the Ministry of Health, Kingdom of Cambodia and World Health Organization (WHO). Twenty first Human Case of Avian Influenza H5N1 in Cambodia.28 May 2012
------
Strain designation A/Cambodian/W0329318/2012 must be either CB20 or CB21 respectfully!
See: Proposed new HA clade 1.1A and Lineages 1 to 6
Snip:
Figure 2. . Phylogenetic relationship of the hemagglutinin (HA) gene among various influenza A(H5N1) strains; HA sequences for 48 strains (36 from Cambodia, 11 from Vietnam and one from China) were included in the analysis. Black triangles indicate viruses detected during this study of environmental samples from live poultry markets in Cambodia. Phylogenetic trees were generated by using the distance method and applying the neighbor-joining algorithm with bootstrap analysis (1,000 replicates). Analysis was based on nt 1?1,661 of the HA gene. The trees were rooted to A/goose/China/Guangdong/1/96 (H5N1). Numbers above and below branch nodes indicate bootstrap value of >70%. Scale bar represents the number of nucleotide changes per site. Lineage numbers 1?6, clades, and subclades indicate strains that are grouped in closely related phylogenetic lineages, as described (14). All sequences included in the analysis are available in GenBank.
Horm SV, Sorn S, Allal L, Buchy P. Influenza A(H5N1) virus surveillance at live poultry markets, Cambodia, 2011. Emerg Infect Dis. 2013 Feb http://dx.doi.org/10.3201/eid1902.121201
------------------------------------------------------------------------
WHO HA Clades:HA Clade 1 ,HA Clade 1.1
Cases: Strain designation
Case 1: A/Cambodia/JP52a/2005 (Odagiri et al. 2005 and Buchy et al. 09 only case in January); IRD: RERRRKKR
Case 2: A/Cambodia/P0322095/2005; IRD: RERRRKKR; M2 Ser31Asn
Case 3: A/Cambodia/408008/2005; IRD: RERRRKKR; PB2-E627K; M2-Ser31Asn
Case 4: A/Cambodia/VN05-103/2005; IRD: RERRRKKR
Case 5: A/Cambodia/Q0321176/2006; IRD: M2-31N
Case 6: A/Cambodia/Q0405047/2006; IRD: RERRRKKR
Case 7: A/Cambodia/R0405050/2007; IRD: M2-Ser31Asn; (VC-NIBRG-88*)
Case 8: A/Cambodia/S1211394/2008; IRD: M2-Ser31Asn
Case 9: N/A
Case 10:A/Cambodia/U0417030/2010; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 11:A/Cambodia/V0203306/2011; IRD: PB1-F2 N66S; PB2 E627K; M2-Ser31Asn
Case 12:N/A
Case 13:A/Cambodia/V0219301/2011; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 14:A/Cambodia/V0401301/2011; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 15:A/Cambodia/V0417301/2011; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 16:A/Cambodia/V0606311/2011; IRD: HA S227N; M2-Ser31Asn and A/Cambodia/V0606321/2011; No Comment for:NA and NS (both collected 6-June in Prey Veng)
Case 17:A/Cambodia/V0719348/2011; IRD: M2-Ser31Asn
Case 18:A/Cambodia/V0813302/2011; IRD: M2-Ser31Asn
Case 19:A/Cambodia/W0112303/2012; IRD: PB1-F2 N66S; PB2 D701N; M2 31N
Case 20:CB20 IVTM pending designation (Original sample CDC ID# 2012788599)
Case 21: CB21 IVTM pending designation (Original sample CDC ID# 2012788600)
Case 22:Pending
Case 23:Pending
Case 24:Pending
Case 25:Pending
Case 26:Pending
Case 27:Pending
Case 28:Pending
"Mutations comments do show increase in Mutations/Motifs possibly related to increase adaptation, virulence, and pathogenicity of Cambodian 1 and 1.1 HA Clades"
To support this personal comment see:
H5N1 Genetic Changes Inventory
Michael Fraser RN (Biological)
Buchy et al. 2009 Molecular Epidemiology of Clade 1 Influenza A Viruses (H5N1), Southern Indochina Peninsula, 2004?2007 Volume 15, Number 10?October 2009 - Emerging Infectious Disease journal ? CDC-http://wwwnc.cdc.gov/eid/article/15/10/09-0115_article.htm
Sorn, S., et al. Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade. Infect. Genet. Evol. (2012), http://dx.doi.org/10.1016/j.meegid.2012.05.013 http://www.sciencedirect.com/science...67134812002158
and now
Horm et al.2013 Influenza A(H5N1) Virus Surveillance at Live Poultry Markets, Cambodia, 2011 - Vol. 19 No. 2 - February 2013 - Emerging Infectious Disease journal CDC
(Also in 2009 see Guti?rrez, Ramona A.; Naughtin, Monica J.; Horm, Srey V.; San, Sorn; Buchy, Philippe et al. 2009. "A(H5N1) Virus Evolution in South East Asia." Viruses 1, no. 3: 335-361. 6 October 2009
The following chronological articles of Cambodian isolates in HA clade1, 1.1 and proposed 1.1A by researchers with epidemiological evidence of proposed sublinaeges 1-6!
Notable strain designation A/Cambodian/W0329318/2012 is an HA 1.1 clade however is a new designation which I haven?t come across in GISAID or any other public database!
It's "W0" is similar to anther human case in January A/Cambodia/W0112303/2012 or CB19 in Influenza Virus Traceability Mechanism (IVTM)
----------------------------------------------------------------------
Summary of Diagnostic Results
Influenza type A (H5N1): 1 of 1 materials
Source IVTM-SRC363, Human, Cambodia
Source Type Human
Country/Area Cambodia
Notes CDC ID# 2012788593
CB19
Deceased
Created on 29-Aug-2012 15:38:03 | Last modified on 29-Aug-2012 15:38:03
Original Specimen IVTM-ORG703, Human, Cambodia
Date of
collection 10-Jan-2012
IVTM Parent IVTM-SRC363
Notes CDC ID# 2012788593
CB19
Deceased
Influenza type A (H5N1)
Specimen Type virus isolate cell culture
Place of collection Cambodia
Created on 29-Aug-2012 15:38:53 | Last modified on 29-Aug-2012 15:38:53
Influenza Virus Traceability Mechanism
Case CB19 background:
"Avian influenza ? situation in Cambodia
16 January 2012 - The Ministry of Health (MoH) of the Kingdom of Cambodia has announced a confirmed case of human infection with avian influenza A (H5N1) virus.
The case was a 2 year-old male from Banteay Meanchey Province. He developed symptoms on 3 January 2012 and was admitted to hospital on 9 January 2012. He is on Tamiflu and has been ventilated.
There have been reports that the boy was exposed to sick poultry in his village. He is the 19th person in Cambodia to become infected with the H5N1 virus; to date, 16 of these cases have died from complications of the disease.
The National and local Rapid Response Teams (RRT) are conducting outbreak investigation and response following the national protocol. Hospital staff who had contact with the case have been offered oseltamivir. To date, none of the human contacts have tested positive for A (H5N1)."
or see
Joint Statement by the Ministry of Health, Kingdom of Cambodia and World Health Organization (WHO). Nineteenth Human Case of Avian Influenza H5N1 in Cambodia.13 January 2012
-------------------------------------------------------------------------
The other cases are CB "case" 20 and CB "case" 21 in 2012
-----------------------------------------------------------------------
Influenza Virus Traceability Mechanism:WHO
Summary of Diagnostic Results
Influenza type A (H5N1): 1 of 1 materials
Source IVTM-SRC364, Human, Cambodia
Source Type Human
Country/Area Cambodia
Notes CDC ID# 2012788599
CB20
Deceased
Created on 29-Aug-2012 15:39:42 | Last modified on 29-Aug-2012 15:39:42
Original Specimen IVTM-ORG704, Human, Cambodia
Date of collection 28-Mar-2012
IVTM Parent IVTM-SRC364
Notes CDC ID# 2012788599
CB20
Deceased
Influenza type A (H5N1)
Specimen Type virus isolate cell culture
Place of collection Cambodia
Created on 29-Aug-2012 15:39:42 | Last modified on 29-Aug-2012 15:39:42
Influenza Virus Traceability Mechanism
Case CB20 background:
Avian influenza ? situation in Cambodia ? update
5 April 2012 - The Ministry of Health (MoH) of the Kingdom of Cambodia has announced a confirmed case of human infection with avian influenza A (H5N1) virus.
"The 6 year-old female from Kampong Chhnang Province developed symptoms on 22 March 2012. After initial treatment at the village, she was later admitted to hospital in Phnom Penh on 28 March. She died on 30 March. Infection with avian influenza A (H5N1) virus was confirmed by Institut Pasteur du Cambodge on 30 March.
It was reported that the patient had contact with sick or dead poultry prior to onset of illness.
The National and local Rapid Response Teams (RRT) are conducting outbreak investigation and response following the national protocol. In addition, a public health education campaign is being conducted to inform families on how to protect themselves from contracting avian influenza.
To date, of the 20 cases reported in Cambodia since 2005, 18 have been fatal."
or see
Joint Statement by the Ministry of Health, Kingdom of Cambodia and World Health Organization (WHO). Twentieth Human Case of Avian Influenza H5N1 in Cambodia.2 April 2012
-----------------------------------------------
Summary of Diagnostic Results
Influenza type A (H5N1): 1 of 1 materials
Source IVTM-SRC365, Human, Cambodia
Source Type Human
Country/Area Cambodia
Notes CDC ID# 2012788600
CB21
Deceased
Created on 29-Aug-2012 15:41:20 | Last modified on 29-Aug-2012 15:41:20
Original Specimen IVTM-ORG705, Human, Cambodia
Date of collection 25-May-2012
IVTM Parent IVTM-SRC365
Notes CDC ID# 2012788600
CB21
Deceased
Influenza type A (H5N1)
Specimen Type virus isolate cell culture
Place of collection Cambodia
Created on 29-Aug-2012 15:42:11 | Last modified on 29-Aug-2012 15:42:11
Influenza Virus Traceability Mechanism
Case CB21 background:
WHO | Avian influenza ? situation in Cambodia ? update
"Avian influenza ? situation in Cambodia ? update
29 May 2012 - The Ministry of Health (MoH) of the Kingdom of Cambodia has announced a confirmed case of human infection with avian influenza A (H5N1) virus.
The case was a 10 years old female from Kampong Speu Province. She developed symptoms on 20 May 2012 and after initial treatment at the village was eventually admitted to the hospital on 25 May with symptoms of fever and shortness of breath. Infection with avian influenza A(H5N1) virus was confirmed by Institute Pasteur du Cambodge on 26 May 2012, however, despite intensive medical care, she died on 27 May 2012.
There are reports of recent deaths among poultry in her village and the patient prepared sick chicken for food prior to becoming sick.
The girl is the twenty-first person in Cambodia to become infected with A(H5N1) virus and 19 have died from the disease.
The National and local Rapid Response Teams (RRT) are conducting outbreak investigation and response following the national protocol. In addition, a public health education campaign is being conducted in the village to inform families on how to protect themselves from contracting avian influenza."
or see
Joint Statement by the Ministry of Health, Kingdom of Cambodia and World Health Organization (WHO). Twenty first Human Case of Avian Influenza H5N1 in Cambodia.28 May 2012
------
Strain designation A/Cambodian/W0329318/2012 must be either CB20 or CB21 respectfully!
See: Proposed new HA clade 1.1A and Lineages 1 to 6
Snip:
Figure 2. . Phylogenetic relationship of the hemagglutinin (HA) gene among various influenza A(H5N1) strains; HA sequences for 48 strains (36 from Cambodia, 11 from Vietnam and one from China) were included in the analysis. Black triangles indicate viruses detected during this study of environmental samples from live poultry markets in Cambodia. Phylogenetic trees were generated by using the distance method and applying the neighbor-joining algorithm with bootstrap analysis (1,000 replicates). Analysis was based on nt 1?1,661 of the HA gene. The trees were rooted to A/goose/China/Guangdong/1/96 (H5N1). Numbers above and below branch nodes indicate bootstrap value of >70%. Scale bar represents the number of nucleotide changes per site. Lineage numbers 1?6, clades, and subclades indicate strains that are grouped in closely related phylogenetic lineages, as described (14). All sequences included in the analysis are available in GenBank.
Horm SV, Sorn S, Allal L, Buchy P. Influenza A(H5N1) virus surveillance at live poultry markets, Cambodia, 2011. Emerg Infect Dis. 2013 Feb http://dx.doi.org/10.3201/eid1902.121201
------------------------------------------------------------------------
WHO HA Clades:HA Clade 1 ,HA Clade 1.1
Cases: Strain designation
Case 1: A/Cambodia/JP52a/2005 (Odagiri et al. 2005 and Buchy et al. 09 only case in January); IRD: RERRRKKR
Case 2: A/Cambodia/P0322095/2005; IRD: RERRRKKR; M2 Ser31Asn
Case 3: A/Cambodia/408008/2005; IRD: RERRRKKR; PB2-E627K; M2-Ser31Asn
Case 4: A/Cambodia/VN05-103/2005; IRD: RERRRKKR
Case 5: A/Cambodia/Q0321176/2006; IRD: M2-31N
Case 6: A/Cambodia/Q0405047/2006; IRD: RERRRKKR
Case 7: A/Cambodia/R0405050/2007; IRD: M2-Ser31Asn; (VC-NIBRG-88*)
Case 8: A/Cambodia/S1211394/2008; IRD: M2-Ser31Asn
Case 9: N/A
Case 10:A/Cambodia/U0417030/2010; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 11:A/Cambodia/V0203306/2011; IRD: PB1-F2 N66S; PB2 E627K; M2-Ser31Asn
Case 12:N/A
Case 13:A/Cambodia/V0219301/2011; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 14:A/Cambodia/V0401301/2011; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 15:A/Cambodia/V0417301/2011; IRD: PB1-F2 N66S; M2-Ser31Asn
Case 16:A/Cambodia/V0606311/2011; IRD: HA S227N; M2-Ser31Asn and A/Cambodia/V0606321/2011; No Comment for:NA and NS (both collected 6-June in Prey Veng)
Case 17:A/Cambodia/V0719348/2011; IRD: M2-Ser31Asn
Case 18:A/Cambodia/V0813302/2011; IRD: M2-Ser31Asn
Case 19:A/Cambodia/W0112303/2012; IRD: PB1-F2 N66S; PB2 D701N; M2 31N
Case 20:CB20 IVTM pending designation (Original sample CDC ID# 2012788599)
Case 21: CB21 IVTM pending designation (Original sample CDC ID# 2012788600)
Case 22:Pending
Case 23:Pending
Case 24:Pending
Case 25:Pending
Case 26:Pending
Case 27:Pending
Case 28:Pending
"Mutations comments do show increase in Mutations/Motifs possibly related to increase adaptation, virulence, and pathogenicity of Cambodian 1 and 1.1 HA Clades"
To support this personal comment see:
H5N1 Genetic Changes Inventory
Michael Fraser RN (Biological)
Comment