Biology subjects

Pitts, J.

Publications and source records attributed to Pitts, J..

13 recordsLinked to original sources

bioRxiv2025

YOLito: A generalizable model for automated mosquito detection

Understanding mosquito behavior is key to advancing research in ecology, evolution, and disease control, yet most behavioral assays rely on human-dependent methods, such as real-time observation or manual frame-by-frame annotation, limiting throughput and reproducibility. We present YOLito, a domain-generalized AI model for automated mosquito detection and behavioral quantification. Built on the Ultralytics YOLO framework and enhanced with Slicing-Aided Hyper Inference (SAHI), YOLito accurately detects multiple mosquitoes across diverse backgrounds and imaging conditions. Trained on a globally assembled dataset of 38,547 annotated images from 35 experimental setups across six laboratories and three public datasets, YOLito achieved high performance on unseen data (precision = 0.95; recall = 0.91) and generalized across mosquito species (Aedes, Anopheles, Culex) and assay types, including blood-feeding, sugar-feeding, and oviposition. By automating behavioral scoring, YOLito transforms traditional assays into scalable and reproducible experimental platforms. The accompanying open-source toolkit enables high-throughput extraction of metrics such as visit frequency, duration, and distance traveled, providing a standardized and extensible framework that bridges computer vision and vector biology.

animal behavior and cognition↗

bioRxiv2025

Oral dosing of the nucleoside analog obeldesivir is efficacious against RSV infection in African green monkeys

Respiratory syncytial virus (RSV) is a significant cause of morbidity and mortality in high-risk populations. Although prophylactic options are available, there are no effective oral therapeutics for RSV infection. Obeldesivir (ODV) is an orally bioavailable prodrug of the nucleoside analog GS-441524, which is converted intracellularly to its active nucleoside triphosphate and inhibits the RSV RNA polymerase. Here we report the potent antiviral activity of ODV against geographically and temporally diverse RSV A and B clinical isolates (EC50: 0.20-0.66 M). Resistance selection studies with ODV and GS-441524 against RSV identified a single amino acid substitution, I777L, in the L polymerase with reduced susceptibility (3.3-3.8-fold) to ODV and GS-441524, indicating a high barrier for resistance development. In an African green monkey RSV infection model, once-daily oral ODV doses of 30 or 90 mg/kg initiated [~]24 hours post-infection significantly reduced log10 viral RNA copies/mLxday area under the curve by 69-92% in the upper and lower respiratory tracts. Together, these preclinical data support the clinical evaluation of ODV for the treatment of RSV infection.

microbiology↗

bioRxiv2024

Mechanism and spectrum of inhibition of a 4'-cyano modified nucleotide analog against diverse RNA polymerases of prototypic respiratory RNA viruses

The development of safe and effective broad-spectrum antivirals that target the replication machinery of respiratory viruses is of high priority in pandemic preparedness programs. Here, we studied the mechanism of action of a newly discovered nucleotide analog against diverse RNA-dependent RNA polymerases (RdRp) of prototypic respiratory viruses. GS-646939 is the active 5'-triphosphate (TP) metabolite of a 4'-cyano modified C-adenosine analog phosphoramidate prodrug GS-7682. Enzyme kinetics show that the RdRps of human rhinovirus type 16 (HRV-16) and enterovirus 71 (EV-71) incorporate GS-646939 with unprecedented selectivity; GS-646939 is incorporated 20-50-fold more efficiently than its natural ATP counterpart. The RdRp complex of respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) incorporate GS-646939 and ATP with similar efficiency. In contrast, influenza B RdRp shows a clear preference for ATP and human mitochondrial RNA polymerase (h-mtRNAP) does not show significant incorporation of GS-646939. Once incorporated into the nascent RNA strand, GS-646939 acts as a chain-terminator although higher NTP concentrations can partially overcome inhibition for some polymerases. Modeling and biochemical data suggest that the 4'-modification inhibits RdRp translocation. Comparative studies with GS-443902, the active triphosphate form of the 1'-cyano modified prodrugs remdesivir and obeldesivir, reveal not only different mechanisms of inhibition, but also differences in the spectrum of inhibition of viral polymerases. In conclusion, 1'-cyano and 4'-cyano modifications of nucleotide analogs provide complementary strategies to target the polymerase of several families of respiratory RNA viruses.

biochemistry↗

bioRxiv2024

Discovery and Synthesis of GS-7682, a Novel Prodrug of a 4'-CN-4-Aza-7,9-Dideazaadenosine C-Nucleoside with Broad-Spectrum Potency Against Pneumo- and Picornaviruses and Efficacy in RSV-Infected African Green Monkeys.

Acute respiratory viral infections (ARVI), such as pneumovirus and respiratory picornavirus infections, exacerbate disease in COPD and asthma patients. A research program targeting respiratory syncytial virus (RSV) led to the discovery of GS-7682 (1) a novel phosphoramidate prodrug of a 4'-CN-4-aza-7,9-dideazaadenosine C-nucleoside GS-646089 (2) with broad antiviral activity against RSV EC50 = 3-46 nM, human metapneumovirus (hMPV) EC50 = 210 {+/-} 50 nM, human rhinovirus (RV) EC50 = 54-61 nM, and enterovirus (EV) EC50 = 83-90 nM. Prodrug optimization for cellular potency and lung cell metabolism identified the 5-methyl((S)-hydroxy(phenoxy)phosphoryl)-L-alaninate in combination with 2,3-diisobutyrate promoieties as optimal for high intracellular triphosphate formation in vitro and in vivo. 1 demonstrated significant reductions of viral loads in the lower respiratory tract of RSV-infected African green monkeys when administered once daily via intratracheal nebulized aerosol. Together these finding support additional evaluation of 1 and its analogs as a potential therapeutic for pneumo- and picornaviruses.

biochemistry↗

bioRxiv2023

Aedes aegypti (Dipetera: Culicidae) odorant receptors respond to floral and plant derived volatiles.

Adult mosquitoes require regular sugar meals, usually floral nectar, to survive and flourish in natural habitats. Both males and females locate potential sugar sources using sensory proteins called odorant receptors activated by plant volatiles that facilitate orientation toward flowers or honeydew. The Yellow Fever mosquito, Aedes aegypti (Linnaeus, 1762), possesses a large repertoire of odorant receptors, many of which are likely to support floral odor detection and nectar-seeking. In this study, we have employed a heterologous expression system and the two-electrode voltage clamping technique to identify environmentally relevant chemical compounds that activate specific odorant receptors. Importantly, we have uncovered ligand-receptor pairings for a suite of Aedes aegypti odorant receptors likely to mediate appetitive or aversive behavioral responses, thus shaping a critical aspect of the life history of a medically important mosquito. Moreover, the high degree of conservation of these receptors in other disease-transmitting species suggests common mechanisms of floral odor detection. This knowledge can be used to further investigate mosquito foraging behavior to either enhance existing, or develop novel, control strategies, especially those that incorporate mosquito bait-and-kill or attractive toxic sugar bait technologies.

molecular biology↗

bioRxiv2023

The evolution of borneol repellency in culicine mosquitoes

The use of essential oils derived from the camphor tree to repel mosquitoes is an ancient practice that originated in Southeast Asia and gradually spread to China and across Europe via the Maritime Silk Road. The olfactory mechanisms by which these oils elicit avoidance behavior are unclear. Here we show that plant bicyclic monoterpenoids and borneol specifically activate a neural pathway that originates in the orphan olfactory receptor neuron of the capitate peg sensillum in the maxillary palp, and projects to the mediodorsal glomerulus 3 in the antennal lobe. This neuron co-locates with two olfactory receptor neurons tuned to carbon dioxide and octenol that mediate human-host detection. We also confirm that borneol elicits repellency against human-seeking female mosquitoes. Understanding the functional role of the mosquito maxillary palp is essential to investigating olfactory signal integration and host-selection behavior.

evolutionary biology↗

bioRxiv2023

Discovery of GS-5245 (Obeldesivir), an Oral Prodrug of Nucleoside GS-441524 that Exhibits Antiviral Efficacy in SARS-CoV-2 Infected African Green Monkeys

Remdesivir 1 is an amidate prodrug that releases the monophosphate of nucleoside GS-441524 (2) into lung cells thereby forming the bioactive triphosphate 2-NTP. 2-NTP, an analog of ATP, inhibits the SARS-CoV-2 RNA-dependent RNA polymerase replication and transcription of viral RNA. Strong clinical results for 1 have prompted interest in oral approaches to generate 2-NTP. Here we describe the discovery of a 5-isobutyryl ester prodrug of 2 (GS-5245, Obeldesivir, 3) that has low cellular cytotoxicity and three to seven-fold improved oral delivery of 2 in monkeys. Prodrug 3 is cleaved pre-systemically to provide high systemic exposures of 2 that overcome its less efficient metabolism to 2-NTP leading to strong SARS-CoV-2 antiviral efficacy in an African green monkey infection model. Exposure-based SARS-CoV-2 efficacy relationships resulted in an estimated clinical dose of 350-400 mg twice-daily. Importantly, all SARS-CoV-2 variants remain susceptible to 2 which supports development of 3 as a promising COVID-19 treatment.

pharmacology and toxicology↗

bioRxiv2023

Diols and sugar substitutes in attractive toxic sugar baits targeting Aedes aegypti and Aedes albopictus (Diptera: Culicidae) mosquitoes.

Around the world, mosquitoes continue to transmit disease-causing pathogens while also developing resistance to insecticides. We previously discovered that a generally regarded as safe (GRAS) compound, 1,2-propanediol, reduces adult mosquito survivorship when ingested. In this study, we assess and compare five more chemically related compounds for mosquito lethality and eight GRAS sugar substitutes to determine toxic effects. We conducted a series of feeding assays to determine if ingesting the compounds influenced mosquito mean survivorship in locally collected lab-reared populations of Aedes aegypti (Linnaeus, 1762) and Aedes albopictus (Skuse, 1894) mosquitoes. Our results indicate that 1,2-propanediol, 1,3-propanediol, 1,5-pentanediol, 1,6-hexanediol, 2-methyl-1,3-propanediol, DL-dithiothreitol, acesulfame potassium, allulose, erythritol, sodium saccharin, stevia, and sucralose significantly reduced the mean survivorship of one or both species. Short-term trials with the most toxic compounds revealed that they could substantially affect survivorship after 24 hours. We also found that many of the compounds yielded different responses in the two species and that male mosquitoes expired to a greater extent than female mosquitoes. These findings indicate that several of the compounds may be highly effective for local mosquito vector population and disease control through functioning as components in attractive toxic sugar bait systems (ATSBs)

pharmacology and toxicology↗

bioRxiv2022

Carboxylic acids that drive mosquito attraction to humans activate ionotropic receptors

The mosquito, Aedes aegypti, is highly anthropophilic and continues to transmit debilitating arboviruses within human populations. Female mosquitoes are attracted to sources of blood by responding to odor plumes that are emitted by their preferred hosts. Acidic volatile compounds, including carboxylic acids, represent particularly salient odors driving this attraction. Importantly, carboxylic acids are major constituents of human sweat and volatiles generated by skin microbes. As such, they are likely to impact human host preference, which is a dominant factor in disease transmission cycles. A more complete understanding of mosquito host attraction will necessitate the elucidation of molecular mechanisms of volatile odor detection that function in peripheral sensory neurons. Recent studies have shown that members of the variant ionotropic glutamate receptor gene family are necessary for physiological and behavioral responses to acidic volatiles in Aedes. In this study, we have identified a subfamily of variant ionotropic receptors that share sequence homology across several important vector species and are likely to be activated by carboxylic acids. Moreover, we demonstrate that selected members of this subfamily are activated by short chain carboxylic acids in a heterologous cell expression system. Our results are consistent with the hypothesis that members of this receptor class underlie acidic volatile sensitivity in vector mosquitoes and provide a frame of reference for future development of novel mosquito attractant and repellent technologies.

molecular biology↗

bioRxiv2022

Anellovirus Structure Reveals a Mechanism for Immune Evasion

The significant impact of the human virome on human physiology is beginning to emerge thanks to modern sequencing methods and bioinformatic tools1. Anelloviruses, the principal constituent of the commensal human virome, are universally acquired in infancy and found throughout the body2,3,4. Since the discovery of the original torque teno virus in 19975, three genera of the Anelloviridae family, each extremely diverse genetically, have been found in humans. These viruses elicit weak immune responses that permit multiple strains to co-exist and persist for years in a typical individual6. However, because they do not cause disease7 and due to the lack of an in vitro culture system, anelloviruses remain poorly understood8,9. Basic features of the virus, such as the identity of its structural protein, have been unclear until now. Here, we describe the first structure of an anellovirus particle, which includes a jelly roll domain that forms a 60-mer icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axes to form crown-like features. Relatively conserved patches of amino acids are near the base of the spike domain while a hypervariable region is at the apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved epitopes while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. This would contrast with viruses such as beak and feather disease virus, canine parvovirus or adeno-associated virus which lack such pronounced surface features. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.

biochemistry↗

bioRxiv2022

Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants

Genetic variation of SARS-CoV-2 has resulted in the emergence and rapid spread of multiple variants throughout the pandemic, of which Omicron is currently the predominant variant circulating worldwide. SARS-CoV-2 variants of concern or interest (VOC/VOI) have evidence of increased viral transmission, disease severity, or decreased effectiveness of vaccines and neutralizing antibodies. Remdesivir (RDV, VEKLURY(R)) is a nucleoside analog prodrug and the first FDA-approved antiviral treatment of COVID-19. Here we present a comprehensive antiviral activity assessment of RDV and its parent nucleoside, GS-441524, against 10 current and former SARS-CoV-2 VOC/VOI clinical isolates by nucleoprotein ELISA and plaque reduction assay. Delta and Omicron variants remained susceptible to RDV and GS-441524, with EC50 values 0.31 to 0.62-fold of those observed against the ancestral WA1 isolate. All other tested variants exhibited EC50 values ranging from 0.15 to 2.3-fold of the observed EC50 values against WA1. Analysis of nearly 6 million publicly available variant isolate sequences confirmed that Nsp12, the RNA-dependent RNA polymerase (RdRp) target of RDV and GS-441524, is highly conserved across variants with only 2 prevalent changes (P323L and G671S). Using recombinant viruses, both RDV and GS-441524 retained potency against all viruses containing frequent variant substitutions or their combination. Taken together, these results highlight the conserved nature of SARS-CoV-2 Nsp12 and provide evidence of sustained SARS-CoV-2 antiviral activity of RDV and GS-441524 across the tested variants. The observed pan-variant activity of RDV supports its continued use for the treatment of COVID-19 regardless of the SARS-CoV-2 variant.

microbiology↗

bioRxiv2021

Reduced binding and neutralization of infection- and vaccine-induced antibodies to the B.1.351 (South African) SARS-CoV-2 variant

The emergence of SARS-CoV-2 variants with mutations in the spike protein is raising concerns about the efficacy of infection- or vaccine-induced antibodies to neutralize these variants. We compared antibody binding and live virus neutralization of sera from naturally infected and spike mRNA vaccinated individuals against a circulating SARS-CoV-2 B.1 variant and the emerging B.1.351 variant. In acutely-infected (5-19 days post-symptom onset), convalescent COVID-19 individuals (through 8 months post-symptom onset) and mRNA-1273 vaccinated individuals (day 14 post-second dose), we observed an average 4.3-fold reduction in antibody titers to the B.1.351-derived receptor binding domain of the spike protein and an average 3.5-fold reduction in neutralizing antibody titers to the SARS-CoV-2 B.1.351 variant as compared to the B.1 variant (spike D614G). However, most acute and convalescent sera from infected and all vaccinated individuals neutralize the SARS-CoV-2 B.1.351 variant, suggesting that protective immunity is retained against COVID-19.

immunology↗

bioRxiv2020

Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 M). Weaker activity was observed in Vero E6 cells (EC50 = 1.65 M) due to their low capacity to metabolize RDV. To rapidly evaluate in vivo efficacy, we engineered a chimeric SARS-CoV encoding the viral target of RDV, the RNA-dependent RNA polymerase, of SARS-CoV-2. In mice infected with chimeric virus, therapeutic RDV administration diminished lung viral load and improved pulmonary function as compared to vehicle treated animals. These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19.

microbiology↗