Biology subjects

Coleman, C. M.

Publications and source records attributed to Coleman, C. M..

4 recordsLinked to original sources

bioRxiv2026

Molecular and Structural Characterisation of the MERS-Coronavirus Polymerase

MERS-CoV (Middle East respiratory syndrome coronavirus) belongs to the Betacoronavirus genus, which also includes SARS-CoV-2, the causative agent of the COVID-19 pandemic. MERS-CoV is the pathogen responsible for Middle East Respiratory Syndrome (MERS), a respiratory disease with a 36.5% case fatality rate. Given the capacity of coronaviruses for genetic recombination and mutation, MERS-CoV remains a pathogen of significant pandemic potential, with viral evolution potentially facilitating enhanced adaptation and transmission in humans. There are no approved treatments for MERS-CoV infection. The MERS-CoV replication-transcription complex (RTC), a multimeric protein complex key to genome amplification, has no cellular analogues and a highly conserved sequence, making it a useful target for antiviral compounds; however, structural and biochemical characterisation of the MERS-CoV RTC is limited. Here, we characterise the minimal MERS-CoV RTC using in vitro and single-molecule assays and show that it is susceptible to the RNA-dependent-RNA-polymerase inhibitor suramin. We present a structure of the minimal MERS-CoV RTC in complex with an RNA duplex, which shows strong structural similarity to the SARS-CoV-2 RTC. We use cross-subunit swapping experiments to show that the MERS-CoV NSP12 core can efficiently utilise SARS-CoV-2 cofactors NSP7 and NSP8, whereas SARS-CoV-2 NSP12 exhibits reduced in vitro activity with the MERS-CoV NSP8. This asymmetric cross-species compatibility highlights both the evolutionary conservation and virus-specific adaptation of coronavirus polymerase-cofactor interactions. Together, these findings provide a structural and mechanistic framework for understanding MERS-CoV RNA synthesis and establish its conserved RTC as a potential target for the development of broadly acting coronavirus antivirals.

microbiology↗

bioRxiv2025

An ultra-long heavy chain bovine antibody neutralizes SARS-CoV-2 and reacts broadly with sarbecoviruses.

The ongoing threat of new SARS-CoV-2 variants and other sarbecoviruses has driven efforts to develop broadly neutralizing monoclonal antibodies (mAbs). This study used immunized cattle, known for producing antibodies with ultra-long CDRH3 domains, to generate 33 mAbs, ten of which had ultra-long CDRH3s (>50 amino acids). Of these, mAbs P7 and 99, demonstrated broad and potent neutralization. Notably, mAb P7 neutralized all tested variants, including SARS-CoV-1, with IC50 values between 0.05 and 9.2 {micro}g/mL, and showed cross-reactivity with RBDs from various sarbecoviruses. Structural analysis revealed that mAb 99 binds the spike proteins RBD at the ACE2 binding site. Although the exact binding of P7 wasnt resolved, evidence suggests it targets a hidden epitope, promoting spike trimer dissociation via its extended CDRH3. In Syrian hamsters, both mAbs significantly reduced lung viral loads. These results support the potential of bovine-derived mAbs, particularly those with ultra-long CDRH3s, for future antiviral therapies.

immunology↗

bioRxiv2021

A novel bivalent DNA vaccine encoding both spike protein receptor-binding domain and nucleocapsid protein of SARS-CoV-2 to elicit T cell and neutralising antibody responses that cross react with variants

Although the efficacy of vaccines targeting SARS-CoV-2 is apparent now that the approved mRNA and adenovirus vector vaccines are in widespread use, the longevity of the protective immune response and its efficacy against emerging variants remains to be determined. We have therefore designed a DNA vaccine encoding both the SARS-CoV-2 spike receptorbinding domain ( RBD) and nucleocapsid proteins, the latter of which is highly conserved amongst beta coronaviruses. The vaccine elicits strong pro-inflammatory CD4+ Th1 and CD8+ T-cell responses to both proteins in mice and rats, with responses being significantly enhanced by fusing the nucleocapsid sequence to a modified Fc domain. We have shown that the vaccine also stimulates high titre antibody responses to RBD in mice that efficiently neutralise in pseudotype and live virus neutralisation assays and show cross reactivity with spike proteins from the variants B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). The vaccine also showed good protection in a viral challenge model in ACE2 receptor transgenic mice. This DNA platform can be easily adapted to target variant proteins and we show that a vaccine variant encoding the Beta variant sequence stimulates cross-reactive humoral and T cell responses. These data support the translation of this DNA vaccine platform into the clinic, thereby offering a particular advantage for rapidly targeting emerging SARS-CoV-2 variants.

immunology↗

bioRxiv2020

Single-molecule sequencing of long DNA molecules allows high contiguity de novo genome assembly for the fungus fly, Sciara coprophila

The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in aiding these studies. We approached assembling the Sciara genome using multiple sequencing technologies: PacBio, Oxford Nanopore MinION, and Illumina. To find an optimal assembly using these datasets, we generated 44 Illumina assemblies using 7 short-read assemblers and 50 long-read assemblies of PacBio and MinION sequence data using 6 long-read assemblers. We ranked assemblies using a battery of reference-free metrics, and scaffolded a subset of the highest-ranking assemblies using BioNano Genomics optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. Moreover, we anchored nearly half of the Sciara genome sequence into chromosomes. Finally, we used the signal level of both the PacBio and Oxford Nanopore data to explore the presence or absence of DNA modifications in the Sciara genome since DNA modifications may play a role in imprinting in Sciara, as they do in mammals. These data serve as the foundation for future research by the growing community studying the unique features of this emerging model system.

genomics↗