Biology subjects

Reeves, D. B.

Publications and source records attributed to Reeves, D. B..

9 recordsLinked to original sources

bioRxiv2026

Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity

SARS-CoV-2 evolution enhanced viral fitness and immune evasion, extending the COVID-19 pandemic and resulting in millions of excess deaths. Viral diversity is generated within infected individuals, yet the timing and interplay of viral and immunological forces that drive transmissible evolution are incompletely understood. We developed a multi-scale within host phylodynamic (WiPhy) model of SARS-CoV-2 infection which couples viral replication, innate and acquired immune responses, and viral mutation. We then validated the model against quantitative viral and phylodynamic metrics. Model output predicts that typical acute infections rapidly generate genetic diversity due to accumulation of minor variants which in most cases do not achieve sufficient concentrations for transmission. Delayed innate immune responses correlate with higher peak viral load and diversification, allowing higher transmission risk of the founder virus or with a novel variant that is equally or less fit. In contrast, the risk of transmitting a fitter variant is highest during the ~10% of infections in which viral loads remain sufficiently high for transmission after 10-14 days. In these cases, non-sustained innate and/or weak acquired immune responses allow sufficient time for selection of a variant with one or more fitness enhancing non-synonymous mutations. Across a simulated cohort of ~1500 individuals, 5% of transmission risk came from variants with enhanced fitness from nonsynonymous mutations, and 13% of simulated infections accounted for 90% of fitter variant transmission risk. Our results highlight how the timing and interplay of viral and immunological forces within a host create bottlenecks that severely limit between host evolution.

evolutionary biology↗

bioRxiv2026

Modeling quantifies in vivo neutralization, Fc-mediated killing, and resistance in human clinical trials of five anti-HIV broadly neutralizing antibodies

Broadly neutralizing antibodies (bnAbs) are a promising intervention for HIV prevention, therapy, and cure. bnAb optimization requires precise quantification of in vivo functions, many of which cannot be directly measured in humans. We therefore performed a mathematical modeling meta-analysis which integrated four clinical trials and reproduced serial bnAb concentrations, viral loads, and bnAb sensitivities (IC50) in 43 viremic trial participants who received an infusion of VRC01, VRC01LS, VRC07-523LS, 3BNC117 or 10-1074. We compared >300 mathematical models for their ability to recapitulate multi-strain HIV dynamics following bnAb infusion. For each bnAb, our best model identified a scaling factor of 36-462 to project in vivo activity from in vitro IC50, quantified Fc-mediated infected cell killing in humans over time, and projected the timing of bnAb-resistant strain emergence. Using this holistic profile, VRC07-523-LS was generally optimal.

immunology↗

bioRxiv2025

VRC01 Selects Rare HIV Escape Mutations After Acquisition in Antibody-Mediated Prevention Trials

Broadly neutralizing antibodies (bnAbs) show promise in HIV prevention, yet viral escape remains a challenge. In the Antibody Mediated Prevention (AMP) trials, the CD4 binding site (CD4bs) bNAb VRC01 blocked acquisition by VRC01-sensitive strains. However, its influence on viral evolution post-acquisition is not fully understood. Here we analyzed >12,000 HIV env sequences from 47 participants from the AMP trials, identifying VRC01-mediated de novo escape mutations in 8 of 26 VRC01-treated participants but none in 21 placebo participants. These mutations were found at very low frequency (<1%) in global viruses. Escape mutations, primarily located in the Loop-D and {beta}23/V5 regions of Env, conferred cross-resistance to several CD4bs bnAbs, while more potent CD4bs bnAbs like N6 and 1-18 largely retained their activity. Our findings demonstrate that prophylactic VRC01 can select for viral escape after infection, underscoring the need for next-generation bnAbs with improved breadth and potency to enhance durability and efficacy of antibody-based HIV prevention.

microbiology↗

bioRxiv2025

Q4ddPCR (May the Fourth Be Precise): A Flexible, 4-Target Assay for High-Resolution HIV Reservoir Profiling

Precise and scalable quantification of the genetically intact HIV reservoir is critical for advancing curative strategies. However, current HIV reservoir assays such as the intact proviral DNA assay (IPDA) are limited by quantification failures or misclassification of defective proviral genomes due to HIV sequence heterogeneity. Q4ddPCR is a modular, droplet digital PCR assay that simultaneously targets four conserved regions in the HIV genome to improve specificity, reduce quantification gaps, and provide multi-layered readouts. We benchmarked Q4ddPCR against 3,650 near full-length proviral sequences from 13 virally suppressed people with HIV (PWH) generated by Q4PCR using the same primer/probe sets. Q4ddPCR enabled intact reservoir quantification in 95% of samples from three independent cohorts and closely matched sequence-confirmed Q4PCR reservoir measurements. In addition, multi-probe readouts revealed clonal intact reservoir dynamics that are not detectable by IPDA. In longitudinal samples from 42 participants over the first 4.5 years on antiretroviral therapy (ART), Q4ddPCR reported lower proviral frequencies and a steeper decline in intact proviral DNA compared to IPDA. Collectively, our findings confirm key predictions from mathematical modeling, demonstrating that multi-target assays provide greater specificity and more accurately capture the dynamics of the intact HIV reservoir.

immunology↗

bioRxiv2025

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

In the HIV antibody mediated prevention (AMP) trials, the broadly neutralizing antibody VRC01 demonstrated protective efficacy against new diagnoses with susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, we performed deep sequencing on 172 participants in the placebo and treatment arms, generating 63,444 gag-{Delta}pol (2.5 kb) and 53,088 rev-env-{Delta}nef (3 kb) sequences. Sequences were classified into transmitted founder lineages (TFLs), and infections with multiple distinct lineages were determined. Multilineage infections were detected in [~]38% of participants in both the African (HVTN 703/HPTN 081) and Americas/Europe (HVTN 704/HPTN 085) cohorts, regardless of placebo or treatment group, or cohort. The high levels of multilineage infections could be attributed to minor lineages (<5% abundance) identified in 20% of participants. Infection with VRC01 discordant viruses (IC80s >3-fold different) was observed in 40% of multilineage infections, with a trend toward greater intra-host neutralization differences with increasing VRC01 dose (Jonckheere-Terpstra test, p=0.072). In six VRC01 treated participants who acquired both sensitive (IC80<1{micro}g/ml) and resistant viruses (IC80>3{micro}g/ml), the sensitive lineages declined over time. Recombination was pervasive, observed in 63% of multilineage infections at the time of HIV diagnosis. In one treated participant infected with VRC01 discordant lineages, recombinant viruses preferentially inherited the resistance mutation (binomial p=0.004). In conclusion, our in-depth analysis of breakthrough viruses in the AMP trials revealed a high frequency of multilineage infections, including infections with viruses with different VRC01 sensitivities. This analysis also highlights the role of recombination in shaping intra-host viral evolution and facilitating escape from VRC01. SignificanceThis work advances our understanding of the diversity of initial viral infection and evolution and in vivo activity of broadly neutralizing antibodies (bNAbs). Deep sequencing revealed [~]38% of HIV acquisitions with multiple transmitted founder lineages, higher than previous studies. These occurrences were similar in the placebo and VRC01 groups. Viral recombination among post-acquisition variants was common under antibody selection and appeared to favor resistant sequences in the treatment group. These data suggest as with single antiviral therapy, passive and active immunization of bNAbs should be directed at multiple antigen targets of HIV-1.

molecular biology↗

bioRxiv2020

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Here we analyzed SARS-CoV-2 sequence diversity across 5,700 sequences sampled since December 2019. The Spike protein, which is the target immunogen of most vaccine candidates, showed 93 sites with shared polymorphisms; only one of these mutations was found in more than 1% of currently circulating sequences. The minimal diversity found among SARS-CoV-2 sequences can be explained by drift and bottleneck events as the virus spread away from its original epicenter in Wuhan, China. Importantly, there is little evidence that the virus has adapted to its human host since December 2019. Our findings suggest that a single vaccine should be efficacious against current global strains. One Sentence SummaryThe limited diversification of SARS-CoV-2 reflects drift and bottleneck events rather than adaptation to humans as the virus spread.

evolutionary biology↗

bioRxiv2019

Thresholds for post-rebound viral control after CCR5 gene-edited autologous hematopoietic cell transplantation

Autologous, CCR5 gene-edited hematopoietic stem and progenitor cell (HSPC) transplantation is a promising strategy for achieving HIV remission. However, only a fraction of HSPCs can be edited ex vivo to provide protection against infection prior to autologous transplantation. The optimal transplantation conditions for achieving viral control in the absence of suppressive antiretroviral therapy (ART) are still unknown. We analyzed data from SHIV-1157ipd3N4-infected juvenile pig-tailed macaques that underwent autologous HSPC transplantation with and without CCR5 gene editing. We developed a mathematical model that recapitulates reconstitution of T cell subset counts and SHIV plasma viral loads in control and transplanted macaques. The model predicts that viral control can be obtained following ART treatment interruption (ATI) when: 1) levels of transplanted HSPCs are at least 10-fold higher than residual endogenous HSPCs after total body irradiation and 2) the fraction of protected HSPCs in the transplant achieves a threshold (73%-90%) sufficient to overcome transplantation-dependent loss of SHIV immunity. Under these conditions, if ATI is withheld until transplanted gene-modified cells engraft and reconstitute to a steady state, then spontaneous viral control is projected to occur immediately. Our results support strategies that 1) increase stem cell dose, 2) enhance potency of conditioning regimen, 3) elevate fraction of gene modified SHIV-resistant cells, 4) extend periods between HSPC transplantation and ATI with tracking of CD4+CCR5- cell recovery and / or 5) augment anti-SHIV immunity to achieve sustained SHIV remission. One Sentence SummaryAutologous transplantation of {Delta}CCR5 HSPCs may induce post-ATI SHIV control when the gene-edited cell dose is sufficient to overcome SHIV immunity loss.

microbiology↗

bioRxiv2018

Viral diversity is an obligate consideration in CRISPR/Cas9 designs for HIV cure

RNA-guided CRISPR/Cas9 systems can be designed to mutate or excise the integrated HIV genome from latently infected cells and have therefore been proposed as a curative approach for HIV. However, most studies to date have focused on molecular clones with ideal target site recognition and do not account for target site variability observed within and between patients. For clinical success and broad applicability, guide RNA (gRNA) selection must account for circulating strain diversity and incorporate the within-host diversity of HIV. To address this, we identified a set of gRNAs targeting HIV LTR, gag and pol using publicly available sequences for these genes. We ranked gRNAs according to global conservation across HIV-1 group M and within subtypes A-C. By considering paired and triplet combinations of gRNAs, we found triplet sets of target sites such that at least one of the gRNAs in the set was present in over 98% of all globally-available sequences. We then selected 59 gRNAs from our list of highly-conserved LTR target sites and evaluated in vitro activity using a loss-of-function LTR-GFP fusion reporter. We achieved efficient GFP knockdown with multiple gRNAs and found clustering of highly active gRNA target sites near the middle of the LTR. Using published deep-sequence data from HIV-infected patients, we found that globally conserved sites also had greater within-host target conservation. Lastly, we developed a mathematical model based on varying distributions of within-host HIV sequence diversity and enzyme efficacy. We used the model to estimate the number of doses required to deplete the latent reservoir and achieve functional cure thresholds. Our modeling results highlight the importance of within-host target site conservation. While increased doses may overcome low target cleavage efficiency, inadequate targeting of rare strains is predicted to lead to rebound upon ART cessation even with many doses.\n\nAuthor summaryThe field of genome engineering has exploded over the last decade with the discovery of targeted endonucleases such as CRISPR/Cas9. Endonucleases are now being used to develop a wide range of therapeutics and their use has expanded into antiviral therapy against latent viral infections like HIV. The idea is to induce mutations in latent viral genomes that will render them replication-incompetent, thereby producing a functional cure. Although a great deal of progress has been made, most studies to date have relied on molecular clones that represent \"ideal\" targets. For clinical success and broad applicability, these therapies need to account for viral genetic diversity within and between individuals. Our paper examines the impact of HIV diversity on CRISPR-based cure strategies to determine the predictors of future clinical success. We performed an exhaustive and detailed computational analysis to identify optimal CRISPR target sites, taking into consideration both within-host and global viral diversity. We coupled this with laboratory testing of highly-conserved guides and compared measured activity to predicted results. Finally, we developed a mathematical model to predict the impact of enzyme activity and viral diversity on the number of doses of a CRISPR-based therapy needed to achieve a functional cure of HIV.

bioinformatics↗

bioRxiv2017

HIV persistence during antiviral therapy occurs due to cellular proliferation

Antiretroviral therapy (ART) suppresses viral replication in people living with HIV. Yet, infected cells persist for decades on ART and viremia returns if ART is stopped. Persistence has been attributed to viral replication in an ART sanctuary and long-lived and1or proliferating latently infected cells. Using ecological methods and existing data, we infer that >99% of infected cells are members of clonal populations after one year of ART. We reconcile our results with observations from the first months of ART, demonstrating mathematically how a \"fossil record\" of historic HIV replication permits observed viral evolution even while most new infected cells arise from proliferation. Together, our results imply cellular proliferation generates a majority of infected cells during ART. Therefore, reducing proliferation could decrease the size of the HIV reservoir and help achieve a functional cure.

immunology↗