1
|
Véras NMC, Santoro MM, Gray RR, Tatem AJ, Presti AL, Olearo F, Cappelli G, Colizzi V, Takou D, Torimiro J, Russo G, Callegaro A, Salpini R, D'Arrigo R, Perno CF, Goodenow MM, Ciccozzi M, Salemi M. Molecular epidemiology of HIV type 1 CRF02_AG in Cameroon and African patients living in Italy. AIDS Res Hum Retroviruses 2011; 27:1173-82. [PMID: 21453131 DOI: 10.1089/aid.2010.0333] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 CRF02_AG accounts for >50% of infected individuals in Cameroon. CRF02_AG prevalence has been increasing both in Africa and Europe, particularly in Italy because of migrations from the sub-Saharan region. This study investigated the molecular epidemiology of CRF02_AG in Cameroon by employing Bayesian phylodynamics and analyzed the relationship between HIV-1 CRF02_AG isolates circulating in Italy and those prevalent in Africa to understand the link between the two epidemics. Among 291 Cameroonian reverse transcriptase sequences analyzed, about 70% clustered within three distinct clades, two of which shared a most recent common ancestor, all related to sequences from Western Africa. The major Cameroonian clades emerged during the mid-1970s and slowly spread during the next 30 years. Little or no geographic structure was detected within these clades. One of the major driving forces of the epidemic was likely the high accessibility between locations in Southern Cameroon contributing to the mobility of the population. The remaining Cameroonian sequences and the new strains isolated from Italian patients were interspersed mainly within West and Central African sequences in the tree, indicating a continuous exchange of CRF02_AG viral strains between Cameroon and other African countries, as well as multiple independent introductions in the Italian population. The evaluation of the spread of CRF02_AG may provide significant insight about the future dynamics of the Italian and European epidemic.
Collapse
Affiliation(s)
- Nazle Mendonca Collaço Véras
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Pós-Graduação em Biologia Molecular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
| | - Rebecca R. Gray
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | - Andrew J. Tatem
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | | | | | | | - Vittorio Colizzi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Desiré Takou
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Judith Torimiro
- International Chantal Biya Reference Centre, Yaoundé, Cameroon
| | - Gianluca Russo
- Department of Tropical and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Romina Salpini
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
| | - Roberta D'Arrigo
- Monitoring Unit of Antiretroviral Therapies, INMI, Lazzaro Spallanzani, Rome, Italy
| | - Carlo-Federico Perno
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Rome, Italy
- Monitoring Unit of Antiretroviral Therapies, INMI, Lazzaro Spallanzani, Rome, Italy
| | - Maureen M. Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
| | | | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| |
Collapse
|
2
|
Djoko CF, Wolfe ND, Vidal N, Tamoufe U, Montavon C, LeBreton M, Pike BL, Fair J, Mbacham WF, Benito A, Rimoin AW, Saylors K, Mpoudi-Ngole E, Grillo MP, Peeters M. HIV type 1 pol gene diversity and genotypic antiretroviral drug resistance mutations in Malabo, Equatorial Guinea. AIDS Res Hum Retroviruses 2010; 26:1027-31. [PMID: 20718620 DOI: 10.1089/aid.2010.0046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, HIV strains circulating among military personnel were characterized, in Malabo, the capital city of Equatorial Guinea. One sample was found to be HIV-2 group A while a high degree of genetic diversity was recorded in the pol region of 41 HIV-1-positive samples. CRF02_AG accounted for 53.7% of the strains, and 11 different variants were obtained in the remaining 19 samples: subtype G (n = 3), A3 (n = 2), C (n = 2), CRF26_A5U (n = 2), F2 (n = 1), CRF06 (n = 1), CRF09 (n = 1), CRF11 (n = 1), CRF22 (n = 1), and divergent subtype A (n = 1) and F (n = 1). One strain could not be classified and three were unique recombinants. Analysis of antiretroviral drug resistance mutations revealed two patients each harboring one major mutation, M46I in protease and D67N in reverse transcriptase sequences, respectively. The high genetic diversity and emerging ARV resistance mutations call for frequent surveys and appropriate monitoring of ARV considering the increasing access to ARV in the country.
Collapse
Affiliation(s)
- Cyrille F. Djoko
- Biotechnology Center & Department of Biochemistry, University of Yaounde I, Yaounde, Cameroon
- Global Viral Forecasting Initiative (GVFI), San Francisco, California, and Yaounde, Cameroon
| | - Nathan D. Wolfe
- Global Viral Forecasting Initiative (GVFI), San Francisco, California, and Yaounde, Cameroon
- Stanford University, Program in Human Biology, Stanford, California
| | - Nicole Vidal
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier I, Montpellier, France
| | - Ubald Tamoufe
- Global Viral Forecasting Initiative (GVFI), San Francisco, California, and Yaounde, Cameroon
| | - Celine Montavon
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier I, Montpellier, France
| | - Matthew LeBreton
- Global Viral Forecasting Initiative (GVFI), San Francisco, California, and Yaounde, Cameroon
| | - Brian L. Pike
- Global Viral Forecasting Initiative (GVFI), San Francisco, California, and Yaounde, Cameroon
| | - Joseph Fair
- Global Viral Forecasting Initiative (GVFI), San Francisco, California, and Yaounde, Cameroon
| | - Wilfred F. Mbacham
- Biotechnology Center & Department of Biochemistry, University of Yaounde I, Yaounde, Cameroon
| | - Alogos Benito
- Division of Military Health, Ministry of National Defence, Malabo, Equatorial Guinea
| | - Anne W. Rimoin
- Department of Epidemiology, UCLA School of Public Health, University of California, Los Angeles, California
| | - Karen Saylors
- Global Viral Forecasting Initiative (GVFI), San Francisco, California, and Yaounde, Cameroon
| | | | - Michael P. Grillo
- U.S. Department of Defense HIV AIDS Prevention Program, San Diego, California
| | - Martine Peeters
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier I, Montpellier, France
| |
Collapse
|
3
|
Lihana RW, Khamadi SA, Kiptoo MK, Kinyua JG, Lagat N, Magoma GN, Mwau MM, Makokha EP, Onyango V, Osman S, Okoth FA, Songok EM. HIV type 1 subtypes among STI patients in Nairobi: a genotypic study based on partial pol gene sequencing. AIDS Res Hum Retroviruses 2006; 22:1172-7. [PMID: 17147506 DOI: 10.1089/aid.2006.22.1172] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Circulating strains of human immunodeficiency virus (HIV) exhibit an extraordinary degree of genetic diversity and have been classified on the basis of relationships into distinct lineages called groups, types, subtypes, and subsubtypes. Sexually transmitted infections (STIs) are known to be a risk factor for HIV infection. To establish HIV-1 subtype diversity among STI patients in Nairobi, 140 samples were collected and partial pol gene sequencing done. From the analysis it was established that subtype A1 was the major subtype (64%) followed by D (17%), C (9%), G (1%), and recombinants AD (4%), AC (3%), CRF02()AG (1%), and CRF16()A2D (1%). These results suggest that the HIV-1 epidemic may be evolving toward more virulent and complex subtypes through transmission of complex recombinants due to viral mixing. Any use of ARVs may therefore require initial testing for de novo resistance before commencement of treatment and/or management.
Collapse
Affiliation(s)
- Raphael W Lihana
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya., KEMRI/JICA Project, Nairobi, Kenya.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Lospitao E, Alvarez A, Soriano V, Holguín A. HIV-1 subtypes in Spain: a retrospective analysis from 1995 to 2003. HIV Med 2005; 6:313-20. [PMID: 16156878 DOI: 10.1111/j.1468-1293.2005.00313.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVE To perform a retrospective analysis of all HIV-1 non-B variants circulating in Spain from 1995 to 2003 and extend their virological characterization. METHODS Samples from a total of 396 HIV-infected subjects with epidemiological suspicion of being infected with non-B clades were analysed during the study period. Subtyping was carried out on the protease (PR), reverse transcriptase (RT) and envelope (env) genes. RESULTS PR sequences belonging to non-B subtypes were recognized in 43.2% of cases (23 A, 13C, 6D, 3F, 118 G, 3H, 4 J and 1 U). Subtype G and AG recombinants were the most frequent variants (69%), and were found most often in subjects from West and Central Africa. Up to 70% of pol (PR, RT) sequences belonging to subtype G harboured env sequences belonging to clade A (55%), B (13.8%) or K (3.4%). Nearly half were mosaic GA viruses, and a few were CRF 14 BG viruses. Up to 14 new recombinant viruses, which could not be assigned to previously described circulating recombinant forms (CRFs), were found. CONCLUSIONS There is great diversity in the HIV-1 variants and recombinant viruses circulating in Spain. Non-B sequences may be underestimated if only the env region is examined in phylogenetic analyses. Drug resistance testing provides the advantage of pol subtyping, and its additional use for this purpose should be encouraged.
Collapse
Affiliation(s)
- E Lospitao
- Infectious Diseases Service, Hospital Carlos III, Madrid, Spain
| | | | | | | |
Collapse
|
5
|
Njai HF, Van der Auwera G, Ngong CA, Heyndrickx L, Sawadago S, Whittle H, Nyambi P, Colebunders R, van der Groen G, Janssens W. Development, evaluation, and validation of an oligonucleotide probe hybridization assay to subtype human immunodeficiency virus type 1 circulating recombinant form CRF02_AG. J Clin Microbiol 2004; 42:1428-33. [PMID: 15070984 PMCID: PMC387545 DOI: 10.1128/jcm.42.4.1428-1433.2004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed and validated an oligonucleotide probe hybridization assay for human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) CRF02_AG. In the p17 coding region of the gag gene, a CRF02_AG-specific signature pattern was observed. Five working probes were designed to discriminate CRF02_AG infections from infections by all other documented subtypes and CRFs in an enzyme-linked immunosorbent assay-based oligonucleotide probe hybridization assay. Nucleic acids were extracted from a panel of HIV-1-positive plasma samples from Cameroon, Bénin, Côte d'Ivoire, Kenya, Zambia, and Belgium and from blood spots from The Gambia. CRF02_AG (n = 147) and non-CRF02 (n = 100) samples were analyzed to evaluate and validate the oligonucleotide probe hybridization assay. The CRF02_AG-specific oligonucleotide probe hybridization assay has a high sensitivity and specificity, with good positive and negative predictive values in regions of high and low prevalence. A validation of the assay with West and West Central African samples indicated a sensitivity of 98.4% and a specificity of 96.7%. The oligonucleotide probe hybridization assay as a diagnostic tool will allow for rapid screening for CRF02_AG. This could be used to track the HIV epidemic in terms of documenting the real prevalence of CRF02_AG strains and will complement efforts in vaccine development. Moreover, this technology can easily be applied in laboratories in developing countries.
Collapse
Affiliation(s)
- Harr F Njai
- Department of Microbiology, Institute of Tropical Medicine, Antwerp
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Tramuto F, Vitale F, Bonura F, Romano N. Detection of HIV type 1 non-B subtypes in Sicily, Italy. AIDS Res Hum Retroviruses 2004; 20:251-4. [PMID: 15018714 DOI: 10.1089/088922204773004987] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To evaluate the presence of HIV-1 non-B subtypes in Sicily, we sequenced and genotyped HIV-1 PR and RT regions of the pol gene using plasma from 169 HIV-1-infected adult patients. All samples were obtained from a study of antiretroviral-associated resistance mutations resulting in virological failure during highly active antiretroviral therapy (HAART). Eight (4.7%) patients had the non-B HIV-1 subtype including some circulating recombinant forms (CRFs). All of these individuals acquired the infection by heterosexual transmission. The detection of HIV-1 non-B strains was significantly associated with younger age of HIV-1 acquisition. Our findings indicate, for the first time, the presence of HIV-1 non-B subtypes in Sicily in patients who experienced virological failure during HAART, and highlight the need for implementing a network for the epidemiological surveillance of HIV-1 subtypes in Southern Europe.
Collapse
Affiliation(s)
- Fabio Tramuto
- Centro di Riferimento Regionale per la Diagnosi Sierologica e Virologica dell'AIDS, Dipartimento di Igiene e Microbiologia, Università degli Studi di Palermo, I-90127 Palermo, Italy
| | | | | | | |
Collapse
|
7
|
Fischetti L, Opare-Sem O, Candotti D, Sarkodie F, Lee H, Allain JP. Molecular epidemiology of HIV in Ghana: Dominance of CRF02_AG. J Med Virol 2004; 73:158-66. [PMID: 15122787 DOI: 10.1002/jmv.20070] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent studies showed the importance of CRF02_AG in West Africa, although the clinical relevance of these recombinant forms of HIV remains unknown. The present study aimed at determining the molecular diversity of HIV in Ghana and investigating the possible epidemiologic advantage of recombinant HIV-1. Plasma samples collected in 1999-2002 from two populations of HIV infected individuals (144 asymptomatic candidate blood donors and 169 AIDS patients) were studied and 249 of them were molecularly characterised in gag, pol, and env regions. Five molecular groups were identified: strains clustering with CRF02_AG in all regions (147/249 or 59%), recombinant strains clustering with CRF02_AG in one or two regions (50/249 or 20%), other subtypes, pure or recombinant, but not involving CRF02_AG (37/249 or 15%), HIV-2 (11/249 or 4.5%), and double infections (4/249 or 1.5%). There was no significant difference in the distribution of HIV-1 recombinant strains according to clinical presentation. No evidence of a significant increase in CRF02_AG prevalence between 1999 and 2002 was found. Irrespective of clinical condition, CRF02_AG is the predominant molecular form of HIV-1 in Kumasi, Ghana.
Collapse
Affiliation(s)
- Lucia Fischetti
- Department of Haematology, Division of Transfusion Medicine, University of Cambridge, Cambridge, England
| | | | | | | | | | | |
Collapse
|
8
|
Fleury H, Recordon-Pinson P, Caumont A, Faure M, Roques P, Plantier JC, Couturier E, Dormont D, Masquelier B, Simon F. HIV type 1 diversity in France, 1999-2001: molecular characterization of non-B HIV type 1 subtypes and potential impact on susceptibility to antiretroviral drugs. AIDS Res Hum Retroviruses 2003; 19:41-7. [PMID: 12596719 DOI: 10.1089/08892220360473952] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Non-B HIV-1 samples collected in France between 1999 and 2001 were sequenced in the env, reverse transcriptase (RT), and protease genes (1) to characterize further the non-B strains circulating in the country, (2) to assess the importance of recombination, and (3) to describe the polymorphism of RT and protease genes and appreciate a possible impact on susceptibility to antiretroviral (ARV) drugs. The results show that, within a background of CRF02_AG predominance, there is a high genetic diversity of non-B isolates, including intersubtype recombinants. There is an extensive polymorphism of protease and RT genes compared with B consensus sequences; we have so far no data indicating that these non-B isolates may have reduced sensitivity to ARV drugs.
Collapse
Affiliation(s)
- Herve Fleury
- Laboratoire de Virologie, Hôpital Pellegrin, CHU de Bordeaux, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Visco-Comandini U, Cappiello G, Liuzzi G, Tozzi V, Anzidei G, Abbate I, Amendola A, Bordi L, Budabbus MA, Eljhawi OA, Mehabresh MI, Girardi E, Antinori A, Capobianchi MR, Sönnerborg A, Ippolito G. Monophyletic HIV type 1 CRF02-AG in a nosocomial outbreak in Benghazi, Libya. AIDS Res Hum Retroviruses 2002; 18:727-32. [PMID: 12167281 DOI: 10.1089/088922202760072366] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A cluster of HIV-1 infection has been identified in Libya in 1999, involving 402 children admitted to "El-Fath" Children's Hospital in Benghazi (BCH) during 1998 and 19 of their mothers. Nosocomial transmission has been indicated as responsible for the spread of infection. Out of this group, 104 children and 19 adult women have been followed at the National Institute for Infectious Diseases L. Spallanzani in Rome during 1 year. At BCH, all children had received intravenous infusions but not blood or blood products. A single child receiving a blood transfusion in 1997 and the 17 infected mothers were never hospitalized in Benghazi. In addition, two nurses were diagnosed as HIV-1 infected. In 40 subjects out of this group HIV-1 gag, env, and pol fragments were amplified and sequenced. The phylogenetic analyses showed that a monophyletic recombinant HIV-1 form CRF02-AG was infecting all of the HIV-1-seropositive patients admitted at BCH with no close similarities to the other CRF02-AG reported to GenBank. A different strain was found in the child infected by blood transfusion. The data thus suggest a highly contagious nosocomial spread of HIV-1 infection and possibly transmission of the virus from child to mother during breastfeeding in connection with primary HIV-1 infection.
Collapse
|
10
|
García-Albert L, Ortiz M, García-Saiz A. HIV type 1 non-B subtype prevalence in Spain, 1997-1998. AIDS Res Hum Retroviruses 2001; 17:1317-20. [PMID: 11602041 DOI: 10.1089/08892220152596560] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have evaluated the prevalence of HIV-1 non-B subtypes in Spain by means of an enzyme immunoassay (EIA) for discrimination between B and non-B subtypes. Samples were obtained from newly diagnosed patients attended at internal medicine outpatient clinics between October 1997 and October 1998. Discrimination between HIV-1 B and non-B subtypes was carried out by means of the EIA, with V3 synthetic peptides specific to the different subtypes. Non-B-serotyped samples were genetically analyzed in the gp41 region from the original sera. During the study period, 909 samples were collected from 21 medical units located in various Spanish geographical regions. Serotyping was possible in 885 cases, of which 791 were assigned as B serotype (89.38%), 70 showed no reactivity to any of the peptides (7.91%), and the remaining samples displayed other reaction patterns (2.72%). Of the 94 non-B-assigned samples, 65 were genetically characterized in the gp41 region of the env gene: 55 were B subtype, 5 were A subtype (4 clustered with CRF02AG reference strains), 3 were C subtype, and 2 were G subtype. The prevalence rate for non-B subtypes in Spain was established at 1.13% (95% CI, 0.59-2.21). Although the B subtype is predominant in the Spanish population, other subtypes have been detected.
Collapse
Affiliation(s)
- L García-Albert
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
| | | | | |
Collapse
|