1
|
Siqueira JD, Alves BM, Castelo Branco AB, Duque KC, Bustamante-Teixeira MT, Soares EA, Levi JE, Azevedo e Silva G, Soares MA. Comparison of four different human papillomavirus genotyping methods in cervical samples: Addressing method-specific advantages and limitations. Heliyon 2024; 10:e25474. [PMID: 38327440 PMCID: PMC10847660 DOI: 10.1016/j.heliyon.2024.e25474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/05/2023] [Accepted: 01/28/2024] [Indexed: 02/09/2024] Open
Abstract
Since human papillomavirus (HPV) is recognized as the causative agent of cervical cancer and associated with anogenital non-cervical and oropharyngeal cancers, the characterization of the HPV types circulating in different geographic regions is an important tool in screening and prevention. In this context, this study compared four methodologies for HPV detection and genotyping: real-time PCR (Cobas® HPV test), nested PCR followed by conventional Sanger sequencing, reverse hybridization (High + Low PapillomaStrip® kit) and next-generation sequencing (NGS) at an Illumina HiSeq2500 platform. Cervical samples from patients followed at the Family Health Strategy from Juiz de Fora, Minas Gerais, Brazil, were collected and subjected to the real-time PCR. Of those, 114 were included in this study according to the results obtained with the real-time PCR, considered herein as the gold standard method. For the 110 samples tested by at least one methodology in addition to real-time PCR, NGS showed the lowest concordance rates of HPV and high-risk HPV identification compared to the other three methods (67-75 %). Real-time PCR and Sanger sequencing showed the highest rates of concordance (97-100 %). All methods differed in their sensitivity and specificity. HPV genotyping contributes to individual risk stratification, therapeutic decisions, epidemiological studies and vaccine development, supporting approaches in prevention, healthcare and management of HPV infection.
Collapse
Affiliation(s)
- Juliana D. Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Brunna M. Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | | | - Kristiane C.D. Duque
- Diretoria de Ensino, Pesquisa e Extensão, Instituto Federal de Santa Catarina, Joinville, SC, Brazil
| | | | - Esmeralda A. Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - José Eduardo Levi
- Instituto de Medicina Tropical de São Paulo Medical School, Universidade de São Paulo, São Paulo, Brazil
- Pesquisa e Desenvolvimento, Dasa Laboratories, Barueri, SP, Brazil
| | - Gulnar Azevedo e Silva
- Departamento de Epidemiologia, Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcelo A. Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
2
|
Tornatore M, Amaral SC, Alves BM, de Oliveira GR, Finger-Jardim F, Avila EC, Pivato AF, Lobato RC, Chies JAB, Ellwanger JH, Soares EA, Sánchez-Luquez K, Gonçalves CV, Martínez AMBD, Soares MA, da Hora VP. HLA-G alleles and their impacts on placental HSV-1 infection in women from southern Brazil. J Reprod Immunol 2023; 159:104134. [PMID: 37634319 DOI: 10.1016/j.jri.2023.104134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/29/2023]
Abstract
The Human Leukocyte Antigen G (HLA-G) is an immunoregulatory molecule with a critical role in pregnancy success. HLA-G alleles are associated with differential susceptibility to multiple conditions, including gestational problems, infectious diseases, and viral persistence. Of note, both herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) can impair HLA-G expression, interfering with HLA-G-associated immunoregulation. On the other hand, the impacts of HLA-G alleles on susceptibility to Herpesviridae infection is a neglected issue. Therefore, this study evaluated HLA-G allele frequencies and their associations with placental Herpesviridae infection in women from southern Brazil. Placenta samples were collected soon after delivery, and detection of viral DNA of HSV-1, HSV-2 and human cytomegalovirus (HCMV) was performed by polymerase chain reaction (PCR). A fragment of HLA-G (exons 2-4) was amplified by PCR, sequenced, and analyzed to allele determination. One hundred and seventy women had their alleles determined. Overall, 25 HLA-G alleles were found, distributed into 56 different genotypes. The most frequent alleles were G* 01:01:01 and G* 01:01:02, found in 37.9 % and 16.5 % of samples, respectively. Among the 170 women, 89 (52.4 %) tested positive for Herpesviridae DNA in the placenta, 55 (32.3 %) tested negative, 3 (1.8 %) were negative for HSV-1 and HSV-2 (with absent HCMV data), and 23 (13.5 %) were undetermined. The G* 01:01:01 allele was significantly associated with an increased risk of placental HSV-1 infection (p = 0.0151; OR=1.837; IC=1.108-3.045). This study describes new information concerning placental HLA-G alleles in women from southern Brazil and helps explain how genetic background can modify susceptibility to placental infections.
Collapse
Affiliation(s)
- Michele Tornatore
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | | | - Brunna M Alves
- Post-Graduate Program in Oncovirology, Instituto Nacional do Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | | | - Fabiana Finger-Jardim
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Emiliana Claro Avila
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Andressa Fernandes Pivato
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Rubens Caurio Lobato
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - José Artur Bogo Chies
- Laboratory of Immunobiology and Immunogenetics, Post-Graduate Program in Genetics and Molecular Biology (PPGBM), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Joel Henrique Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Post-Graduate Program in Genetics and Molecular Biology (PPGBM), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Esmeralda A Soares
- Post-Graduate Program in Oncovirology, Instituto Nacional do Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Karen Sánchez-Luquez
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Carla Vitola Gonçalves
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Ana Maria Barral de Martínez
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Marcelo A Soares
- Post-Graduate Program in Oncovirology, Instituto Nacional do Câncer (INCA), Rio de Janeiro, RJ, Brazil; Department of Genetics, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Vanusa Pousada da Hora
- Post-Graduate Program in Health Sciences, Faculty of Medicine, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil.
| |
Collapse
|
3
|
Botelho OM, Basso RP, Da Mota LD, Da Hora VP, Garrido MM, Machado ES, Alves BM, Soares MA. Evaluation of HIV-1 antiretroviral drug resistance profiles in the peripheral blood reservoir of successfully treated persons using massive sequencing and viral full genome characterization. J Antimicrob Chemother 2023:7113319. [PMID: 37039023 DOI: 10.1093/jac/dkad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/17/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Antiretroviral therapy has revolutionized HIV treatment, increasing quality and life expectancy of people living with HIV (PLWH). However, the expansion of treatment has resulted in an increase in antiretroviral-resistant viruses, which can be an obstacle to maintenance of successful ART. OBJECTIVES This study analysed the genetic composition of the HIV near full-length genome (NFLG) from archived proviruses of PLWH under successful ART, and determined the presence/frequency of drug resistance mutations (DRMs) and viral subtype. PATIENTS AND METHODS Forty-six PLWH from Rio de Janeiro (RJ) and 40 from Rio Grande (RS) had proviral HIV NFLG PCR-amplified and ultradeep sequenced. The presence/frequency of DRMs were analysed in Geneious. Phylogenetic analyses were performed using PhyML and SimPlot. RESULTS All samples included in the study were sequenced and 69 (80.2%) had the HIV NFLG determined. RJ and RS showed a predominance of HIV subtypes B (78.3%) and C (67.5%), respectively. Overall, 168 DRMs were found in 63 (73.3%) samples, and 105 (62.5%) of them were minority variants. Among DRMs, 41 (39.0%) minority variants and 33 (52.4%) variants with frequency above 20.0% in the viral population were able to confer some degree of resistance to at least one drug in use by respective patients, yet no one showed signs of therapeutic failure. CONCLUSIONS Our study contributes to the understanding of the impact of DRMs on successful therapy and supports the sustainability of combinatorial ART, because all patients maintained their successful treatment despite the high prevalence of DRMs at low (62.5%) or high (37.5%) frequency.
Collapse
Affiliation(s)
- Ornella M Botelho
- Programa de Genética e Virologia Tumoral, Instituto Nacional do Câncer, Rua André Cavalcanti, 37 - 4° andar, 20.231-050, Rio de Janeiro, Brazil
| | - Rossana P Basso
- Hospital Universitário Dr. Miguel Riet Corrêa Jr., Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Luisa D Da Mota
- Hospital Universitário Dr. Miguel Riet Corrêa Jr., Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Vanusa P Da Hora
- Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Marianne M Garrido
- Serviço de Infectologia, Hospital Federal de Ipanema, Rio de Janeiro, Brazil
| | - Elizabeth S Machado
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Brunna M Alves
- Programa de Genética e Virologia Tumoral, Instituto Nacional do Câncer, Rua André Cavalcanti, 37 - 4° andar, 20.231-050, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Genética e Virologia Tumoral, Instituto Nacional do Câncer, Rua André Cavalcanti, 37 - 4° andar, 20.231-050, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
4
|
Goes LR, Siqueira JD, Garrido MM, Alves BM, Cicala C, Arthos J, Viola JPB, Soares MA. Evidence of recurrent selection of mutations commonly found in SARS-CoV-2 variants of concern in viruses infecting immunocompromised patients. Front Microbiol 2022; 13:946549. [PMID: 35958144 PMCID: PMC9362983 DOI: 10.3389/fmicb.2022.946549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Chronically immunosuppressed patients infected with SARS-CoV-2 often experience prolonged virus shedding, and may pave the way to the emergence of mutations that render viral variants of concern (VOC) able to escape immune responses induced by natural infection or by vaccination. We report herein a SARS-CoV-2+ cancer patient from the beginning of the COVID-19 pandemic whose virus quasispecies across multiple timepoints carried several immune escape mutations found in more contemporary VOC, such as alpha, delta and omicron, that appeared to be selected for during infection. We hypothesize that immunosuppressed patients may represent the source of VOC seen throughout the COVID-19 pandemics.
Collapse
Affiliation(s)
- Livia R. Goes
- Oncovirology Program, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
- *Correspondence: Livia R. Goes,
| | - Juliana D. Siqueira
- Oncovirology Program, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Marianne M. Garrido
- Hospital Infection Control Committee, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Brunna M. Alves
- Oncovirology Program, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - João P. B. Viola
- Immunology and Tumor Biology Program, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Marcelo A. Soares
- Oncovirology Program, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Marcelo A. Soares,
| |
Collapse
|
5
|
Goes LR, Siqueira JD, Garrido MM, Alves BM, Pereira ACPM, Cicala C, Arthos J, Viola JPB, Soares MA. New infections by SARS-CoV-2 variants of concern after natural infections and post-vaccination in Rio de Janeiro, Brazil. Infect Genet Evol 2021; 94:104998. [PMID: 34252616 PMCID: PMC8270730 DOI: 10.1016/j.meegid.2021.104998] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022]
Abstract
After a one-year rollout of the pandemic caused by SARS-CoV-2, the continuous dissemination of the virus has generated a number of variants with increased transmissibility and infectivity, called variants of concern (VOC), which now predominate worldwide. Concerns about the susceptibility of humans that have already been infected before or those already vaccinated to infection by VOC rise among scientists and clinicians. Herein, we assessed the prevalence of different VOC among recent infections at the Brazilian National Cancer Institute (Rio de Janeiro, Brazil). By using a Sanger-based sequencing approach targeting the viral S gene to identify VOC, we have analyzed 72 recent infections. The overall prevalence of VOC was 97%. Among the subjects analyzed, six had been vaccinated with the ChAdOx1-S/nCoV-19 (n = 4; one with two doses and three with one dose) or the CoronaVac (n = 2; both with 2 doses) vaccine, while five subjects represented reinfection cases, being two of them also part of the vaccinated group (each one with one vaccine type). All vaccinated and re-infected subjects carried VOC irrespective of the vaccine type taken, the number of doses taken, IgG titers or being previously infected during the first wave of the Brazilian pandemic. Importantly, all six vaccinees only had mild symptoms. We present here several examples of how natural infections or vaccination may not be fully capable of conferring sterilizing immunity against VOC.
Collapse
Affiliation(s)
- Livia R Goes
- Oncovirology Program, Brazilian National Cancer Institute, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - Juliana D Siqueira
- Oncovirology Program, Brazilian National Cancer Institute, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil.
| | - Marianne M Garrido
- Hospital Infection Control Committee, Brazilian National Cancer Institute, Praça Cruz Vermelha, 23, Rio de Janeiro, RJ 20230-130, Brazil.
| | - Brunna M Alves
- Oncovirology Program, Brazilian National Cancer Institute, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil.
| | - Ana Cristina P M Pereira
- Section of Anesthesiology, Brazilian National Cancer Institute, Praça Cruz Vermelha, 23, Rio de Janeiro, RJ 20230-130, Brazil.
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - João P B Viola
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil.
| | - Marcelo A Soares
- Oncovirology Program, Brazilian National Cancer Institute, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil; Department of Genetics, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ 21941-590, Brazil.
| |
Collapse
|
6
|
Siqueira JD, Goes LR, Alves BM, da Silva ACP, de Carvalho PS, Cicala C, Arthos J, Viola JPB, Soares MA. Distinguishing SARS-CoV-2 bonafide re-infection from pre-existing minor variant reactivation. Infect Genet Evol 2021; 90:104772. [PMID: 33592317 PMCID: PMC7882217 DOI: 10.1016/j.meegid.2021.104772] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/22/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
Different groups have recently reported events of SARS-CoV-2 reinfection, where patients had a sequence of positive-negative-positive RT-PCR tests. However, such events could be explained by different scenarios such as intermittent viral shedding, bonafide re-infection or multiple infection with alternating predominance of different viruses. Analysis of minor variants is an important tool to distinguish between these scenarios. Using ARTIC network PCR amplification and next-generation sequencing, we obtained SARS-CoV-2 sequences from two timepoints (with a time span of 102 days) of a patient followed at the Brazilian National Cancer Institute. Within-host variant analysis evidenced three single nucleotide variants (SNVs) at the consensus viral sequence in the second timepoint that were already present in the first timepoint as minor variants. Another five SNVs found in the second timepoint were not detected in the first sample sequenced, suggesting an additional infection by a yet another new virus. Our observation shed light into the existence of different viral populations that are present in dynamic frequencies and fluctuate during the course of SARS-CoV-2 infection. The detection of these variants in distinct disease events of an individual highlights a complex interplay between viral reactivation from a pre-existing minority variant and reinfection by a different virus.
Collapse
Affiliation(s)
- Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Livia R Goes
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Ana Carla P da Silva
- Hospital do Câncer II, Instituto Nacional de Câncer, Avenida Via Binário do Porto, 831, Rio de Janeiro, RJ 20081-250, Brazil
| | - Pedro S de Carvalho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - João P B Viola
- Programa de Imunologia e Biologia de Tumores, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ 21941-402, Brazil.
| |
Collapse
|
7
|
Siqueira JD, Goes LR, Alves BM, de Carvalho PS, Cicala C, Arthos J, Viola JPB, de Melo AC, Soares MA. SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. Virus Evol 2021; 7:veab013. [PMID: 33738124 PMCID: PMC7928633 DOI: 10.1093/ve/veab013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Numerous factors have been identified to influence susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (non-cancer controls) by deep sequencing and investigated the within-host viral population of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers from the Brazilian National Cancer Institute were collected in April to May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4%–19.7%) among the consensus sequences. Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to healthcare workers. This difference was independent of SARS-CoV-2 Ct values obtained at the diagnostic tests, which did not differ between the two groups. The most common nucleotide changes of intrahost SNVs in both groups were consistent with APOBEC and ADAR activities. Intrahost genetic diversity in cancer patients was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Moreover, the presence of metastasis, either in general or specifically in the lung, was not associated with intrahost diversity among cancer patients. Cancer patients carried significantly higher numbers of minor variants compared to non-cancer counterparts. Further studies on SARS-CoV-2 diversity in especially vulnerable patients will shed light onto the understanding of the basis of COVID-19 different outcomes in humans.
Collapse
Affiliation(s)
- Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ 20.231-050, Brazil
| | - Livia R Goes
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ 20.231-050, Brazil.,Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ 20.231-050, Brazil
| | - Pedro S de Carvalho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ 20.231-050, Brazil
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - João P B Viola
- Programa de Imunologia e Biologia de Tumores, Instituto Nacional de Câncer, Rio de Janeiro, RJ 20.231-050, Brazil
| | - Andréia C de Melo
- Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico, Instituto Nacional de Câncer, Rio de Janeiro, RJ 20.231-050, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ 20.231-050, Brazil
| |
Collapse
|
8
|
Pham HT, Alves BM, Yoo S, Xiao MA, Leng J, Quashie PK, Soares EA, Routy JP, Soares MA, Mesplède T. Progressive emergence of an S153F plus R263K combination of integrase mutations in the proviral DNA of one individual successfully treated with dolutegravir. J Antimicrob Chemother 2021; 76:639-647. [PMID: 33184634 DOI: 10.1093/jac/dkaa471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/19/2020] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES The development of HIV drug resistance against the integrase strand transfer inhibitor dolutegravir is rare. We report here the transient detection, by near full-genome ultradeep sequencing, of minority HIV-1 subtype B variants bearing the S153F and R263K integrase substitutions in the proviral DNA from blood cells of one patient who successfully initiated dolutegravir-based ART, over 24 weeks. Our objective was to study the effects of these substitutions. METHODS Strand transfer and DNA-binding activities of recombinant integrase proteins were measured in cell-free assays. Cell-based resistance, infectivity and replicative capacities were measured using molecular clones. Structural modelling was performed to understand experimental results. RESULTS R263K emerged first, followed by the addition of S153F at Week 12. By Week 24, both mutations remained present, but at lower prevalence. We confirmed the coexistence of S153F and R263K on single viral genomes. Combining S153F or S153Y with R263K decreased integration and viral replicative capacity and conferred high levels of drug resistance against all integrase inhibitors. Alone, S153Y and S153F did little to infectivity or dolutegravir resistance. We identified altered DNA binding as a mechanism of resistance. The patient remained with undetectable viral loads at all timepoints. CONCLUSIONS Drug-resistant minority variants have often been reported under suppressive ART. Our study adds to these observations by unravelling a progression towards higher levels of resistance through a novel pathway despite continuous undetectable viral loads. Poorly replicative HIV drug-resistant minority proviral variants did not compromise viral suppression in one individual treated with dolutegravir.
Collapse
Affiliation(s)
- Hanh T Pham
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Sunbin Yoo
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Meng A Xiao
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Jing Leng
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Peter K Quashie
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- The Francis Crick Institute, London, UK
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Jean-Pierre Routy
- For Montreal PHI Cohort Study Group, Division of Hematology, McGill University Health Centre, Montréal, Québec, Canada
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thibault Mesplède
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| |
Collapse
|
9
|
Siqueira JD, Goes LR, Alves BM, de Carvalho PS, Cicala C, Arthos J, Viola JP, de Melo AC, Soares MA. SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. bioRxiv 2020:2020.08.26.267831. [PMID: 32869023 PMCID: PMC7457605 DOI: 10.1101/2020.08.26.267831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (HCW; non-cancer controls) by deep sequencing and investigated the within-host viral quasispecies of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2 + swabs from 57 cancer patients and 14 healthcare workers (HCW) from the Brazilian Cancer Institute were collected in April-May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants (iSNVs) were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%). Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to HCW (p = 0.009). Intrahost genetic diversity in cancer patients was independent of SARS-CoV-2 Ct values, and was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Such a feature may explain, at least in part, the more adverse outcomes to which cancer/COVID-19 patients experience. AUTHOR SUMMARY Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. In this study, phylogenetic and variation analysis of SARS-CoV-2 genomes from cancer patients and non-cancer healthcare workers at the Brazilian National Cancer Institute were characterized by deep sequencing. Viral genomes showed signatures characteristic of Brazilian viruses, consistent with the hypothesis of local, community transmission rather than virus importation from abroad. Despite most genomes in patients and healthcare workers belonging to the same lineage, intrahost variability was higher in cancer patients when compared to non-cancer counterparts. The intrahost genomic diversity analysis presented in our study highlights the relaxed evolution of SARS-CoV-2 in a vulnerable population of cancer patients. The high number of minor variations can result in the selection of immune escape variants, resistance to potential drugs, and/or increased pathogenicity. The impact of this higher intrahost variability over time warrants further investigation.
Collapse
Affiliation(s)
- Juliana D. Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer. Rio de Janeiro, RJ, Brazil
| | - Livia R. Goes
- Programa de Oncovirologia, Instituto Nacional de Câncer. Rio de Janeiro, RJ, Brazil
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Brunna M. Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer. Rio de Janeiro, RJ, Brazil
| | - Pedro S. de Carvalho
- Programa de Oncovirologia, Instituto Nacional de Câncer. Rio de Janeiro, RJ, Brazil
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - João P.B. Viola
- Programa de Imunologia e Biologia de Tumores, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Andréia C. de Melo
- Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Marcelo A. Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer. Rio de Janeiro, RJ, Brazil
| |
Collapse
|
10
|
Alves BM, Siqueira JD, Prellwitz IM, Botelho OM, Da Hora VP, Sanabani S, Recordon-Pinson P, Fleury H, Soares EA, Soares MA. Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing. Front Microbiol 2019; 10:749. [PMID: 31024510 PMCID: PMC6465556 DOI: 10.3389/fmicb.2019.00749] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/25/2019] [Indexed: 12/26/2022] Open
Abstract
Approximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with the virus. As a touristic and commercial hub in Latin America, Brazil harbors an elevated HIV genetic variability, further contributed by the selective pressure exerted by the host immune system and by antiretroviral treatment. Through the progress of the next-generation sequencing (NGS) techniques, it has been possible to expand the study of HIV genetic diversity, evolutionary, and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity in the detection of viral recombinant forms represents one of the major improvements associated with this development. It is possible to identify unique or circulating recombinant forms using the near full-length viral genomes with increasing accuracy. It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections. These data unveiled unprecedented high rates of viral recombination and highlighted that novel recombinants are continually arising in the Brazilian epidemic. In the pooled analysis depicted in this report, HIV subtypes have been determined from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul). Combined data analysis showed a significant prevalence of recombinant forms (29%; 101/350), and a similar 26% when only NFLGs were considered. Moreover, the analysis was able to evidence the occurrence of multiple infections in some individuals. Our data highlight the great HIV genetic diversity found in Brazil and unveils a more accurate scenario of the HIV evolutionary dynamics in the region.
Collapse
Affiliation(s)
- Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ornella M Botelho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Vanusa P Da Hora
- Laboratório de Biologia Molecular, Escola de Medicina, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Sabri Sanabani
- LIM-3, Hospital das Clinicas FMUSP, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Hervé Fleury
- CNRS MFP-UMR 5234, University Hospital of Bordeaux, University of Bordeaux, Bordeaux, France
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
11
|
Recordon-Pinson P, Alves BM, Tumiotto C, Bellecave P, Bonnet F, Neau D, Soares EA, Soares MA, Fleury H. A New HIV-1 Circulating Recombinant Form (CRF98_cpx) Between CRF06_cpx and Subtype B Identified in Southwestern France. AIDS Res Hum Retroviruses 2018; 34:1005-1009. [PMID: 29947242 DOI: 10.1089/aid.2018.0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
During a recent study on the sequencing data of our database between 2012 and 2016 in Southwestern France, we observed that eight patients harbored what seemed to be the same virus. Indeed, routine genotyping at the time of HIV diagnosis showed that protease and reverse transcriptase were related to CRF06_cpx and subtype B, respectively. The integrase sequences (available for three patients) were clustering with CRF06_cpx and envelope (Env) gp120 sequences (available for two patients) with subtype B. Since such a recombinant has not been recorded in the Los Alamos database, we decided to characterize the full-length genome of this virus. The data suggest the identification of a new circulating recombinant form (CRF) between CRF06_cpx and subtype B, the structure of which is very complex with multiple breakpoints. We will refer this CRF as CRF98_cpx.
Collapse
Affiliation(s)
| | | | - Camille Tumiotto
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Fabrice Bonnet
- Department of Internal Medicine, University Hospital of Bordeaux, Bordeaux, France
| | - Didier Neau
- Department of Infectious and Tropical Diseases, University Hospital of Bordeaux, Bordeaux, France
| | | | | | - Hervé Fleury
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| |
Collapse
|
12
|
Alves BM, Siqueira JD, Garrido MM, Botelho OM, Prellwitz IM, Ribeiro SR, Soares EA, Soares MA. Characterization of HIV-1 Near Full-Length Proviral Genome Quasispecies from Patients with Undetectable Viral Load Undergoing First-Line HAART Therapy. Viruses 2017; 9:v9120392. [PMID: 29257103 PMCID: PMC5744166 DOI: 10.3390/v9120392] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/16/2017] [Accepted: 12/18/2017] [Indexed: 12/16/2022] Open
Abstract
Increased access to highly active antiretroviral therapy (HAART) by human immunodeficiency virus postive (HIV+) individuals has become a reality worldwide. In Brazil, HAART currently reaches over half of HIV-infected subjects. In the context of a remarkable HIV-1 genetic variability, highly related variants, called quasispecies, are generated. HIV quasispecies generated during infection can influence virus persistence and pathogenicity, representing a challenge to treatment. However, the clinical relevance of minority quasispecies is still uncertain. In this study, we have determined the archived proviral sequences, viral subtype and drug resistance mutations from a cohort of HIV+ patients with undetectable viral load undergoing HAART as first-line therapy using next-generation sequencing for near full-length virus genome (NFLG) assembly. HIV-1 consensus sequences representing NFLG were obtained for eleven patients, while for another twelve varying genome coverage rates were obtained. Phylogenetic analysis showed the predominance of subtype B (83%; 19/23). Considering the minority variants, 18 patients carried archived virus harboring at least one mutation conferring antiretroviral resistance; for six patients, the mutations correlated with the current ARVs used. These data highlight the importance of monitoring HIV minority drug resistant variants and their clinical impact, to guide future regimen switches and improve HIV treatment success.
Collapse
Affiliation(s)
- Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Marianne M Garrido
- Serviço de Doenças Infecciosas, Hospital Federal de Ipanema, Rio de Janeiro 22411-020, Brazil.
| | - Ornella M Botelho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Sayonara R Ribeiro
- Serviço de Doenças Infecciosas, Hospital Federal de Ipanema, Rio de Janeiro 22411-020, Brazil.
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, Brazil.
| |
Collapse
|
13
|
Abstract
The aims of this study were to assess the linear relationships between agronomic and nutritional traits and to identify promising traits for indirect selection in early and super-early maturing maize genotypes. Two trials were run in the 2009/2010 agricultural year, each consisting of a randomized block design with three replications. One trial was run on 36 early maturing maize genotypes and the other on 22 super-early maturing genotypes. Six agronomic traits, 11 protein-nutritional traits, and four energetic-nutritional traits were measured. Error normality assumptions were verified using the Kolmogorov-Smirnov test and residual variance homogeneity assumptions using the Levene test. Analysis of variance and the F-test were run for each of the 21 traits. Next, the genotype correlation coefficient matrix was estimated for the 21 traits and each trial. Ridge path analysis was based on values of k = 0.00 and k = 0.10 on the diagonal of X'X correlation matrix, taking the nutritional traits as principal variables and agronomic traits as explanatory variables. The number of days from sowing to male flowering, the number of days from sowing to female flowering, plant height, ear insertion height, ear weight and grain yield can be used in indirect selection as indicators of grain nutritional quality.
Collapse
Affiliation(s)
- B M Alves
- Departamento de Fitotecnia, , , Brasil
| | | |
Collapse
|
14
|
Abstract
The objective of this study was to evaluate the effects of multicollinearity under two methods of canonical correlation analysis (with and without elimination of variables) in maize (Zea mays L.) crop. Seventy-six maize genotypes were evaluated in three experiments, conducted in a randomized block design with three replications, during the 2009/2010 crop season. Eleven agronomic variables (number of days from sowing until female flowering, number of days from sowing until male flowering, plant height, ear insertion height, ear placement, number of plants, number of ears, ear index, ear weight, grain yield, and one thousand grain weight), 12 protein-nutritional variables (crude protein, lysine, methionine, cysteine, threonine, tryptophan, valine, isoleucine, leucine, phenylalanine, histidine, and arginine), and 6 energetic-nutritional variables (apparent metabolizable energy, apparent metabolizable energy corrected for nitrogen, ether extract, crude fiber, starch, and amylose) were measured. A phenotypic correlation matrix was first generated among the 29 variables for each of the experiments. A multicollinearity diagnosis was later performed within each group of variables using methodologies such as variance inflation factor and condition number. Canonical correlation analysis was then performed, with and without the elimination of variables, among groups of agronomic and protein-nutritional, and agronomic and energetic-nutritional variables. The canonical correlation analysis in the presence of multicollinearity (without elimination of variables) overestimates the variability of canonical coefficients. The elimination of variables is an efficient method to circumvent multicollinearity in canonical correlation analysis.
Collapse
Affiliation(s)
- B M Alves
- Departamento de Fitotecnia, Universidade Federal de Santa Maria, Santa Maria, RS, Brasil
| | - A Cargnelutti Filho
- Departamento de Fitotecnia, Universidade Federal de Santa Maria, Santa Maria, RS, Brasil
| | - C Burin
- Departamento de Fitotecnia, Universidade Federal de Santa Maria, Santa Maria, RS, Brasil
| |
Collapse
|
15
|
Siqueira JD, Alves BM, Prellwitz IM, Furtado C, Meyrelles ÂR, Machado ES, Seuánez HN, Soares MA, Soares EA. Identification of novel human papillomavirus lineages and sublineages in HIV/HPV-coinfected pregnant women by next-generation sequencing. Virology 2016; 493:202-8. [PMID: 27060563 DOI: 10.1016/j.virol.2016.03.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 01/04/2023]
Abstract
Infection by human papillomavirus (HPV) is a necessary condition for development of cervical cancer, and has also been associated with malignancies of other body anatomical sites. Specific HPV types have been associated with premalignant lesions and invasive carcinoma, but mounting evidence suggests that within-type lineages and sublineages also display distinct biological characteristics associated with persistent infections and evolution to cervical cancer. In the present study, we have assessed HPV multiple infection and variation from a cohort of highly susceptible, HIV(+) pregnant women using next-generation sequencing and an in-house pipeline for HPV full-length genome assembly. Seventy-two consensus sequences representing complete or near-complete (>97%) HPV genomes were assembled, spanning 28 different types. Genetic distance and phylogenetic analyses allowed us to propose the classification of novel HPV lineages and sublineages across nine HPV types, including two high-risk types. HPV diversity may be a hallmark of immunosuppressed patients upon HIV infection and AIDS progression.
Collapse
Affiliation(s)
- Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ângela R Meyrelles
- Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizabeth S Machado
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| |
Collapse
|
16
|
Alves BM, Prellwitz IM, Siqueira JD, Meyrelles ÂR, Bergmann A, Seuánez HN, Machado ES, Soares MA, Soares EA. The effect of human leukocyte antigen G alleles on human papillomavirus infection and persistence in a cohort of HIV-positive pregnant women from Brazil. Infect Genet Evol 2015; 34:339-43. [PMID: 26134300 DOI: 10.1016/j.meegid.2015.06.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 06/25/2015] [Accepted: 06/28/2015] [Indexed: 01/01/2023]
Abstract
Patients with compromised immune systems have more severe intraepithelial lesions and more rapid disease progression, in addition to increased risk for cervical cancer. Persistent infection by the human papillomavirus (HPV) is a necessary step in that process. By inducing expression of inhibitory ligands of natural killer cells, like HLA-G, HPV avoids the elimination of infected cells. Recent studies have investigated polymorphisms in HLA-G that may be associated with susceptibility to HPV infection and persistence. One hundred-forty HIV(+) pregnant women from Brazil had a DNA fragment comprising HLA-G exons 2-4 PCR-amplified, cloned, sequenced and analyzed for allele determination. Altogether, 22 alleles comprising 52 different genotypes were found. Four novel HLA-G alleles were characterized. We have not observed association of specific HLA-G alleles with HPV infection, but found a protective effect of the G:01:01:02 allele against the occurrence of intraepithelial lesions. In addition to describing new HLA-G alleles and defining new reference sequences, our data provide a better understanding of the impact of HLA-G alleles on HPV-related disease.
Collapse
Affiliation(s)
- Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ângela R Meyrelles
- Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anke Bergmann
- Programa de Epidemiologia Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizabeth S Machado
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| |
Collapse
|
17
|
Mata H, Gongora J, Eizirik E, Alves BM, Soares MA, Ravazzolo AP. Identification and characterization of diverse groups of endogenous retroviruses in felids. Retrovirology 2015; 12:26. [PMID: 25808580 PMCID: PMC4373062 DOI: 10.1186/s12977-015-0152-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 02/23/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Endogenous retroviruses (ERVs) are genetic elements with a retroviral origin that are integrated into vertebrate genomes. In felids (Mammalia, Carnivora, Felidae), ERVs have been described mostly in the domestic cat, and only rarely in wild species. To gain insight into the origins and evolutionary dynamics of endogenous retroviruses in felids, we have identified and characterized partial pro/pol ERV sequences from eight Neotropical wild cat species, belonging to three distinct lineages of Felidae. We also compared them with publicly available genomic sequences of Felis catus and Panthera tigris, as well as with representatives of other vertebrate groups, and performed phylogenetic and molecular dating analyses to investigate the pattern and timing of diversification of these retroviral elements. RESULTS We identified a high diversity of ERVs in the sampled felids, with a predominance of Gammaretrovirus-related sequences, including class I ERVs. Our data indicate that the identified ERVs arose from at least eleven horizontal interordinal transmissions from other mammals. Furthermore, we estimated that the majority of the Gamma-like integrations took place during the diversification of modern felids. Finally, our phylogenetic analyses indicate the presence of a genetically divergent group of sequences whose position in our phylogenetic tree was difficult to establish confidently relative to known retroviruses, and another lineage identified as ERVs belonging to class II. CONCLUSIONS Retroviruses have circulated in felids along with their evolution. The majority of the deep clades of ERVs exist since the primary divergence of felids' base and cluster with retroviruses of divergent mammalian lineages, suggesting horizontal interordinal transmission. Our findings highlight the importance of additional studies on the role of ERVs in the genome landscaping of other carnivore species.
Collapse
|
18
|
Prellwitz IM, Alves BM, Ikeda MLR, Kuhleis D, Picon PD, Jarczewski CA, Osório MR, Sánchez A, Seuánez HN, Larouzé B, Soares MA, Soares EA. HIV behind bars: human immunodeficiency virus cluster analysis and drug resistance in a reference correctional unit from southern Brazil. PLoS One 2013; 8:e69033. [PMID: 23874857 PMCID: PMC3706441 DOI: 10.1371/journal.pone.0069033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/05/2013] [Indexed: 02/06/2023] Open
Abstract
People deprived of liberty in prisons are at higher risk of infection by the human immunodeficiency virus (HIV) due to their increased exposure through intravenous drug use, unprotected sexual activity, tattooing in prison and blood exposure in fights and rebellions. Yet, the contribution of intramural HIV transmission to the epidemic is scarcely known, especially in low- and middle-income settings. In this study, we surveyed 1,667 inmates incarcerated at Presídio Central de Porto Alegre, located in southern Brazil, for HIV infection and molecular characterization. The HIV seroprevalence was 6.6% (110/1,667). Further analyses were carried out on 40 HIV-seropositive inmates to assess HIV transmission clusters and drug resistance within the facility with the use of molecular and phylogenetic techniques. The molecular epidemiology of HIV-1 subtypes observed was similar to the one reported for the general population in southern Brazil, with the predominance of HIV-1 subtypes C, B, CRF31_BC and unique BC recombinants. In particular, the high rate (24%) of URF_BC found here may reflect multiple exposures of the population investigated to HIV infection. We failed to find HIV-infected inmates sharing transmission clusters with each other. Importantly, the analysis of HIV-1 pol genomic fragments evidenced high rates of HIV primary and secondary (acquired) drug resistance and an alarming proportion of virologic failure among patients under treatment, unveiling suboptimal access to antiretroviral therapy (ARV), low ARV adherence and dissemination of drug resistant HIV strains in primary infections. Our results call for immediate actions of public authority to implement preventive measures, serological screening and, for HIV-seropositive subjects, clinical and treatment follow-up in order to control HIV infection and limit the spread of drug resistance strains in Brazilian prisons.
Collapse
Affiliation(s)
| | - Brunna M. Alves
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Maria Letícia R. Ikeda
- Secretaria de Saúde de Viamão, Prefeitura de Viamão, Viamão, Brazil
- Departamento de Ensino e Pesquisa, Hospital Sanatório Partenon, Porto Alegre, Brazil
| | - Daniele Kuhleis
- Secretaria de Segurança Pública, Governo do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pedro D. Picon
- Secretaria de Segurança Pública, Governo do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carla A. Jarczewski
- Departamento de Ensino e Pesquisa, Hospital Sanatório Partenon, Porto Alegre, Brazil
| | - Marta R. Osório
- Fundação Estadual de Produção e Pesquisa em Saúde, Governo do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexandra Sánchez
- Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Secretaria de Estado de Administração Penitenciária, Governo do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N. Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bernard Larouzé
- Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- INSERM U707, Paris, France
- Université Pierre et Marie Curie - Paris 6, Paris, France
| | - Marcelo A. Soares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Esmeralda A. Soares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- * E-mail:
| |
Collapse
|