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. 2023 Nov 8;13(1):2281356. doi: 10.1080/22221751.2023.2281356

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© 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

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Figure 3. — Identification of SARS-CoV-2 variants of concern in nasal swab and tissues. Next-generation sequencing was used to determine the percent composition of the SARS-CoV-2 variants of concern Delta and Omicron BA.2, present in the inoculum, swab samples and tissues collected from the co-infected calves. Reads were analyzed using the VirStrain (Version 1.12) software package to determine the genetic composition (% of each lineage) of SARS-CoV-2 RNA present in samples. The genome sequences from the virus stocks used in our challenge experiment were used to construct the reference database for VirStrain lineage assignment.