Biology subjects

Thippeshappa, R.

Publications and source records attributed to Thippeshappa, R..

4 recordsLinked to original sources

bioRxiv2026

APOBEC3G Splicing Defects in Nonhuman Primate Models Result in Disparate Viral Mutational Profiles Relative to Humans

Nonhuman primates (NHPs), particularly macaques, are indispensable models for studying human infectious diseases due to their close immunological and physiological similarities. Understanding species-specific molecular differences is essential for maximizing the translational value of these models. Here we report that APOBEC3G (A3G), a potent antiviral restriction factor and the major source of genetic variations in HIV, exhibits a widespread mRNA splicing defect in the Cercopithecinae subfamily, which includes the commonly used NHP models. Driven by intronic polymorphisms, this splicing defect substantially reduces A3G protein levels and consequently results in a markedly reduced A3G-mediated mutation signatures, fewer defective viral genomes, and greater viral diversification in SIV compared to HIV. This species-specific effect is not restricted to lentiviruses: reduced A3G signatures have also been reported in simian foamy virus and simian T-cell leukemia virus, suggesting broader effects across primate retroviruses. These findings reveal a lineage-specific alteration in a major antiviral restriction factor, with important implications for viral restriction, evolution, drug resistance, and immune evasion. They also highlight the importance of incorporating naturally occurring genetic variation into NHP model selection to improve the reproducibility, translational fidelity, and biological relevance of preclinical research.

genomics↗

bioRxiv2025

Single dose alum adjuvanted RBD protein vaccine provides protection against homologous challenge with SARS-CoV-2 Washington strain and heterologous rechallenge with Delta and Omicron BA.5 variants in K18 hACE2 mouse model

Most COVID-19 vaccination strategies require at least two doses-a primary vaccine followed by a booster dose with the updated variant-specific vaccine. However, vaccine and booster dose hesitancy make it challenging to administer multiple doses of vaccines in the unvaccinated and vaccinated populations, respectively. Thus, it is important to determine if vaccinated individuals exposed to SARS-CoV-2 infection develop immune responses that may protect them against emerging variants of concern (VoCs). We have developed mouse models to understand the protective efficacy of an RBD-based vaccine against challenge and rechallenge with SARS-CoV-2 VoCs. Mice were vaccinated with RBD protein vaccine formulated in 2% Alhydrogel (alum) adjuvant by subcutaneous route. To determine the efficacy of RBD vaccine, mice were challenged approximately 4 weeks post-vaccination with SARS-CoV-2 variants by intranasal route. To determine the efficacy of RBD vaccine against SARS-CoV-2 rechallenge, mice were rechallenged with SARS-CoV-2 Delta and Omicron BA.5 variants at day 14 post SARS-CoV-2 Washington (WA) strain challenge. Our data suggest that single dose alum adjuvanted RBD protein from Wuhan strain provides protection against homologous challenge with SARS-CoV-2 WA strain but failed to provide protection against heterologous challenge with Delta and Omicron BA.5 variants. Interestingly, vaccinated mice that survived homologous challenge with the WA strain showed protection against heterologous rechallenge with Delta and omicron BA.5 variants. Furthermore, infectious viral loads of Delta and Omicron BA.5 were not detected in the lung tissues collected from the rechallenged mice at 3 days post-rechallenge. The data suggest that a single dose RBD vaccine from the ancestral Wuhan strain together with survival from WA strain challenge induces protective immune responses against Delta and Omicron BA.5 variants rechallenge. These mouse models will be useful to determine the immune responses that correlate with protection against challenge and rechallenge with SARS-CoV-2 VoCs.

microbiology↗

bioRxiv2021

In vivo serial passaging of human-simian immunodeficiency virus clones identifies viral characteristics that enhance persistent viral replication

We previously reported that a human immunodeficiency virus type 1 with a simian immunodeficiency virus vif substitution (HSIV-vifNL4-3) could replicate in pigtailed macaques (PTMs), demonstrating that Vif is a species-specific tropism factor of primate lentiviruses. However, infections did not result in high peak viremia or setpoint plasma viral loads, as observed during SIV infection of PTMs. Here, we characterized variants isolated from one of the original infected animals with CD4 depletion after nearly four years of infection to identify determinants of increased replication fitness. In our studies, we found that the HSIV-vif clones did not express the HIV-1 Vpr protein due to interference from the vpx open reading frame in singly spliced vpr mRNA. To examine whether these viral genes contribute to persistent viral replication, we generated infectious HSIV-vif clones expressing either the HIV-1 Vpr or SIV Vpx protein. And then to determine viral fitness determinants of HSIV-vif, we conducted three rounds of serial in vivo passaging in PTMs, starting with an initial inoculum containing a mixture of CXCR4-tropic (Vpr- HSIV-vifNL4-3 isolated at 196 (C/196) and 200 (C/200) weeks post-infection from a PTM with depressed CD4 counts) and CCR5-tropic HSIV (Vpr+ HSIV-vif derivatives based NL-AD8 and Bru-Yu2 and a Vpx expressing HSIV-vifYu2). Interestingly, all infected PTMs showed peak plasma viremia close to or above 105 copies/ml and persistent viral replication for more than 20 weeks. The passage 3 PTM showed peak viral loads greater than 105 viral RNA copies/ml. Infectious molecular clones (IMCs) recovered from the passage 3 PTM (HSIV-P3 IMCs) included mutations required for HIV-1 Vpr expression and those mutations encoded by the CXCR4-tropic HSIV-vifNL4-3 isolates C/196 and C/200. The data indicate that the biological isolates selected during long-term infection acquired HIV-1 Vpr expression to enhance their replication fitness in PTMs. Further passaging of HSIV-P3 IMCs in vivo may generate pathogenic variants with higher replication capacity, which will be a valuable resource as challenge virus in vaccine and cure studies.

microbiology↗

bioRxiv2020

SARS-CoV-2 infection leads to acute infection with dynamic cellular and inflammatory flux in the lung that varies across nonhuman primate species

There are no known cures or vaccines for COVID-19, the defining pandemic of this era. Animal models are essential to fast track new interventions and nonhuman primate (NHP) models of other infectious diseases have proven extremely valuable. Here we compare SARS-CoV-2 infection in three species of experimentally infected NHPs (rhesus macaques, baboons, and marmosets). During the first 3 days, macaques developed clinical signatures of viral infection and systemic inflammation, coupled with early evidence of viral replication and mild-to-moderate interstitial and alveolar pneumonitis, as well as extra-pulmonary pathologies. Cone-beam CT scans showed evidence of moderate pneumonia, which progressed over 3 days. Longitudinal studies showed that while both young and old macaques developed early signs of COVID-19, both groups recovered within a two-week period. Recovery was characterized by low-levels of viral persistence in the lung, suggesting mechanisms by which individuals with compromised immune systems may be susceptible to prolonged and progressive COVID-19. The lung compartment contained a complex early inflammatory milieu with an influx of innate and adaptive immune cells, particularly interstitial macrophages, neutrophils and plasmacytoid dendritic cells, and a prominent Type I-interferon response. While macaques developed moderate disease, baboons exhibited prolonged shedding of virus and extensive pathology following infection; and marmosets demonstrated a milder form of infection. These results showcase in critical detail, the robust early cellular immune responses to SARS-CoV-2 infection, which are not sterilizing and likely impact development of antibody responses. Thus, various NHP genera recapitulate heterogeneous progression of COVID-19. Rhesus macaques and baboons develop different, quantifiable disease attributes making them immediately available essential models to test new vaccines and therapies.

immunology↗