Classification of viral strains is essential in monitoring and managing the COVID-19 pandemic, but patient privacy and data security concerns often limit the extent of the open sharing of full viral genome sequencing data. We propose a framework called CoVnita, that supports private training of a classification model and secure inference with the same model. Using genomic sequences from eight common SARS-CoV-2 strains, we simulated scenarios where the data was distributed across multiple data providers. Our framework produces a private federated model, over 8 parties, with a classification AUROC of 0.99, given a privacy budget of\documentclass[12pt]{minimal}
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				\begin{document}$$\varepsilon =1$$\end{document}ε=1. The roundtrip time, from encryption to decryption, took a total of 0.298 s, with an amortized time of 74.5 ms per sample.