Rapid repeat infection of SARS-CoV-2 by two highly distinct delta-lineage viruses

Gorzalski, Andrew; Boyles, Christina; Sepcic, Victoria; Verma, Subhash C.; Sevinsky, Joel; Libuit, Kevin; Hooser, Stephanie Van; Pandori, Mark

doi:10.1016/j.diagmicrobio.2022.115747

Cited by 3 publications

(3 citation statements)

References 26 publications

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“…NPS and plasma samples were sequenced using amplicon-based protocols using either a MiSeq instrument (Illumina, La Jolla, CA, USA) with ARTIC primers (version 3 for Case 1, version 4.1 for Case 2) or the Clear Dx SARS-CoV-2 WGS v3.0 platform (Clear Labs, San Carlos, CA, USA) for Case 2 only. Detailed protocols and quality control criteria were described previously [ 15 , 16 ]. Illumina sequencing data and Clear Labs consensus genomes were analyzed on Terra.bio using the TheiaCoV_Illumina_PE v2.3.0 and TheiaCoV_FASTA v2.3.0 workflows, respectively, (Theiagen Genomics, Highlands Ranch, CO) [ 17 , 18 , 19 , 20 , 21 ] with Wuhan-Hu-1/2019 (GenBank MN908947) used as the reference genome.…”

Section: Methodsmentioning

confidence: 99%

Transient SARS-CoV-2 RNA-Dependent RNA Polymerase Mutations after Remdesivir Treatment for Chronic COVID-19 in Two Transplant Recipients: Case Report and Intra-Host Viral Genomic Investigation

Yang,

Multani,

Garrigues

et al. 2023

Microorganisms

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Remdesivir is the first FDA-approved drug for treating severe SARS-CoV-2 infection and targets RNA-dependent RNA polymerase (RdRp) that is required for viral replication. To monitor for the development of mutations that may result in remdesivir resistance during prolonged treatment, we sequenced SARS-CoV-2 specimens collected at different treatment time points in two transplant patients with severe COVID-19. In the first patient, an allogeneic hematopoietic stem cell transplant recipient, a transient RdRp catalytic subunit mutation (nsp12:A449V) was observed that has not previously been associated with remdesivir resistance. As no in vitro study had been conducted to elucidate the phenotypic effect of nsp12:A449V, its clinical significance is unclear. In the second patient, two other transient RdRp mutations were detected: one in the catalytic subunit (nsp12:V166A) and the other in an accessory subunit important for processivity (nsp7:D67N). This is the first case report for a potential link between the nsp12:V166A mutation and remdesivir resistance in vivo, which had only been previously described by in vitro studies. The nsp7:D67N mutation has not previously been associated with remdesivir resistance, and whether it has a phenotypic effect is unknown. Our study revealed SARS-CoV-2 genetic dynamics during remdesivir treatment in transplant recipients that involved mutations in the RdRp complex (nsp7 and nsp12), which may be the result of selective pressure. These results suggest that close monitoring for potential resistance during the course of remdesivir treatment in highly vulnerable patient populations may be beneficial. Development and utilization of diagnostic RdRp genotyping tests may be a future direction for improving the management of chronic COVID-19.

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Section: Methodsmentioning

confidence: 99%

Transient SARS-CoV-2 RNA-Dependent RNA Polymerase Mutations after Remdesivir Treatment for Chronic COVID-19 in Two Transplant Recipients: Case Report and Intra-Host Viral Genomic Investigation

Yang,

Multani,

Garrigues

et al. 2023

Microorganisms

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“…Nasal and nasopharyngeal swab specimens were received at the Nevada State Public Health Lab (NSPHL) or Southern Nevada Public Health Lab (SNPHL) and RNA extraction was completed as previously described ( Hartley et al, 2021 ; Tillett et al, 2021 ; Gorzalski et al, 2022 ). Specimens were tested for the presence of coronaviral RNA using FDA-approved kits for clinical laboratories that employed RT-qPCR to detect SARS-COV-2 RNA corresponding to Spike and Nucleocapsid, and a cellular target control.…”

Section: Methodsmentioning

confidence: 99%

“…Specimens were tested for the presence of coronaviral RNA using FDA-approved kits for clinical laboratories that employed RT-qPCR to detect SARS-COV-2 RNA corresponding to Spike and Nucleocapsid, and a cellular target control. Positive specimens were selected for whole genome sequencing using the Clear Labs DX platform and data files from the sequencing reaction were processed as previously described ( Gorzalski et al, 2022 ). The data files are available at GISAID, accession numbers are listed in Supplemental Table 1.…”

Section: Methodsmentioning

confidence: 99%

Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021

Payen

Gorzalski

Siao

et al. 2023

Infection, Genetics and Evolution

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Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities

Uppal

Hartley

et al. 2022

Sci Rep

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Detection of SARS-CoV-2 viral load in wastewater has been highly informative in estimating the approximate number of infected individuals in the surrounding communities. Recent developments in wastewater monitoring to determine community prevalence of COVID-19 further extends into identifying SARS-CoV-2 variants, including those being monitored for having enhanced transmissibility. We sequenced genomic RNA derived from wastewater to determine the variants of coronaviruses circulating in the communities. Wastewater samples were collected from Truckee Meadows Water Reclamation Facility (TMWRF) from November 2020 to June 2021. SARS-CoV-2 variants resulting from wastewater were compared with the variants detected in infected individuals' clinical specimens (nasal/nasopharyngeal swabs) during the same period and found conclusively in agreement. Therefore, wastewater monitoring for SARS-CoV-2 variants in the community is a feasible strategy as a complementary tool to clinical specimen testing in the latter's absence.

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Rapid repeat infection of SARS-CoV-2 by two highly distinct delta-lineage viruses

Cited by 3 publications

References 26 publications

Transient SARS-CoV-2 RNA-Dependent RNA Polymerase Mutations after Remdesivir Treatment for Chronic COVID-19 in Two Transplant Recipients: Case Report and Intra-Host Viral Genomic Investigation

Transient SARS-CoV-2 RNA-Dependent RNA Polymerase Mutations after Remdesivir Treatment for Chronic COVID-19 in Two Transplant Recipients: Case Report and Intra-Host Viral Genomic Investigation

Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021

Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities

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