AUTHOR=Lueking Richard , Clark Andrew E. , Narasimhan Madhusudhanan , Mahimainathan Lenin , Muthukumar Alagarraju , Larsen Christian P. , SoRelle Jeffrey A. TITLE=SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis JOURNAL=Frontiers in Genetics VOLUME=13 YEAR=2022 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.942713 DOI=10.3389/fgene.2022.942713 ISSN=1664-8021 ABSTRACT=

Immunocompromised patients can experience prolonged SARS-CoV-2 infections in the setting of a lack of protectivity immunity despite vaccination. As circulating SARS-CoV-2 strains become more heterogeneous, concomitant infection with multiple SARS-CoV-2 variants has become an increasing concern. Immunocompromised patient populations represent potential reservoirs for the emergence of novel SARS-CoV-2 variants through mutagenic change or coinfection followed by recombinatory events. Identification of SARS-CoV-2 coinfections is challenging using traditional next generation sequencing pipelines; however, targeted genotyping approaches can facilitate detection. Here we describe five COVID-19 cases caused by coinfection with different SARS-CoV-2 variants (Delta/Omicron BA.1 and Omicron BA.1/BA.2) as identified by multiplex fragment analysis.