Article
Multidisciplinary Sciences
Matthijs Meijers, Kanika Vanshylla, Henning Gruell, Florian Klein, Michael Laessig
Summary: Broadly neutralizing antibodies show promise in treating and preventing HIV-1 infections, but the virus often evolves resistance. A fitness model based on in vivo data accurately predicts the dynamics of HIV-1 escape during antibody treatment, highlighting an evolutionary trade-off between antibody resistance and its collateral cost.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Sandile Cele, Farina Karim, Gila Lustig, James Emmanuel San, Tandile Hermanus, Houriiyah Tegally, Jumari Snyman, Thandeka Moyo-Gwete, Eduan Wilkinson, Mallory Bernstein, Khadija Khan, Shi-Hsia Hwa, Sasha W. Tilles, Lavanya Singh, Jennifer Giandhari, Ntombifuthi Mthabela, Matilda Mazibuko, Yashica Ganga, Bernadett Gosnell, Salim S. Abdool Karim, Willem Hanekom, Wesley C. Van Voorhis, Thumbi Ndung'u, Richard J. Lessells, Penny L. Moore, Mahomed-Yunus S. Moosa, Tulio de Oliveira, Alex Sigal
Summary: Characterizing the evolution of SARS-CoV-2 in an individual with advanced HIV disease in South Africa, this study found that the evolved virus showed immune escape of vaccines and enhanced escape of Delta immunity. This suggests that immune-compromised hosts may play a significant role in the evolution of the virus.
CELL HOST & MICROBE
(2022)
Article
Biochemistry & Molecular Biology
Nametso Kelentse, Sikhulile Moyo, Kesaobaka Molebatsi, Olorato Morerinyane, Shatho Bitsang, Ontlametse T. Bareng, Kwana Lechiile, Tshepo B. Leeme, David S. Lawrence, Ishmael Kasvosve, Rosemary Musonda, Mosepele Mosepele, Thomas S. Harrison, Joseph N. Jarvis, Simani Gaseitsiwe
Summary: This study investigated CSF viral escape and HIV-1 viral load in individuals treated for HIV-associated cryptococcal meningitis. The results showed a decreasing trend of CSF viral escape during antifungal treatment, indicating the potential of antifungal therapy in reversing CSF viral escape.
Article
Immunology
Baitshepi Mokaleng, Wonderful Tatenda Choga, Ontlametse Thato Bareng, Dorcas Maruapula, Doreen Ditshwanelo, Nametso Kelentse, Patrick Mokgethi, Natasha Onalenna Moraka, Modisa Sekhamo Motswaledi, Leabaneng Tawe, Catherine Kegakilwe Koofhethile, Sikhulile Moyo, Matshediso Zachariah, Simani Gaseitsiwe
Summary: HIV accumulates escape mutations in response to immune response, and the prevalence of CTL escape mutations in Botswana remains similar between two time points. The P17 protein has the most mutations, and unique mutations are found in both early and late time point sequences.
Article
Virology
Aparajitha Vaidyanathan, Harry E. Taylor, Thomas J. Hope, Richard T. D'Aquila, Elizabeth T. Bartom, Judd F. Hultquist, Marcus E. Peter
Summary: HIV infection leads to depletion of CD4(+) T cells, but some cells can survive and become part of the latent reservoir. Understanding the mechanisms of HIV-mediated cell death could potentially help clear the latent reservoir.
JOURNAL OF VIROLOGY
(2023)
Article
Cell Biology
Phillip Pymm, Stefan Tenzer, Edmund Wee, Mirjana Weimershaus, Anne Burgevin, Simon Kollnberger, Jan Gerstoft, Tracy M. Josephs, Kristin Ladell, James E. McLaren, Victor Appay, David A. Price, Lars Fugger, John I. Bell, Hansjoerg Schild, Peter van Endert, Maria Harkiolaki, Astrid K. N. Iversen
Summary: This study discovers that the cytotoxic T lymphocyte (CTL) and natural killer (NK) cell responses to a specific epitope in the human immunodeficiency virus are associated with enhanced immune control. The length and mutations of the epitope influence the CTL and NK cell responses, leading to viral escape.
Article
Virology
Aurelie Drouin, Julie Migraine, Marie-Alice Durand, Alain Moreau, Julien Burlaud-Gaillard, Maxime Beretta, Philippe Roingeard, Melanie Bouvin-Pley, Martine Braibant
Summary: The cellular factor IFITM3 reduces HIV-1 infectivity through an unclear mechanism. IFITM3 interacts with Env of sensitive viruses, inducing conformational changes that decrease viral infectivity, but this antiviral action is modulated by the nature of Env, particularly the V1V2 and V3 loops, which may escape this interaction after processing in the Golgi apparatus.
JOURNAL OF VIROLOGY
(2021)
Review
Microbiology
Alexis Carpenter, Rollie J. Clem
Summary: Arboviral diseases transmitted by mosquitoes are a major global health concern. Current treatment and prevention methods are limited, so controlling the disease at the vector level is ideal. The midgut of the mosquito plays a crucial role in preventing the spread of arboviruses. Understanding the midgut escape barrier may aid in developing effective control strategies.
Article
Infectious Diseases
Nametso Kelentse, Sikhulile Moyo, Wonderful T. Choga, Kwana Lechiile, Tshepo B. Leeme, David S. Lawrence, Ishmael Kasvosve, Rosemary Musonda, Mosepele Mosepele, Thomas S. Harrison, Joseph N. Jarvis, Simani Gaseitsiwe
Summary: This study compared the patterns of HIV-1 drug resistance mutations between the cerebrospinal fluid (CSF) and plasma of individuals with HIV-associated cryptococcal meningitis. The results showed high concordance in HIV-1 drug resistance mutations between the CSF and plasma, suggesting intercompartmental mixing and possibly a lack of compartmentalization. Some individuals also harbored minority HIV-1 drug resistance mutations.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Microbiology
Steven A. Kemp, Oscar J. Charles, Anne Derache, Werner Smidt, Darren P. Martin, Collins Iwuji, John Adamson, Katya Govender, Tulio de Oliveira, Francois Dabis, Deenan Pillay, Richard A. Goldstein, Ravindra K. Gupta
Summary: This study analyzed the whole-genome sequences of chronically infected HIV-1-positive individuals failing 2nd-line regimens under non-suppressive antiretroviral therapy. The findings revealed dramatic changes in virus population structure and highlighted viral diversification, recombination, and haplotype competition during non-suppressive ART.
Letter
Medicine, General & Internal
Erin M. Scherer, Ahmed Babiker, Max W. Adelman, Brent Allman, Autum Key, Jennifer M. Kleinhenz, Rose M. Langsjoen, Phuong-Vi Nguyen, Ivy Onyechi, Jacob D. Sherman, Trevor W. Simon, Hannah Soloff, Jessica Tarabay, Jay Varkey, Andrew S. Webster, Daniela Weiskopf, Daniel B. Weissman, Yongxian Xu, Jesse J. Waggoner, Katia Koelle, Nadine Rouphael, Stephanie M. Pouch, Anne Piantadosi
Summary: This report examines the evolution of SARS-CoV-2 in response to immunologic and monoclonal-antibody pressure in five patients with B-cell deficiency.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Plant Sciences
Sergey Ivashuta, Alberto Iandolino, Greg Watson
Summary: Environmental RNAi (eRNAi) is a process where exogenous RNA regulates endogenous gene expression in a responsive organism, with potential applications in agriculture. Despite mixed results from previous attempts, the concept remains attractive for agricultural use. Understanding the biological significance of eRNAi is crucial for its successful practical applications in agriculture.
Article
Biochemical Research Methods
Erik Lundgren, Ethan Romero-Severson, Jan Albert, Thomas Leitner
Summary: We have developed a multi-biomarker augmented phylogenetic inference method to reconstruct HIV transmission history more accurately by incorporating probabilistic information about infection times obtained from observed biomarkers. Testing on multiple epidemiological scenarios demonstrated that the method can achieve up to 90% accuracy in ideal situations and around 50% accuracy in realistic within-host HIV-1 evolution. The addition of more biomarkers and sequence data per infected host improved the performance of the method.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Jonathan M. O. Rawson, Olga A. Nikolaitchik, Jennifer A. Yoo, Xayathed Somoulay, Matthew A. Brown, Franck S. Mbuntcha Bogni, Vinay K. Pathak, Ferri Soheilian, Ryan L. Slack, Stefan G. Sarafianos, Wei-Shau Hu
Summary: Novel retroviruses can emerge from recombination between distantly related retroviruses. These recombinants may initially have replication defects, but they can adapt and enhance their replication by acquiring substitutions.
Article
Medicine, General & Internal
Sander F. Garrelfs, Yaacov Frishberg, Sally A. Hulton, Michael J. Koren, William D. O'Riordan, Pierre Cochat, Georges Deschenes, Hadas Shasha-Lavsky, Jeffrey M. Saland, William G. van't Hoff, Daniel G. Fuster, Daniella Magen, Shabbir H. Moochhala, Gesa Schalk, Eva Simkova, Jaap W. Groothoff, David J. Sas, Kristin A. Meliambro, Jiandong Lu, Marianne T. Sweetser, Pushkal P. Garg, Akshay K. Vaishnaw, John M. Gansner, Tracy L. McGregor, John C. Lieske
Summary: Primary hyperoxaluria type 1 is a rare genetic disease caused by hepatic overproduction of oxalate, leading to kidney stones, nephrocalcinosis, kidney failure, and systemic oxalosis. This trial tested the efficacy of lumasiran, an RNAi therapeutic agent, in reducing hepatic oxalate production. The results showed that lumasiran significantly reduced urinary oxalate excretion, alleviating the cause of kidney failure in PH1 patients.
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
Editorial Material
Microbiology
Miguel Angel Martinez
Summary: While some drugs have shown limited impact on COVID-19, recent research has indicated that plitidepsin has potent antiviral activity, making it a promising alternative therapeutic option for COVID-19.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Editorial Material
Immunology
Miguel Angel Martinez
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Sandra Franco, Daniela Buccione, Cristina Tural, Miguel Angel Martinez
Summary: This study found that specific miRNAs in plasma may be associated with liver injury in patients with HIV-1 infections. A signature of seven miRNAs was identified to be highly correlated with liver fibrosis progression. Two miRNAs, 100-5p and 192-5p, showed high sensitivity and specificity for detecting liver fibrosis progression.
Editorial Material
Virology
Miguel Angel Martinez
Review
Microbiology
Ana Jordan-Paiz, Sandra Franco, Miguel Angel Martinez
Summary: Synonymous mutations within protein coding regions can introduce changes in DNA or messenger RNA without affecting protein structure. Recoding virus genomes through synonymous mutations has helped identify new virus features and mechanisms and improved our understanding of virus genome structures, gene expression regulation, mutational robustness, and adaptability. Advances in understanding how synonymous substitutions impact virus phenotype, coupled with improved DNA synthesis methods, have enhanced our ability to study HIV-1 and potential therapeutic targets.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Sandra Franco, Judith Horneros, Laura Soldevila, Dan Ouchi, Ivan Galvan-Femenia, Rafael de Cid, Montserrat Tenesa, Jordi Bechini, Ricardo Perez, Josep M. Llibre, Bonaventura Clotet, Cristina Tural, Miguel Angel Martinez
Summary: Nonalcoholic fatty liver disease (NAFLD), insulin resistance, and liver fibrosis are common in individuals co-infected with HIV-1/HCV, even after HCV eradication. This study aimed to evaluate the association of single nucleotide polymorphisms (SNPs) with advanced liver fibrosis in HIV-1/HCV co-infected patients.
Article
Virology
Lucia Gutierrez-Chamorro, Eva Riveira-Munoz, Clara Barrios, Vanesa Palau, Maria Nevot, Sonia Pedreno-Lopez, Jordi Senserrich, Marta Massanella, Bonaventura Clotet, Cecilia Cabrera, Oriol Mitja, Marta Crespo, Julio Pascual, Marta Riera, Ester Ballana
Summary: The study found that soluble functional ACE2 levels increase upon SARS-CoV-2 infection in swabs and plasma of infected patients, but rapidly decrease during the course of infection alongside ACE2 gene expression. Similarly, SARS-CoV-2 infection induced the expression of inflammatory cytokines, which correlated positively with viral load.
Article
Cell Biology
Ana Jordan-Paiz, Sandra Franco, Miguel Angel Martinez
Summary: Deoptimizing synonymous codon pair bias in the HIV-1 envelope gene did not always lead to virus attenuation, while optimization of codon pair bias attenuated virus replication. The study also revealed that increasing CpG dinucleotides in the 5' end of the env gene did not always reduce the replication capacity of HIV-1.
Review
Pharmacology & Pharmacy
Miguel Angel Martinez
Summary: This article discusses whether drug repurposing is the best strategy for developing effective therapies to treat COVID-19 and other viral human infections.
DRUG DISCOVERY TODAY
(2022)
Editorial Material
Microbiology
Miguel Angel Martinez
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Virology
Ana Jordan-Paiz, Sandra Franco, Miguel Angel Martinez
Summary: Reducing the frequency of CpG dinucleotides in the HIV-1 envelope can enhance viral replication capacity and may be associated with differences in clinical progression rates in infected individuals.
Review
Virology
Miguel Angel Martinez, Cristina Tural, Sandra Franco
Summary: MicroRNAs (miRNAs) are crucial regulators of gene expression and contribute to various physiological and pathological processes. Liver disease affects the function of liver-associated miRNAs, and these miRNAs can also circulate in body fluids. Circulating miRNAs have the potential to serve as biomarkers for liver disease and can aid in the diagnosis and prediction of different stages of liver disease.
Article
Multidisciplinary Sciences
Sandra Franco, Raquel Pluvinet, Jose Francisco Sanchez-Herrero, Lauro Sumoy, Miguel Angel Martinez
Summary: This study presents a simple reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) assay for quantifying the miR-100-5p_iso_3p:-2 variant. The assay was validated in 57 plasma samples and showed high concordance with high-throughput RNA sequencing results. The method can be easily adapted for quantifying other identified isomiRs, providing greater resolution and accuracy compared to using canonical sequences.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Sandra Franco, Josep M. Llibre, Toni Jou, Cristina Tural, Miguel Angel Martinez
Summary: In a previous study, three plasma circulating miRNAs (miR-100-5p_iso3p:-2, miR-122-5p, and miR-192-5p) that correlate with liver fibrosis evolution in HIV-1/HCV co-infected patients were identified. This study investigated whether the levels of these miRNAs are associated with liver disease progression in HIV-1/HCV co-infected patients who achieved sustained virologic response (SVR) after treatment. The results showed significant reductions in the levels of these miRNAs in SVR patients, indicating their potential as biomarkers for liver damage progression in these individuals.
Article
Gastroenterology & Hepatology
Miguel Angel Martinez, Sandra Franco
Summary: The novel coronavirus SARS-CoV-2 has caused the global COVID-19 pandemic in a short period of time, with implications for individuals with underlying chronic liver disease who may face increased risk of adverse outcomes and liver damage.
HEPATOLOGY COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)