This document summarizes genetic analysis of HIV-1 strains circulating in Russia. The key points are:
1. Subtype A1 is the most prevalent, accounting for 75% of strains, but subtypes B, G, and CRF03_AB also contribute significantly to the epidemic in Russia.
2. The distribution of subtypes varies by geographical region within Russia. For example, subtype G strains were highly concentrated in two southern cities.
3. Many strains showed natural polymorphisms in protease and reverse transcriptase genes that could influence response to antiretroviral treatment, highlighting the need for genotype testing to guide therapy.
Karyotypic complexity and multiclonality: Two cytogenetic parameters to be co...Georgia Bardi
Karyotypic complexity and multiclonality (either cytogenetically unrelated clones or cytogenetically related clones) represent two parameters of prognostic significance in management of patients with Myelodysplastic syndromes.
Presented by Georgia Bardi, PhD at MDS workshop in Perugia 2008. Cytogenetic data produced by Eugenia Gourgouveli and Despina Iakovaki.
Karyotypic complexity and multiclonality: Two cytogenetic parameters to be co...Georgia Bardi
Karyotypic complexity and multiclonality (either cytogenetically unrelated clones or cytogenetically related clones) represent two parameters of prognostic significance in management of patients with Myelodysplastic syndromes.
Presented by Georgia Bardi, PhD at MDS workshop in Perugia 2008. Cytogenetic data produced by Eugenia Gourgouveli and Despina Iakovaki.
Dhirendra Kumar1, Preety Sinha2, Naresh Chand Sharma3*
1Research Scholar, PG Department of Zoology, A. N. College, Patna, India
2Professor, PG Department of Zoology, A. N. College, Patna, India
3Consultant Bacteriologist, Laboratory Department, Maharishi Valmiki Infectious Diseases Hospital, Delhi, India
*Address for Correspondence: Dr. Naresh Chand Sharma, Consultant Bacteriologist, Laboratory Department,
Maharishi Valmiki Infectious Diseases Hospital, Kingsway Campus, Delhi, India
Received: 17 Sept 2016/Revised: 28 Sept 2016/Accepted: 19 Oct 2016
ABSTRACT- The acute diarrheal disease cholera is caused by Vibrio cholerae, a major public health problem in Asia,
Africa and Latin America. V. cholerae has more than 200 known serotypes but not all the strains are pathogenic. In recent
years, it has been seen that the emergence of new variants of V. cholerae O1 have carried characteristics of both classical
and El Tor biotypes and these variants of V. cholerae O1 are called as ‘atypical El Tor’. These strains might have evolved
from El Tor variants that acquired certain characteristics from classical genome. 30 V. cholerae O1 isolates (Table 1) were
revived from stock cultures maintained at Laboratory Department in Maharishi Valmiki Infectious Diseases Hospital
(MVIDH), Delhi during 2012-2014. Mismatch amplification mutation assay was used for classifying the strains into
prototype El Tor, hybrid, or El Tor variant biotype based on their ctxB gene. All isolates were biochemically identified as
V. cholerae biotype El Tor and serologically O1 Ogawa. All isolates were amplified with classical specific primers.
Cholera continues to be endemic in large number of states in the eastern, western, northern and southern parts of India and
there were 38 cholera outbreak reports published in India during 2007 to 2013. These Indian outbreaks have been
associated with new El Tor variant.
Key-words- V. cholerae O1, El Tor, MAMA PCR, ctxB
Assessment of immunomolecular_expression_and_prognostic_role_of_tlr7_among_pa...dr.Ihsan alsaimary
Dr. ihsan edan abdulkareem alsaimary
PROFESSOR IN MEDICAL MICROBIOLOGY AND MOLECULAR IMMUNOLOGY
ihsanalsaimary@gmail.com
mobile : 009647801410838
university of basrah - college of medicine - basrah -IRAQ
La disponibilidad de un sistema de multiplicación del virus de la hepatitis C (VHC) infeccioso en cultivos celulares está permitiendo investigar nuevos factores de respuesta a tratamientos antivíricos en condiciones controladas. Se presentará evidencia de que el fitness vírico puede ser un factor de multiresistencia a inhibidores y quese pueden obtener eficientes reducciones de carga viral empleando diseños secuenciales de administración de inhibidores que incluyan ribavirina. Se discutirán posibilidades de aplicación clínica.
Dhirendra Kumar1, Preety Sinha2, Naresh Chand Sharma3*
1Research Scholar, PG Department of Zoology, A. N. College, Patna, India
2Professor, PG Department of Zoology, A. N. College, Patna, India
3Consultant Bacteriologist, Laboratory Department, Maharishi Valmiki Infectious Diseases Hospital, Delhi, India
*Address for Correspondence: Dr. Naresh Chand Sharma, Consultant Bacteriologist, Laboratory Department,
Maharishi Valmiki Infectious Diseases Hospital, Kingsway Campus, Delhi, India
Received: 17 Sept 2016/Revised: 28 Sept 2016/Accepted: 19 Oct 2016
ABSTRACT- The acute diarrheal disease cholera is caused by Vibrio cholerae, a major public health problem in Asia,
Africa and Latin America. V. cholerae has more than 200 known serotypes but not all the strains are pathogenic. In recent
years, it has been seen that the emergence of new variants of V. cholerae O1 have carried characteristics of both classical
and El Tor biotypes and these variants of V. cholerae O1 are called as ‘atypical El Tor’. These strains might have evolved
from El Tor variants that acquired certain characteristics from classical genome. 30 V. cholerae O1 isolates (Table 1) were
revived from stock cultures maintained at Laboratory Department in Maharishi Valmiki Infectious Diseases Hospital
(MVIDH), Delhi during 2012-2014. Mismatch amplification mutation assay was used for classifying the strains into
prototype El Tor, hybrid, or El Tor variant biotype based on their ctxB gene. All isolates were biochemically identified as
V. cholerae biotype El Tor and serologically O1 Ogawa. All isolates were amplified with classical specific primers.
Cholera continues to be endemic in large number of states in the eastern, western, northern and southern parts of India and
there were 38 cholera outbreak reports published in India during 2007 to 2013. These Indian outbreaks have been
associated with new El Tor variant.
Key-words- V. cholerae O1, El Tor, MAMA PCR, ctxB
Assessment of immunomolecular_expression_and_prognostic_role_of_tlr7_among_pa...dr.Ihsan alsaimary
Dr. ihsan edan abdulkareem alsaimary
PROFESSOR IN MEDICAL MICROBIOLOGY AND MOLECULAR IMMUNOLOGY
ihsanalsaimary@gmail.com
mobile : 009647801410838
university of basrah - college of medicine - basrah -IRAQ
La disponibilidad de un sistema de multiplicación del virus de la hepatitis C (VHC) infeccioso en cultivos celulares está permitiendo investigar nuevos factores de respuesta a tratamientos antivíricos en condiciones controladas. Se presentará evidencia de que el fitness vírico puede ser un factor de multiresistencia a inhibidores y quese pueden obtener eficientes reducciones de carga viral empleando diseños secuenciales de administración de inhibidores que incluyan ribavirina. Se discutirán posibilidades de aplicación clínica.
Gene therapy is a technique that modifies a person's genes to treat or cure disease. Gene therapies can work by several mechanisms: Replacing a disease-causing gene with a healthy copy of the gene. Inactivating a disease-causing gene that is not functioning properly. Genetic therapies hold promise to treat many diseases, but they are still new approaches to treatment and may have risks. Potential risks could include certain types of cancer, allergic reactions, or damage to organs or tissues if an injection is involved. Recent advances have made genetic therapies much safer. Gene therapy is on course to revolutionize medical care for several conditions. The hope is that gene therapy will be a one-time curative therapeutic intervention for diseases ranging from inherited hemoglobinopathies, such as sickle cell disease and thalassemia, to acquired diseases such as HIV.
Dr. Igor Paploski - Making Epidemiological Sense Out of Large Datasets of PRR...John Blue
Making Epidemiological Sense Out of Large Datasets of PRRS Sequences - Dr. Igor Paploski, from the 2018 Allen D. Leman Swine Conference, September 15-18, 2018, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2018-leman-swine-conference-material
Novel tools for immune quiecense monitoring in kidney transplanation poster a...Kevin Jaglinski
Organ transplant patients face life-long immunosuppression (IS) with increased morbidity. Currently unknown numbers of kidney transplant recipients develop a state of targeted immune quiescence (Operational Tolerance, TOL) allowing them to withdraw IS while retaining stable graft function and continuing immune responses against 3rd party antigens. Transcriptional Profiling Peripheral Blood is a means to provide a gene signature to monitor this state of TOL, to titrate IS in patients with this signature, and to better understand the underlying biology.
Variation analysis of Swine influenza virus (SIV) H1N1 sequences in experimen...Álvaro L. Valiñas
Swine influenza is a highly contagious and widely distributed disease that generates important economic losses in the pig industry. Nowadays, one of the most extended strategy used to control Swine influenza viruses (SIVs) is the trivalent vaccine application, which formulation contains the most frequently circulating SIV subtypes H1N1, H1N2 and H3N2. These vaccines do not provide sterilizing immunity against the virus, potentially favoring viral evolutionary dynamics. To better understand the main mechanisms that shape viral evolution, in this work, the SIV intra-host diversity was analyzed in samples collected from both, vaccinated and non-vaccinated animals challenged with H1N1 influenza A virus. In the present study 276 single nucleotide variants were found within 28 whole SIV genomes obtained by next generation sequencing. Differences in nucleotide variants between groups were established and the impact of each substitution found was hypothesized according to previous literature. Substitutions were allocated along all influenza genetic segments, while the most relevant non-synonymous substitutions were allocated in the NS1 protein on samples collected only from vaccinated animals. These substitutions could affect both, mRNA viral translation and pathogenesis. Moreover, new viral variants were found in both vaccinated and non-vaccinated pigs, showing relevant substitutions in the HA, NA and NP proteins that may be contributing to evasion of host immune system, virulence and host adaptation. Overall, results of the present study suggest that SIV is continuously evolving despite vaccine application, therefore new substitutions may increase viral fitness under field conditions.
Variation analysis of Swine influenza virus (SIV) H1N1 sequences in experimen...Álvaro L. Valiñas
Swine influenza is a highly contagious and widely distributed disease that generates important economic losses in the pig industry. Nowadays, one of the most extended strategy used to control Swine influenza viruses (SIVs) is the trivalent vaccine application, which formulation contains the most frequently circulating SIV subtypes H1N1, H1N2 and H3N2. These vaccines do not provide sterilizing immunity against the virus, potentially favoring viral evolutionary dynamics. To better understand the main mechanisms that shape viral evolution, in this work, the SIV intra-host diversity was analyzed in samples collected from both, vaccinated and non-vaccinated animals challenged with H1N1 influenza A virus. In the present study 276 single nucleotide variants were found within 28 whole SIV genomes obtained by next generation sequencing. Differences in nucleotide variants between groups were established and the impact of each substitution found was hypothesized according to previous literature. Substitutions were allocated along all influenza genetic segments, while the most relevant non-synonymous substitutions were allocated in the NS1 protein on samples collected only from vaccinated animals. These substitutions could affect both, mRNA viral translation and pathogenesis. Moreover, new viral variants were found in both vaccinated and non-vaccinated pigs, showing relevant substitutions in the HA, NA and NP proteins that may be contributing to evasion of host immune system, virulence and host adaptation. Overall, results of the present study suggest that SIV is continuously evolving despite vaccine application, therefore new substitutions may increase viral fitness under field conditions.
Towards Precision Medicine: Tute Genomics, a cloud-based application for anal...Reid Robison
Tute Genomics is cloud-based software that can rapidly analyze entire human genomes. The cost of whole genome sequencing is dropping rapidly and we are in the middle of a genomic revolution. Tute is opening a new door for personalized medicine by helping researchers & healthcare organizations analyze human genomes.
Dr. Yao-Wei Huang - Here we go again? Emergence of a novel swine enteric alph...John Blue
Here we go again? Emergence of a novel swine enteric alphacoronavirus (SeACov) in Southern China - Dr. Yao-Wei Huang, Zhejiang University, from the 2017 North American PRRS/National Swine Improvement Federation Joint Meeting, December 1‐3, 2017, Chicago, Illinois, USA.
More presentations at http://www.swinecast.com/2017-north-american-prrs-nsif-joint-meeting
— We performed analysis of the biological properties of African swine fever virus (ASF) isolate Odintsovo 02/14. Domestic pigs were inoculated with 50 (low) or 5000 (high) hemadsorbing doses (HAD) of the virus via intranasal (IN) or intramuscular (IM) routes, to investigate the pathogenesis of ASF virus Odintsovo 02/14 isolate. Our results indicated that filtered 10% spleen suspension of ASFV isolate Odintsovo 02/14 induced an acute disease in pigs, resulting in 100% mortality rate. For cultural viral suspension (3rd passage), produced in a PBM cells mortality rate was 85.7%. We also present an analysis of the complete genome of African swine fever virus (ASF) Odintsovo 02/14 isolate. It is 189 333 nucleotide long and contains more than 160 open reading frames (ORFs). Complete nucleotide sequence of the genome of Odintsovo 02/14 isolate was obtained using pyrosequencing method and used to determine differences between the nucleotide sequences in the genomes of Odintsovo 02/14 and Georgia 01/2007. The genome of ASF virus Odintsovo 02/14 contains substitutions, insertions and deletions in genes encoding structural, membrane, and regulatory proteins, DNA reparation enzymes, host immune response evasion proteins, and MGF genes. The intergenic region I73R/I329L of Odintsovo 02/14 isolate contains 10-nucleotide long tandem repeat sequence, missing in Georgia 01/2007. Keywords— African swine fever (ASF), experimental challenge, complete genome sequencing, intergenic region, tandem repeats.
1. Conclusions
l The genetic diversity of HIV-1 circulating in Russia is complex & subtype distri-
bution is related to the geographical region of sample collection.
l A1, the most prevalent subtype, accounts for 75% of strains evaluated.
l A1 strains in Russia (AFSU) appear to cluster independently from A1 reference
strains collected in other parts of the world.
l Subtypes B (6.8%), G (9.3%) and CRF03_AB (7%) also contribute to the HIV-1
epidemic in Russia.
l Other strains (2%) include subtypes A3, C, F1, CRF01_AE, CR02_AG, CRF06_cpx
and CRF32_06A1.
l We detected a high frequency of protease polymorphic mutations in positions
associated with drug resistance. The influence of these polymorphisms on the
success of protease inhibitor therapy deserves further investigation.
l Availability of commercial genotyping assay facilitates management of patients
on HAART regimens, and identifies natural polymorphisms in drug naïve patients
that may influence resistance pathways.
Genetic Characterization of Diverse HIV-1 Strains Circulating in Russia
Natalia Marlowe1
*, Priscilla Swanson2
, Lei Fang1
, Vera Holzmayer2
, Peter Smith1
, Robert Bruce1
, Sven Thamm3
, Tatiana Kondrashova3
, John Hackett, Jr.2
and the Russian HIV-1 Study Group4
1
Celera, Alameda, USA; 2
Abbott Diagnostics, Abbott Park, USA; 3
Abbott Molecular, Germany; 4
Russian HIV-1 Study Group
Abstract
Background: Of the European countries, Russia has the largest number of HIV infections. The dominant strain in
Russia has been a variant of subtype A1 (AFSU), followed by subtypes B and an intersubtype recombinant CRF03_AB.
To examine the molecular epidemiology of circulating virus strains, plasma samples were collected from HIV-1
infected subjects attending ten geographically diverse AIDS centers in Russia.
Methods: Plasma samples were collected in 2007-2009 from 611 HIV-1 infected individuals and processed at
the clinical laboratories of Rostov (n=29), Ust-Izhora (n=79), St. Petersburg AIDS & Pasteur Institute (n=70, n=20),
Yekaterinburg (n=43), Kazan (n=62), Vologda (n=89), Krasnoyarsk (n=67), Noyabrsk (n=129), and Khabarovsk (n=23).
Protease and reverse transcriptase were sequenced using the ViroSeq HIV-1 Genotyping System v2.0. Consensus
sequences for each sample were aligned against HIV-1 group M reference strains and Russian genomes from the
Los Alamos HIV Sequence Database. Phylogenetic analysis was performed using Phylip software to assign HIV-1
subtype.
Results: Complete protease and 5' reverse transcriptase sequences were obtained for 556 samples. The subtype
composition of the panel included 6 subtypes and 5 circulating recombinant forms (CRFs): 416 A1 (74.8%), 52 G
(9.3%), 39 CRF03_AB (7.0%), 38 B (6.8%), 3 CRF02_AG (0.5%), 2 CRF01_AE (0.4%), 2 F1 (0.4%) as well as 1 each of
A3, C, CRF06_cpx, and CRF32_06A1 (0.2% each). A1 strains were identified in all regions and clustered with the
Russian AFSU sequences. Subtype G strains were present in nearly 50% of the samples from Rostov and Ust-Izhora
sites, and formed closely related clusters suggesting common ancestors. Subtype B was found at all locations
except three southern cities, and CRF03_AB was primarily restricted to the northwest and central regions.
Conclusions: These data demonstrate complex genetic diversity of the HIV-1 strains circulating in Russia. While
A1 is still the most prevalent subtype, other strains, especially subtype G and CRF03_AB, are contributing to the
increasing genetic diversity of non-B HIV-1 epidemic in this country. The subtype distribution was shown to be
closely related to the geographical region where samples were collected.
Study OBJECTIVEs
l To evaluate performance of the ViroSeq™ HIV-1 Genotyping system v 2.0 (Celera, Alameda, CA) on HIV infected
plasma collected (and processed) by AIDS Centers in Russia
l To determine HIV-1 subtypes and analyze natural polymorphisms in virus strains circulating in Russia
MATERIALS & METHODS
l Number of HIV-1 samples and panel composition were determined by each participating center
l Samples were collected and processed at the participating site using the ViroSeq system
l ViroSeq PCR, sequencing results and sample information (Viral load, treatment history) were sent to Abbott/
Celera for data analysis
l Sequencing data were used for Drug Resistance analysis with ViroSeq v2.8 software
l ViroSeq Protease/Reverse Transcriptase sequences were aligned with reference sequences (Los Alamos HIV
Sequence Database) for HIV-1 group M subtypes and circulating recombinant forms (CRF’s)
l Phylogenetic analysis for subtype determination was performed using the PHYLIP software (v3.5c; J.
Felsenstein, Univ of Washington, Seattle, WA)
RESULTS
Phylogenetic Analysis
Genetic Diversity by site
Site n A1 A3 B C F1 G CRF01 CRF02 CRF03 CRF06 CRF32
Saint Petersburg
Pasteur Institute
20 17 1 2
Saint Petersburg
AIDS
70 54 13 2 1
Ust-Izhora 72 16 1 7 39 2 7
Vologda 59 45 1 12 1
Rostov 28 14 13 1
Kazan 51 50 1
Yekaterinburg 38 29 9
Noyabrsk 129 117 2 2 8
Krasnoyarsk 67 61 6
Khabarovsk 22 13 8 1
Total (n) 556 416 1 38 1 2 52 2 3 39 1 1
% 74.8 0.2 6.8 0.2 0.4 9.3 0.4 0.5 7.0 0.2 0.2
Distribution of HIV-1 Subtypes in Russia (n = 556)
A1
B
G
CRF03_AB
A3
C
St. Petersburg (AIDS)
St. Petersburg (Pasteur)
Ust-Izhora
Vologda Rostov YekaterinburgKazan
Krasnoyarsk
Noyabrsk
Khabarovsk
F1
CRF01_AG
CRF02_AG
CRF06_cpx
CRF32_06A1
A1 (74.8%)
B (6.8%)
G (9.3%)
CRF03_AB
(7%)
All Other
(2.1%)
(85%)
(77.1%)
(18.6%)
(22.2%)
(9.7%)
(54.2%)
(9.7%)
(76.3%)
(20.3%)
(46.4%)(50%)
(98%)
(76.3%)
(23.7%)
(90.7%)
(6.2%)
(91%)
(9%)
(36.4%)
(59.1%)
(10%)
Neighbor-Joining Tree of HIV-1 Subtypes/CRF's in Russia
90
100
97
93
99
97
100
98
83
76
66
100
100
8574
-
-
0
--
-
-
-
1
-
-
-
-
n
v
-1v
-
0.02
B
C
CRF02_AG
CRF01_AE
CRF06_cpx
CRF32_06A1
D
F1
F2
CRF03_AB
HG
A1
A3
Afsu
Representative virus strains from each of 10 sites (black triangle) are shown relative to HIV-1 reference strains. Numbers at
selected nodes indicate bootstrap support (%). Branches are labeled with the HIV-1 subtype or CRF. Outgroup (SIV-cpz)
was removed from the tree. AFSU designates the A1 strains observed in Russia.
Neighbor-Joining Tree of HIV-1 Subtype A1 in Russia (Afsu)
Yekaterinburg
Vologda
A1-RU00051
Ust-Izhora
Ust-Izhora
Rostov
Khabarovsk
St Petersburg Pasteur
St Petersburg AIDS
St Petersburg Pasteur
Krasnoyarsk
St Petersburg AIDS
Noyabrsk
Noyabrsk
Noyabrsk
Yekaterinburg
Rostov
Kazan
Vologda
Krasnoyarsk
A1-RUPok
St Petersburg AIDS
Ust-Izhora
A1-RU20061
Khabarovsk
Krasnoyarsk
Khabarovsk
Rostov
Kazan
Yekaterinburg
Kazan
Vologda
SIV-CPZGAB
0.02
CRF01_AE
Afsu
B
A1
99
100
100
78
63
78
71
St Petersburg Pasteur
A1
Representative A1 virus strains from
each of 10 Russian sites (AFSU) are shown
relative to HIV-1 reference strains A1, B
and CRF01_AE. Numbers at selected
nodes indicate bootstrap support
(%). A1 strains highlighted in red are
full genome Russian reference strains.
The branch labeled A1 represents
reference strains from Kenya, Somalia
& Uganda.
Acknowledgements
We thank the following investigators and institutions for their
collaboration:
St. Petersburg (Pasteur): Tatiana Smolskaya, Ph.D. - Pasteur St. Petersburg
Research Institute for Epidemiology and Microbiology, Northwest
Federal AIDS Center Diagnostical Division
St. Petersburg (AIDS): Natalya Dementyeva - St. Petersburg Municipal
AIDS Center, Clinical Diagnostics Lab
Ust-Izhora: Galina Korovina Ph.D. - Russian Republican Clinical Hospital for
Infectious Diseases, Clinical Diagnostics Lab
Vologda: Lyudmila Chernyshova - Vologda Region AIDS Center, Clinical
Immunology
Rostov: Svetlana Poddubskaya - Rostov Research Institute for Microbiology
and Parasitology, Division of Health Survey and Clinical Laboratory
Monitoring of HIV-infected patients
Kazan: Valery Gerasimov Ph.D. - Tatarstan Republican AIDS Center,
Molecular Biology Research Lab
Yekaterinburg: Tatiana Sandyreva - Sverdlovsk Region AIDS Center,
Division of Clinical Laboratory Diagnostics
Noyabrsk: Lyudmila Volova, Ph.D. - Yamalo-Nenets Region AIDS Center
Clinical Diagnostic Lab
Krasnoyarck: Olga Rumyantseva - Krasnoyarsk Region AIDS Center,
Division of Molecular Genetic Research
Khabarovsk: Valeria Kotova - Khabarovsk Research Institute for
Epidemiology and Microbiology, Diagnostic Lab
#439
Substitutions in Protease/Reverse Transcriptase at Drug Resistance-Associated Amino Acid Positions^
HIV-1 Strains from Drug Naïve Russian Subjects (n = 139)
Protease amino acids 10-93
HXB2 L I G K L E M K I Q D I L I H V V N L I
AA position 10 13 16 20 33 35 36 43 47 58 60 62 63 64 69 77 82 83 89 93
Mutation* I, F, V, C V E R, M, I, T, V I, F, V G I, L, V T V E E V P L, M, V K I A, T, F, I, S, L D V L, M
Subtype (n)
A1 (112) I8, V1 V57 E23, A2 R3 D103 I109 T1 M1 E1 V2 I2, P7, T3, V3 M2, V1 K112 I31 M109 L59
B (10) I2, V1 V2 E1 I2 D2 I1 E1 E1 V5 P4, Q1, S2, T1 L1, M1 Q1 I3 I1 L4
G (2) I1 V2 I2 D2 I2 K2 I2 M2
CRF03_AB (15) I3, V1 V8 D15 I15 T1 K15 Y1 M15 L6
TOTAL (139) I14, V3 V69 E24 R3, I2 I2 I127 T1 E1 E2 V7 P11 L1, M3, V1 K129 I34 I3 L69
% of Total 10.0, 2.2 49.6 17.2 2.2, 1.4 1.4 91.4 0.7 0.7 1.4 5.0 7.9 0.7, 2.2, 0.7 92.8 24.4 2.2 49.6
Amino acid (letter) followed by number indicates the number of strains observed with a selected drug-associated substitution.
^Based on guidelines of IAS, CID 2008:47, 266-285
Reverse Transcriptase amino acids 62-210
HXB2 A D V A K F Q V Y G L
AA position 62 67 90 98 101 116 151 179 188 190 210
Mutation* V N I G E, P Y M D, F, T L A, S W
Subtype (n)
A1 (112) V47 N1 I7 S1 R2, Q1 Y1 M1 I1, G1 M1 A1, S1 F1, M1, S1
B (10) S2 I2 F1
G (2)
CRF03_AB (15) N1 S1 D1
TOTAL (139) V47 N2 I7 S4 R2, Q1 Y1 M1 D1, I3, G1 M1 A1, S1 F2, M1, S1
% of Total 33.8 1.4 5.0 0.7 0.7 0.7 0.7, 0.7
HIV-1 Strains from Drug Treated Russian Subjects (n = 119)
Protease amino acids 10-93
HXB2 L I G K L E M K I Q D I L I H V V N L I
AA position 10 13 16 20 33 35 36 43 47 58 60 62 63 64 69 77 82 83 89 93
Mutation* I, F, V, C V E R, M, I, T, V I, F, V G I, L, V T V E E V P L, M, V K I A, T, F, I, S, L D V L, M
Subtype (n)
A1 (83) I6, V5 V35 A1, E14 R4, T2 D73 I82 T2 E1 V1 C1, I1, P6, T2, V2 K82 I22 F1 I1, M79, T1 L28
B (9) I6, F1 V1 E3 I1 D7 I5 V1 V1 P4, S1, T3 M1, V2 K1 I2 A1 L5
F1 (2) V1 V2 R2 D1 I2 I1 M2
G (21) I6 V21 E4 I17, T1 I2 D17, N2 I21 R3 E1 P1, R1, T3 M1 K20, R1 F1, I19, S1 I4, M14, V3 M2
CRF02_AG (1) V1 E1 I1 D1 I1 R1 L1 K1 M1 V1
CRF03_AB (2) V2 D2 I2 V1 K2 M2 L1
CRF32_06A1 (1) I1 V1 I1 D1 I1 H1 M1 K1 M1
TOTAL (119) I19, F1, V1 V63 E22 R6, I19, T3 I3 I114 T2 V1 E2 V2 P11 L1, M3, V3 K108 I24 A1, F2, I20, S1 V3 L34, M2
% of Total 16, 0.8, 0.8 52.9 18.5 5.0, 16, 2.5 2.5 95.8 1.7 0.8 1.7 1.7 9.2 0.8, 2.5, 2.5 90.8 20.2 0.8, 1.7, 16.8, 0.8 2.5 28.6, 1.7
Resistance mutation analysis on ViroSeq protease/Reverse Transcriptase sequences from 139 drug naive and 119 drug-treated Russian patients showed that mutations of >10% were observed for these populations at protease positions L10I, I13V,
G16E, M36I, H69K, V77I, I93L and reverse transcriptase A62V. Protease K20I and V82I mutations were present in ~16% of only the drug-treated subjects.
Reverse Transcriptase amino acids 62-210
HXB2 A D V A K F Q V Y G L
AA position 62 67 90 98 101 116 151 179 188 190 210
Mutation* V N I G E, P Y M D, F, T L A, S W
Subtype (n)
A1 (83) V24 N1 I7 S1 Q1, R2 Y1 M1 G1, I1 M1 A1, S1 F1, M1, S1
B (9) N2 G1 I4 A1 W1
F1 (2) V1
G (21) N3 G2, S1 E1, Q1 W3
CRF02_AG (1)
CRF03_AB (2) L1
CRF32_06A1 (1)
TOTAL (119) V24 N6 I7 G3 E1 Y1 M1 L1 A2, S1 W3
% of Total 20.2 5.0 5.9 2.5 0.8 0.8 0.8 0.8 1.7, 0.8 2.5
Participating AIDS Centers in Russia
N O R W A Y
E N
F I N L A N D
UKRAINE
I R A N
M O N G O L I A
JAPAN
N. KOREA
KAZAKHSTAN
UZBEKISTAN
KIRGHIZIA
TURKMENISTAN
TAJIKISTAN
AZE
RB
AIJAN
ARMENIA
LITHUANI
ESTONIA
R U S S I A
GEORGIA
Kola
Peninsula
Novaya Zemlya
Yamal
Pen.
Gyda
Pen.
Taymyr
Peninsula
Severnaya
Zemlya
FranzJosef Land
New
Siberian
Islands
Chukchi
Pen.
Kamchatka
Peninsula
Sakhalin
MOSCOW
Novosibirsk
Kazan
Rostov
Chelyabinsk
Omsk
Perm
St. Petersburg
Nizhniy-Novgorod
Ust-Izhora
Vologda
Yekaterinburg Khanty-Mansiysk
Krasnoyarsk Khabarovsk
Noyabrsk
Rostov
Ust-Izhora
Saint Petersburg AIDS
Saint Petersburg
Pasteur Institute
YekaterinburgKazan
Vologda
N O R W A Y
E N
LITHLITII
EESTONININIE AAA
OSCO
Rostov
N
UKRAINE
MO
I R A N
AZE
RB
ARMENIAAAGEORGIA
ssk
KK
k
NN
Proposed sites
SS
Noyabrsk Krasnoyarsk Khabarovsk
Poster presented at 17th Conference on Retroviruses and Opportunistic Infections — February 16–19, 2010 — San Francisco, CA
Contact*
Dr. Natalia Marlowe (natalia.marlowe@celera.com)
Celera, 1401 Harbor Bay Parkway, Alameda, CA 94502