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Massic L, Gorzalski A, Siao DD, Dykema P, Hua C, Schneider E, Van Hooser S, Pandori M, Hess D. Detection of five instances of dual-clade infections of Candida auris with opposite mating types in southern Nevada, USA. Lancet Infect Dis 2023; 23:e328-e329. [PMID: 37478879 DOI: 10.1016/s1473-3099(23)00434-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Affiliation(s)
- Lauryn Massic
- Nevada State Public Health Laboratory, Reno, NV 89503, USA; School of Medicine, University of Nevada, Reno, NV, USA.
| | | | | | - Philip Dykema
- Washington State Department of Health, Olympia, WA, USA
| | - Chi Hua
- Washington State Department of Health, Olympia, WA, USA
| | | | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV 89503, USA; School of Medicine, University of Nevada, Reno, NV, USA
| | - David Hess
- Nevada State Public Health Laboratory, Reno, NV 89503, USA; School of Medicine, University of Nevada, Reno, NV, USA
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Gorzalski A, Ambrosio FJ, Massic L, Scribner MR, Siao DD, Hua C, Dykema P, Schneider E, Njoku C, Libuit K, Sevinsky JR, Van Hooser S, Pandori M, Hess D. The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada. Front Public Health 2023; 11:1198189. [PMID: 37522005 PMCID: PMC10374848 DOI: 10.3389/fpubh.2023.1198189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/06/2023] [Indexed: 08/01/2023] Open
Abstract
A Candida auris outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200 C. auris isolates from patients at several facilities. Genetically distinct subgroups of C. auris were detected from Clade I (3 distinct lineages) and III (1 lineage). Open-source bioinformatic tools were developed and implemented to aid in the epidemiological investigation. The work herein compares three methods for C. auris whole genome analysis: Nullarbor, MycoSNP and a new pipeline TheiaEuk. We also describe a novel analysis method focused on elucidating phylogenetic linkages between isolates within an ongoing outbreak. Moreover, this study places the ongoing outbreaks in a global context utilizing existing sequences provided worldwide. Lastly, we describe how the generated results were communicated to the epidemiologists and infection control to generate public health interventions.
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Affiliation(s)
| | | | - Lauryn Massic
- Nevada State Public Health Laboratory, Reno, NV, United States
| | | | | | - Chi Hua
- Division of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United States
| | - Phillip Dykema
- Division of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United States
| | - Emily Schneider
- Division of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United States
| | - Chidinma Njoku
- Nevada Department of Health and Human Services, Las Vegas, NV, United States
| | - Kevin Libuit
- Theiagen Consulting LLC, Highlands Ranch, CO, United States
| | | | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United States
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV, United States
| | - David Hess
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United States
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Gorzalski AJ, Kerwin H, Verma S, Hess DC, Sevinsky J, Libuit K, Vlasova-St Louis I, Siao D, Siao L, Buñuel D, Van Hooser S, Pandori MW. Rapid Lineage Assignment of Severe Acute Respiratory Syndrome Coronavirus 2 Cases through Automated Library Preparation, Sequencing, and Bioinformatic Analysis. J Mol Diagn 2023; 25:191-196. [PMID: 36754279 PMCID: PMC9902282 DOI: 10.1016/j.jmoldx.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has provided a stage to illustrate that there is considerable value in obtaining rapid, whole-genome-based information about pathogens. This article describes the utility of a commercially available, automated severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) library preparation, genome sequencing, and a bioinformatics analysis pipeline to provide rapid, near-real-time SARS-CoV-2 variant description. This study evaluated the turnaround time, accuracy, and other quality-related parameters obtained from commercially available automated sequencing instrumentation, from analysis of continuous clinical samples obtained from January 1, 2021, to October 6, 2021. This analysis included a base-by-base assessment of sequencing accuracy at every position in the SARS-CoV-2 chromosome using two commercially available methods. Mean turnaround time, from the receipt of a specimen for SARS-CoV-2 testing to the availability of the results, with lineage assignment, was <3 days. Accuracy of sequencing by one method was 100%, although certain sites on the genome were found repeatedly to have been sequenced with varying degrees of read error rate.
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Affiliation(s)
| | | | - Subhash Verma
- Department of Microbiology and Immunology, University of Nevada-Reno, School of Medicine, Reno, Nevada
| | - David C Hess
- Nevada State Public Health Laboratory, Reno, Nevada; Department of Pathology and Laboratory Medicine, University of Nevada-Reno, School of Medicine, Reno, Nevada
| | | | | | | | | | - Lauren Siao
- Nevada State Public Health Laboratory, Reno, Nevada
| | - Diego Buñuel
- Nevada State Public Health Laboratory, Reno, Nevada
| | | | - Mark W Pandori
- Nevada State Public Health Laboratory, Reno, Nevada; Department of Microbiology and Immunology, University of Nevada-Reno, School of Medicine, Reno, Nevada; Department of Pathology and Laboratory Medicine, University of Nevada-Reno, School of Medicine, Reno, Nevada.
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Gorzalski AJ, Boyles C, Sepcic V, Verma S, Sevinsky J, Libuit K, Van Hooser S, Pandori MW. Rapid repeat infection of SARS-CoV-2 by two highly distinct delta-lineage viruses. Diagn Microbiol Infect Dis 2022; 104:115747. [PMID: 35843112 PMCID: PMC9217632 DOI: 10.1016/j.diagmicrobio.2022.115747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 06/01/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
An instance of sequential infection of an individual with, firstly, the Delta variant and secondly a Delta-sub-lineage has been identified. The individual was found positive for the AY.26 lineage 22 days after being found positive for the Delta [B.1.617.2] variant. The viruses associated with the cases showed dramatic genomic difference, including 31 changes that resulted in deletions or amino acid substitutions. Seven of these differences were observed in the Spike protein. The patient in question was between 30 and 35 years old and had no underlying health conditions. Though singular, this case illustrates the possibility that infection with the Delta variant may not itself be fully protective against a population of SARS-CoV-2 variants that are becoming increasingly diverse.
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Affiliation(s)
| | | | - Victoria Sepcic
- Nevada Department of Health and Human Services, Department of Public and Behavioral Health, Carson City, NV, USA
| | - Subhash Verma
- Department of Microbiology and Immunology, University of Nevada, School of Medicine, Reno, NV, USA
| | | | | | | | - Mark W Pandori
- Nevada State Public Health Laboratory, Reno, NV, USA; Department of Pathology and Laboratory Medicine, University of Nevada, School of Medicine, Reno, NV, USA.
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Tillett RL, Sevinsky JR, Hartley PD, Kerwin H, Crawford N, Gorzalski A, Laverdure C, Verma SC, Rossetto CC, Jackson D, Farrell MJ, Van Hooser S, Pandori M. Genomic evidence for reinfection with SARS-CoV-2: a case study. Lancet Infect Dis 2021; 21:52-58. [PMID: 33058797 PMCID: PMC7550103 DOI: 10.1016/s1473-3099(20)30764-7] [Citation(s) in RCA: 481] [Impact Index Per Article: 160.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The degree of protective immunity conferred by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently unknown. As such, the possibility of reinfection with SARS-CoV-2 is not well understood. We describe an investigation of two instances of SARS-CoV-2 infection in the same individual. METHODS A 25-year-old man who was a resident of Washoe County in the US state of Nevada presented to health authorities on two occasions with symptoms of viral infection, once at a community testing event in April, 2020, and a second time to primary care then hospital at the end of May and beginning of June, 2020. Nasopharyngeal swabs were obtained from the patient at each presentation and twice during follow-up. Nucleic acid amplification testing was done to confirm SARS-CoV-2 infection. We did next-generation sequencing of SARS-CoV-2 extracted from nasopharyngeal swabs. Sequence data were assessed by two different bioinformatic methodologies. A short tandem repeat marker was used for fragment analysis to confirm that samples from both infections came from the same individual. FINDINGS The patient had two positive tests for SARS-CoV-2, the first on April 18, 2020, and the second on June 5, 2020, separated by two negative tests done during follow-up in May, 2020. Genomic analysis of SARS-CoV-2 showed genetically significant differences between each variant associated with each instance of infection. The second infection was symptomatically more severe than the first. INTERPRETATION Genetic discordance of the two SARS-CoV-2 specimens was greater than could be accounted for by short-term in vivo evolution. These findings suggest that the patient was infected by SARS-CoV-2 on two separate occasions by a genetically distinct virus. Thus, previous exposure to SARS-CoV-2 might not guarantee total immunity in all cases. All individuals, whether previously diagnosed with COVID-19 or not, should take identical precautions to avoid infection with SARS-CoV-2. The implications of reinfections could be relevant for vaccine development and application. FUNDING Nevada IDEA Network of Biomedical Research, and the National Institute of General Medical Sciences (National Institutes of Health).
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Affiliation(s)
- Richard L Tillett
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, USA; University of Nevada, Reno Center for Bioinformatics, Reno, NV, USA
| | | | - Paul D Hartley
- Nevada Genomics Center, University of Nevada, Reno, NV, USA
| | - Heather Kerwin
- Division of Epidemiology & Public Health Preparedness, Washoe County Health District, Reno, NV, USA
| | | | | | | | - Subhash C Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Cyprian C Rossetto
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - David Jackson
- Forensic Science Division, Washoe County Sheriff's Office, Reno, NV, USA
| | - Megan J Farrell
- Forensic Science Division, Washoe County Sheriff's Office, Reno, NV, USA
| | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, USA; Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, USA.
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Gorzalski AJ, Hartley P, Laverdure C, Kerwin H, Tillett R, Verma S, Rossetto C, Morzunov S, Van Hooser S, Pandori MW. Characteristics of viral specimens collected from asymptomatic and fatal cases of COVID-19. J Biomed Res 2020; 34:431-436. [PMID: 33243941 PMCID: PMC7718074 DOI: 10.7555/jbr.34.20200110] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We sought to determine the characteristics of viral specimens associated with fatal cases, asymptomatic cases and non-fatal symptomatic cases of COVID-19. This included the analysis of 1264 specimens found reactive for at least two SARS-CoV-2 specific loci from people screened for infection in Northern Nevada in March-May of 2020. Of these, 30 were specimens from fatal cases, while 23 were from positive, asymptomatic cases. We assessed the relative amounts of SARS-CoV-2 RNA from sample swabs by real-time PCR and use of the threshold crossing value (Ct). Moreover, we compared the amount of human RNase P found on the same swabs. A considerably higher viral load was found to be associated with swabs from cases involving fatality and the difference was found to be strongly statistically significant. Noting this difference, we sought to assess whether any genetic correlation could be found in association with virus from fatal cases using whole genome sequencing. While no common genetic elements were discerned, one branch of epidemiologically linked fatal cases did have two point mutations, which no other of 156 sequenced cases from northern Nevada had. The mutations caused amino acid changes in the 3′-5′ exonuclease protein, and the product of the gene, orf8.
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Affiliation(s)
| | | | | | | | - Richard Tillett
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154-4022, USA.,Nevada Center for Bioinformatics, University of Nevada Reno, Reno, NV 89557, USA
| | | | | | | | | | - Mark W Pandori
- Nevada State Public Health Laboratory, Reno, NV 89597, USA
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