The paper identifies a 667-nucleotide region in SARS-CoV-2 nsp15 that binds nucleoprotein and enhances defective genome accumulation, revealing a new packaging signal element.

bioRxiv · May 29, 2026 · PreprintMicrobiology

Comparative analysis of serological assays and sero-surveillance for SARS-CoV-2 exposure in US cattle

Santhamani Ramasamy, Meysoon Quraishi, Swastidipa Mukherjee, Sonalika Mahajan, Lindsey Cecelia LaBella, Shubhada K. Chothe, Padmaja Jakka, Abhinay Gontu, Sougat Misra, Meera Surendran Nair, Ruth Helmus Nissly, Suresh Varma Kuchipudi

This study evaluates serological assays for SARS-CoV-2 in US cattle, finding no evidence of natural infection or transmission and highlighting issues with false positives in neutralization assays.

Microorganisms · Mar 5, 2025Peer-reviewedMicrobiology

A trans-amplifying mRNA vaccine with consensus spike elicits broadly cross-neutralizing antibody response against multiple SARS-CoV-2 variants

Abhinay Gontu, Sougat Misra, Shubhada K. Chothe, Santhamani Ramasamy, Padmaja Jakka, Maurice Byukusenge, Lindsey Cecelia LaBella, Meera Surendran Nair, Bhushan M. Jayarao, Marco Archetti, Ruth Helmus Nissly, Suresh Varma Kuchipudi

This study evaluates a trans-amplifying mRNA vaccine with a consensus spike protein, showing it elicits broad cross-neutralizing antibodies against multiple SARS-CoV-2 variants with reduced antigen dose.

bioRxiv · Jan 22, 2025 · PreprintMicrobiology

Enhanced Diversifying Selection on Polymerase Genes in H5N1 Clade 2.3.4.4b: A Key Driver of Altered Species Tropism and Host Range Expansion

Sougat Misra, Elizabeth Gilbride, Santhamani Ramasamy, Sergei L. Kosakovsky Pond, Suresh Varma Kuchipudi

This study identifies enhanced diversifying selection on polymerase genes in H5N1 clade 2.3.4.4b viruses, linking it to expanded host range and increased pathogenicity.

bioRxiv · Aug 19, 2024 · PreprintEvolutionary Biology

Transmission of SARS-CoV-2 from humans to animals and potential host adaptation

Cedric C.S. Tan, Su Datt Lam, Damien Richard, Christopher J. Owen, Dorothea Berchtold, Christine Anne Orengo, Meera Surendran Nair, Suresh Varma Kuchipudi, Vivek Kapur, Lucy van Dorp, François Balloux

The paper analyzes SARS-CoV-2 genomic mutations in mink and deer to identify potential host-specific adaptations and assess spillover risks.

Nature Communications · May 27, 2022Peer-reviewedGenomics

Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality

Jule Goike, Ching‐Lin Hsieh, Andrew P. Horton, Elizabeth C. Gardner, Foteini Bartzoka, Nianshuang Wang, Kamyab Javanmardi, Andrew S. Herbert, Shawn A. Abbasi, Rebecca L. Renberg, Michael J. Johanson, José Cardona, Thomas H. Segall-Shapiro, Ling Zhou, Ruth Helmus Nissly, , Jimmy Gollihar

The paper identifies SARS-CoV-2 neutralizing antibodies from convalescent patients and describes a novel quaternary binding mechanism using high-throughput methods.

bioRxiv · Apr 7, 2021 · PreprintSynthetic Biology

Continued circulation, recombination and evolution of the ancient subcontinent lineage despite predominance of the recent arctic-like lineage rabies viruses (RABV) in India

Jagadeeswaran Deventhiran, Bhuvaneswari Srinivasan, Manoharan Seeralan, Vijayarani Kanagaraj, Sangeetha Raju, Kumanan Kathaperumal, Ruth Nissly, Sunitha Manjari Kasibhatla, Mohan M Kale, Urmila Kulkarni-Kale, Suresh V Kuchipudi

This study analyzes rabies virus genetic diversity and evolution in southern India, finding co-circulation of ancient subcontinent and recent arctic-like lineages with recombination and higher evolutionary rates.

bioRxiv · Aug 22, 2018 · PreprintMicrobiology