Article
Neurosciences
Maxwell A. Sherman, Rachel E. Rodin, Giulio Genovese, Caroline Dias, Alison R. Barton, Ronen E. Mukamel, Bonnie Berger, Peter J. Park, Christopher A. Walsh, Po-Ru Loh
Summary: The contribution of mosaic copy number variants (mCNVs) to the risk of autism spectrum disorder (ASD) was investigated in a study, revealing that probands with ASD carry a significant burden of mCNVs compared to their unaffected siblings, particularly large mCNVs. Additionally, the severity of ASD symptoms correlated positively with the size of mCNVs, and no mosaic analogues of common short de novo CNVs associated with ASD were observed.
NATURE NEUROSCIENCE
(2021)
Article
Immunology
Kai Kammers, Athena Chen, Daniel R. Monaco, Sarah E. Hudelson, Wendy Grant-McAuley, Richard D. Moore, Galit Alter, Steven G. Deeks, Charles S. Morrison, Leigh A. Eller, Joel N. Blankson, Oliver Laeyendecker, Ingo Ruczinski, Susan H. Eshleman, H. Benjamin Larman
Summary: Low HIV viral load is linked to delayed disease progression and reduced transmission, with HIV controllers able to suppress viral load without treatment. The study used the VirScan antibody profiling system to compare antibody reactivity in different HIV groups. Results showed that controllers had higher antibody reactivity to certain peptides compared to non-controllers who were virally suppressed on ART.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Mathematics, Applied
Peng Wu, Zhaosheng Feng, Xuebing Zhang
Summary: In this study, a model is established to study the global dynamical behaviors of HIV/AIDS transmission by considering three-age structure, spatial diffusion, viral load-dependent infection and conversion rates. The global stability of steady states and the uniform persistence of the disease are analyzed. Sensitivity analysis shows that certain parameters significantly impact the transmission rate and intervention measures play a crucial role in controlling HIV infection at the population level. Numerical simulations suggest that intervention measures at both individual and population levels are highly effective in controlling disease transmission.
JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
(2022)
Article
Ecology
Alexander J. Smith, Karen McGlathery, Yaping Chen, Carolyn J. Ewers Lewis, Scott C. Doney, Keryn Gedan, Carly K. LaRoche, Peter Berg, Michael L. Pace, Julie C. Zinnert, Matthew L. Kirwan
Summary: Coastal landscapes consist of shifting mosaics of distinct ecosystems, and rapid losses and gains within these ecosystems largely offset each other, resulting in relatively stable areas and increased carbon storage. However, the strength of these compensatory mechanisms may weaken as climate change exacerbates carbon losses.
Article
Immunology
Prakash Ganesh, Tom Heller, Boniface Chione, Joe Gumulira, Salem Gugsa, Shaukat Khan, Seth McGovern, Angellina Nhlema, Lyse Nkhoma, Jilian A. Sacks, Clement Trapence, Hannock Tweya, Peter Ehrenkranz, Sam Phiri
Summary: The targeted near-POC viral load testing in large HIV clinics in Lilongwe, Malawi showed that it enabled prompt clinical action, effectively managing patients. Although the all-in cost for near-POC testing was slightly higher compared to centralized testing, combining both methods in an optimized national program could further reduce the cost difference.
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES
(2021)
Article
Chemistry, Multidisciplinary
Reza Nouri, Yuqian Jiang, Anthony J. Politza, Tianyi Liu, Wallace H. Greene, Yusheng Zhu, Jonathan J. Nunez, Xiaojun Lian, Weihua Guan
Summary: This study reported a new digital CRISPR-Cas13 assay (dCRISPR) using automated membrane-based partitioning to achieve absolute quantification of HIV-1 viral RNAs. The method does not require amplification and can rapidly quantify RNA samples over a wide range in a short period of time.
Article
Immunology
Wendy Grant-McAuley, William Morgenlander, Sarah E. Hudelson, Manjusha Thakar, Estelle Piwowar-Manning, William Clarke, Autumn Breaud, Joel Blankson, Ethan Wilson, Helen Ayles, Peter Bock, Ayana Moore, Barry Kosloff, Kwame Shanaube, Sue-Ann Meehan, Anneen van Deventer, Sarah Fidler, Richard Hayes, Ingo Ruczinski, Kai Kammers, Oliver Laeyendecker, H. Benjamin Larman, Susan H. Eshleman
Summary: This study analyzed the HIV antibody response in controllers and non-controllers and its association with viral load. It found that specific antibody responses prior to infection were associated with controller status and lower viral load, while another antibody response was associated with non-controller status and higher viral load. These findings may contribute to research on antibody-based interventions for HIV treatment.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Yonatan Woodbridge, Sharon Amit, Amit Huppert, Naama M. Kopelman
Summary: This study demonstrates that recent vaccination reduces Omicron viral load, but its effect wanes rapidly. In contrast, recovered COVID-19 individuals show a significantly slower waning rate. Therefore, a reassessment of future booster campaigns is needed.
NATURE COMMUNICATIONS
(2022)
Article
Pediatrics
Armando B. D. Djiyou, Calixte Ida Penda, Yoann Madec, Grace Dalle Ngondi, Astrid Moukoko, Marie Varloteaux, Laure-Amelie de Monteynard, Cecile Moins, Carole Else Eboumbou Moukoko, Avelin F. Aghokeng
Summary: This study assessed the rate of sustained viral suppression (VS) and factors associated with virological failure (VF) in a cohort of adolescents receiving antiretroviral therapy (ART) in Cameroon. The study found a high rate of VS, indicating that achieving the UNAIDS 95% VS rate is feasible in this population.
Article
Microbiology
Chuyu Zhang, Yun Lan, Linghua Li, Ruiying He, Yu Meng, Jian Li, Weilie Chen
Summary: This study investigated the factors associated with different HIV-1 tropisms in low-level viral load HIV-1 infections in China. The majority of infections in Guangdong receiving highly active antiretroviral therapy for more than 6 months were R5-tropic, and the baseline immune level was lower in X4-tropic infections. Furthermore, certain amino acid variations were associated with X4-tropic HIV-1.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biology
Juliane Schroter, Rob J. de Boer
Summary: An acute HIV infection in young children is characterized by higher viral loads and a poor contraction to a setpoint viral load. We used a mathematical model to investigate why children have a lower viral contraction ratio than adults. Our analysis suggests that an ineffective immune response is the primary reason for the higher viral setpoint in children and their faster disease progression.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Article
Immunology
Jienchi Dorward, Jessica Naidoo, Pravikrishnen Moodley, Yukteshwar Sookrajh, Natasha Samsunder, Fathima Sayed, Nivashnee Naicker, Thomas Fanshawe, Paul K. Drain, Richard J. Lessells, Gail Hayward, Christopher C. Butler, Nigel Garrett
Summary: This study evaluated the analytic performance of three rapid HIV viral load assays. The results showed that all three assays had clinically acceptable accuracy in detecting viremia. In addition, both Xpert assays were also accurate in detecting low-level viremia.
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES
(2022)
Article
Ecology
Anders P. Charmouh, Jane M. Reid, Trine Bilde, Greta Bocedi
Summary: Understanding how genetic and ecological effects interact to shape genetic loads is crucial for understanding the ongoing persistence of systems that should be susceptible to extinction. Our hypothesis suggests that genetic stochasticity and evolving dispersal can facilitate metapopulation persistence by causing fluctuations in metapopulation size and transient gene flow. This mechanism provides an explanation for the continued existence of structured populations with inbreeding mating systems in diverse taxa.
Article
Virology
Lele Zhao, Chris Wymant, Francois Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Matthew Hall, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, M. Kate Grabowski, Barbara Gunsenheimer-Bartmeyer, Huldrych F. Gunthard, Pia Kivela, Roger D. Kouyos, Oliver Laeyendecker, Laurence Meyer, Kholoud Porter, Ard van Sighem, Marc van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Christophe Fraser, Luca Ferretti
Summary: This study investigates the relationship between viral load and transmission fitness in HIV-1. The results suggest that higher set-point viral load is associated with increased infectiousness and transmission fitness. This finding has implications for understanding the evolution and spread of HIV-1.
Article
Biochemistry & Molecular Biology
Maddy L. Newby, Carl A. Fogarty, Joel D. Allen, John Butler, Elisa Fadda, Max Crispin
Summary: The emergence of SARS-CoV-2 variants affects the effectiveness of existing immunity. Understanding the structure of the viral spike helps determine the impact of mutations on the antigenic surface. One type of mutation affects glycosylation attachment sites, which can influence the antigenic structure beyond the immediate attachment site. This study compares the glycosylation of different variants and investigates the effects of specific glycan sites on the spike protein.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Immunology
Manon Ragonnet-Cronin, Tanya Golubchik, Sikhulile Moyo, Christophe Fraser, Max Essex, Vlad Novitsky, Erik Volz
Summary: This study shows that the recency of HIV-1 infection can be inferred from viral sequence diversity even among patients on suppressive ART.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Infectious Diseases
Katherine A. Twohig, Tommy Nyberg, Asad Zaidi, Simon Thelwall, Mary A. Sinnathamby, Shirin Aliabadi, Shaun R. Seaman, Ross J. Harris, Russell Hope, Jamie Lopez-Bernal, Eileen Gallagher, Andre Charlett, Daniela De Angelis, Anne M. Presanis, Gavin Dabrera
Summary: A study in England found that patients with COVID-19 infected with the delta variant were more likely to be admitted to hospital or attend emergency care compared to those infected with the alpha variant. This suggests that outbreaks of the delta variant in unvaccinated populations may pose a greater burden on healthcare services.
LANCET INFECTIOUS DISEASES
(2022)
Article
Immunology
Daniela Bezemer, Alexandra Blenkinsop, Matthew Hall, Ard van Sighem, Marion Cornelissen, Els Wessels, Jeroen van Kampen, Thijs van de Laar, Peter Reiss, Christophe Fraser, Oliver Ratmann
Summary: This study investigates the introductions and spread of different HIV-1 subtypes in the Netherlands. The results show that a considerable proportion of non-B infections amongst both heterosexuals and MSM in the Netherlands have been acquired in-country, although most introductions of non-B subtypes showed little onward transmission.
Article
Health Care Sciences & Services
Carolin Vegvari, Sam Abbott, Frank Ball, Ellen Brooks-Pollock, Robert Challen, Benjamin S. Collyer, Ciara Dangerfield, Julia R. Gog, Katelyn M. Gostic, Jane M. Heffernan, T. Deirdre Hollingsworth, Valerie Isham, Eben Kenah, Denis Mollison, Jasmina Panovska-Griffiths, Lorenzo Pellis, Michael G. Roberts, Gianpaolo Scalia Tomba, Robin N. Thompson, Pieter Trapman
Summary: The reproduction number R has become a popular epidemiological metric during the COVID-19 pandemic, but its interpretation and estimation can vary significantly depending on the definition and statistical methods used. The availability and type of data also play a crucial role in estimating R accurately. Careful consideration and analysis are required when using R as an indicator for managing the epidemic effectively.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2022)
Article
Infectious Diseases
Ben Swallow, Paul Birrell, Joshua Blake, Mark Burgman, Peter Challenor, Luc E. Coffeng, Philip Dawid, Daniela De Angelis, Michael Goldstein, Victoria Hemming, Glenn Marion, Trevelyan J. McKinley, Christopher E. Overton, Jasmina Panovska-Griffiths, Lorenzo Pellis, Will Probert, Katriona Shea, Daniel Villela, Ian Vernon
Summary: This paper discusses four challenges in the estimation paradigm for infectious disease modeling and proposes priorities in estimation methodology to prepare for future pandemics.
Article
Infectious Diseases
Mirjam E. Kretzschmar, Ben Ashby, Elizabeth Fearon, Christopher E. Overton, Jasmina Panovska-Griffiths, Lorenzo Pellis, Matthew Quaife, Ganna Rozhnova, Francesca Scarabel, Helena B. Stage, Ben Swallow, Robin N. Thompson, Michael J. Tildesley, Daniel Villela
Summary: This paper discusses the framework provided by mathematical modelling and statistical inference for controlling epidemics during the COVID-19 pandemic. It highlights the challenges for future pandemic control and emphasizes the importance of data availability, correct parameterization, and modeling various aspects of interventions, including health economics and politics.
Article
Immunology
Kidist Zewdie, Michael Pickles, Sian Floyd, Sarah Fidler, Helen Ayles, Peter Bock, Graeme Hoddinott, Nomtha Mandla, Kwame Shanaube, Musonda Simwinga, Christophe Fraser, Janet Seeley, Estelle Piwowar-Manning, Richard Hayes, Deborah Donnell
Summary: Based on data analysis from 21 research communities in Zambia and South Africa, it was found that traditional male circumcision is not significantly more protective against HIV acquisition compared to medical male circumcision. The uptake of voluntary medical male circumcision was not substantial, even with household-based delivery of HIV testing followed by referral for circumcision.
Article
Infectious Diseases
Suraj Balakrishna, Tom Loosli, Maryam Zaheri, Paul Frischknecht, Michael Huber, Katharina Kusejko, Sabine Yerly, Karoline Leuzinger, Matthieu Perreau, Alban Ramette, Chris Wymant, Christophe Fraser, Paul Kellam, Astrid Gall, Hans H. Hirsch, Marcel Stoeckle, Andri Rauch, Matthias Cavassini, Enos Bernasconi, Julia Notter, Alexandra Calmy, Huldrych F. Gunthard, Karin J. Metzner, Roger D. Kouyos
Summary: This study compared the reliability of Sanger sequencing and Next-generation sequencing (NGS) in detecting HIV drug resistance mutations (DRMs). The results showed good agreement between the two methods when detecting mutations at a threshold of 5% or higher. However, at lower thresholds, NGS detected a substantial number of low-frequency mutations, which were likely to be sequencing errors.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Social Sciences, Mathematical Methods
Lorenzo Pellis, Paul J. Birrell, Joshua Blake, Christopher E. Overton, Francesca Scarabel, Helena B. Stage, Ellen Brooks-Pollock, Leon Danon, Ian Hall, Thomas A. House, Matt J. Keeling, Jonathan M. Read, Daniela JUNIPER Consortium, Daniela De Angelis
Summary: The reproduction number R has been an important metric in the COVID-19 pandemic response, but its estimation is complex and model-dependent. Limited data and challenges in communication further complicate its use.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY
(2022)
Article
Biology
Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, Luca Ferretti
Summary: The raw material for viral evolution comes from intra-host mutations during replication, transcription, or post-transcription. This study explores the mutational spectrum of SARS-CoV-2 and reveals differences in mutation patterns between the negative and positive strands, potentially influenced by host factors.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Michelle Kendall, Daphne Tsallis, Chris Wymant, Andrea Di Francia, Yakubu Balogun, Xavier Didelot, Luca Ferretti, Christophe Fraser
Summary: The NHS COVID-19 app, launched in England and Wales in September 2020, had a Bluetooth-based contact tracing functionality to reduce the transmission of SARS-CoV-2. The study shows that user engagement and the app's impact on the epidemic varied based on social and epidemic characteristics. The authors also discuss the interaction and complementarity of manual and digital contact tracing approaches.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Nick Groves-Kirkby, Ewan Wakeman, Seema Patel, Robert Hinch, Tineke Poot, Jonathan Pearson, Lily Tang, Edward Kendall, Ming Tang, Kim Moore, Scott Stevenson, Bryn Mathias, Ilya Feige, Simon Nakach, Laura Stevenson, Paul O'Dwyer, William Probert, Jasmina Panovska-Griffiths, Christophe Fraser
Summary: This study adapted an agent-based model of COVID-19 to inform planning and decision-making within a healthcare setting. By calibrating the model to health data, it simulated the spread of the virus in England and provided useful projections of future clinical demand for the National Health Service (NHS).
Article
Biology
Katrina A. Lythgoe, Tanya Golubchik, Matthew Hall, Thomas House, Roberto Cahuantzi, George MacIntyre-Cockett, Helen Fryer, Laura Thomson, Anel Nurtay, Mahan Ghafani, David Buck, Angie Green, Amy Trebes, Paolo Piazza, Lorne J. Lonie, Ruth Studley, Emma Rourke, Darren Smith, Matthew Bashton, Andrew Nelson, Matthew Crown, Clare McCann, Gregory R. Young, Rui Andre Nunes dos Santos, Zack Richards, Adnan Tariq, Christophe Fraser, Ian Diamond, Jeff Barrett, Ann Sarah Walker, David Bonsall
Summary: The study analyzed the samples collected by the Office for National Statistics Coronavirus Infection Survey (ONS-CIS) to investigate the epidemiological and evolutionary dynamics of SARS-CoV-2. The findings showed that different lineages had distinct growth advantages during the study period, although there was a gradual decrease in average viral burdens. The study also observed increasing divergence and diversity within lineages, with step increases in divergence associated with major lineages.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Meeting Abstract
Immunology
S. E. Chaudron, L. Zhao, G. Macinthyre-Crockett, L. Thompson, I. Baudi, M. Limbada, S. Floyd, B. Kosloff, K. Shanaube, S. Fidler, R. Hayes, H. Ayles, J. Herbeck, C. Fraser, D. Bonsall
JOURNAL OF THE INTERNATIONAL AIDS SOCIETY
(2022)
Article
Virology
Lele Zhao, Chris Wymant, Francois Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Matthew Hall, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, M. Kate Grabowski, Barbara Gunsenheimer-Bartmeyer, Huldrych F. Gunthard, Pia Kivela, Roger D. Kouyos, Oliver Laeyendecker, Laurence Meyer, Kholoud Porter, Ard van Sighem, Marc van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Christophe Fraser, Luca Ferretti
Summary: This study investigates the relationship between viral load and transmission fitness in HIV-1. The results suggest that higher set-point viral load is associated with increased infectiousness and transmission fitness. This finding has implications for understanding the evolution and spread of HIV-1.