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Picker MA, Karney MMA, Gerson TM, Karabachev AD, Duhart JC, McKenna JA, Wing HJ. Localized modulation of DNA supercoiling, triggered by the Shigella anti-silencer VirB, is sufficient to relieve H-NS-mediated silencing. Nucleic Acids Res 2023; 51:3679-3695. [PMID: 36794722 PMCID: PMC10164555 DOI: 10.1093/nar/gkad088] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
In Bacteria, nucleoid structuring proteins govern nucleoid dynamics and regulate transcription. In Shigella spp., at ≤30°C, the histone-like nucleoid structuring protein (H-NS) transcriptionally silences many genes on the large virulence plasmid. Upon a switch to 37°C, VirB, a DNA binding protein and key transcriptional regulator of Shigella virulence, is produced. VirB functions to counter H-NS-mediated silencing in a process called transcriptional anti-silencing. Here, we show that VirB mediates a loss of negative DNA supercoils from our plasmid-borne, VirB-regulated PicsP-lacZ reporter in vivo. The changes are not caused by a VirB-dependent increase in transcription, nor do they require the presence of H-NS. Instead, the VirB-dependent change in DNA supercoiling requires the interaction of VirB with its DNA binding site, a critical first step in VirB-dependent gene regulation. Using two complementary approaches, we show that VirB:DNA interactions in vitro introduce positive supercoils in plasmid DNA. Subsequently, by exploiting transcription-coupled DNA supercoiling, we reveal that a localized loss of negative supercoils is sufficient to alleviate H-NS-mediated transcriptional silencing independently of VirB. Together, our findings provide novel insight into VirB, a central regulator of Shigella virulence and, more broadly, a molecular mechanism that offsets H-NS-dependent silencing of transcription in bacteria.
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Affiliation(s)
- Michael A Picker
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Monika M A Karney
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Taylor M Gerson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | | | - Juan C Duhart
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Joy A McKenna
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Helen J Wing
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
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2
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Vo V, Harrington A, Afzal S, Papp K, Chang CL, Baker H, Aguilar P, Buttery E, Picker MA, Lockett C, Gerrity D, Kan HY, Oh EC. Identification of a rare SARS-CoV-2 XL hybrid variant in wastewater and the subsequent discovery of two infected individuals in Nevada. Sci Total Environ 2023; 858:160024. [PMID: 36356728 PMCID: PMC9640213 DOI: 10.1016/j.scitotenv.2022.160024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 05/31/2023]
Abstract
The identification of novel SARS-CoV-2 variants can predict new patterns of COVID-19 community transmission and lead to the deployment of public health resources. However, increased access to at-home antigen tests and reduced free PCR tests have recently led to data gaps for the surveillance of evolving SARS-CoV-2 variants. To overcome such limitations, we asked whether wastewater surveillance could be leveraged to detect rare variants circulating in a community before local detection in human cases. Here, we performed whole genome sequencing (WGS) of SARS-CoV-2 from a wastewater treatment plant serving Las Vegas, Nevada in April 2022. Using metrics that exceeded 100× depth at a coverage of >90 % of the viral genome, we identified a variant profile similar to the XL recombinant lineage containing 26 mutations found in BA.1 and BA.2 and three private mutations. Prompted by the discovery of this rare lineage in wastewater, we analyzed clinical COVID-19 sequencing data from Southern Nevada and identified two cases infected with the XL lineage. Taken together, our data highlight how wastewater genome sequencing data can be used to discover rare SARS-CoV-2 lineages in a community and complement local public health surveillance.
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Affiliation(s)
- Van Vo
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Anthony Harrington
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Salman Afzal
- Southern Nevada Health District, Las Vegas, NV 89106, USA
| | - Katerina Papp
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Ching-Lan Chang
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Hayley Baker
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Erin Buttery
- Southern Nevada Health District, Las Vegas, NV 89106, USA
| | | | | | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA.
| | - Horng-Yuan Kan
- Southern Nevada Health District, Las Vegas, NV 89106, USA.
| | - Edwin C Oh
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Department of Internal Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
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3
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Picker MA, Karney MMA, Gerson TM, Karabachev AD, Duhart JC, McKenna JA, Wing HJ. Localized modulation of DNA supercoiling, triggered by the Shigella anti-silencer VirB, is sufficient to relieve H-NS-mediated silencing. bioRxiv 2023:2023.01.09.523335. [PMID: 36711906 PMCID: PMC9882051 DOI: 10.1101/2023.01.09.523335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In Bacteria, nucleoid structuring proteins govern nucleoid dynamics and regulate transcription. In Shigella spp ., at ≤ 30 °C, the histone-like nucleoid structuring protein (H-NS) transcriptionally silences many genes on the large virulence plasmid. Upon a switch to 37 °C, VirB, a DNA binding protein and key transcriptional regulator of Shigella virulence, is produced. VirB functions to counter H-NS-mediated silencing in a process called transcriptional anti-silencing. Here, we show that VirB mediates a loss of negative DNA supercoils from our plasmid-borne, VirB-regulated PicsP-lacZ reporter, in vivo . The changes are not caused by a VirB-dependent increase in transcription, nor do they require the presence of H-NS. Instead, the VirB-dependent change in DNA supercoiling requires the interaction of VirB with its DNA binding site, a critical first step in VirB-dependent gene regulation. Using two complementary approaches, we show that VirB:DNA interactions in vitro introduce positive supercoils in plasmid DNA. Subsequently, by exploiting transcription-coupled DNA supercoiling, we reveal that a localized loss of negative supercoils is sufficient to alleviate H-NS-mediated transcriptional silencing, independently of VirB. Together, our findings provide novel insight into VirB, a central regulator of Shigella virulence and more broadly, a molecular mechanism that offsets H-NS-dependent silencing of transcription in bacteria.
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4
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Li L, Uppal T, Hartley PD, Gorzalski A, Pandori M, Picker MA, Verma SC, Pagilla K. Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities. Sci Rep 2022; 12:16141. [PMID: 36167869 PMCID: PMC9514676 DOI: 10.1038/s41598-022-20219-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
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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Affiliation(s)
- Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV, 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV, 89557, USA
| | - Paul D Hartley
- Nevada Genomics Center, University of Nevada, Reno, NV, 89557, 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
| | - Michael A Picker
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV, USA
| | - Subhash C Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV, 89557, USA.
| | - Krishna Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV, 89557, USA.
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Vo V, Tillett RL, Papp K, Shen S, Gu R, Gorzalski A, Siao D, Markland R, Chang CL, Baker H, Chen J, Schiller M, Betancourt WQ, Buttery E, Pandori M, Picker MA, Gerrity D, Oh EC. Use of wastewater surveillance for early detection of Alpha and Epsilon SARS-CoV-2 variants of concern and estimation of overall COVID-19 infection burden. Sci Total Environ 2022; 835:155410. [PMID: 35469875 PMCID: PMC9026949 DOI: 10.1016/j.scitotenv.2022.155410] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 05/14/2023]
Abstract
A decline in diagnostic testing for SARS-CoV-2 is expected to delay the tracking of COVID-19 variants of concern and interest in the United States. We hypothesize that wastewater surveillance programs provide an effective alternative for detecting emerging variants and assessing COVID-19 incidence, particularly when clinical surveillance is limited. Here, we analyzed SARS-CoV-2 RNA in wastewater from eight locations across Southern Nevada between March 2020 and April 2021. Trends in SARS-CoV-2 RNA concentrations (ranging from 4.3 log10 gc/L to 8.7 log10 gc/L) matched trends in confirmed COVID-19 incidence, but wastewater surveillance also highlighted several limitations with the clinical data. Amplicon-based whole genome sequencing (WGS) of 86 wastewater samples identified the B.1.1.7 (Alpha) and B.1.429 (Epsilon) lineages in December 2020, but clinical sequencing failed to identify the variants until January 2021, thereby demonstrating that 'pooled' wastewater samples can sometimes expedite variant detection. Also, by calibrating fecal shedding (11.4 log10 gc/infection) and wastewater surveillance data to reported seroprevalence, we estimate that ~38% of individuals in Southern Nevada had been infected by SARS-CoV-2 as of April 2021, which is significantly higher than the 10% of individuals confirmed through clinical testing. Sewershed-specific ascertainment ratios (i.e., X-fold infection undercounts) ranged from 1.0 to 7.7, potentially due to demographic differences. Our data underscore the growing application of wastewater surveillance in not only the identification and quantification of infectious agents, but also the detection of variants of concern that may be missed when diagnostic testing is limited or unavailable.
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Affiliation(s)
- Van Vo
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Katerina Papp
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV, 89193, USA
| | - Shirley Shen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Richard Gu
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Danielle Siao
- Nevada State Public Health Laboratory, Reno, NV 89597, USA
| | - Rayma Markland
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89106, USA
| | - Ching-Lan Chang
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Hayley Baker
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Martin Schiller
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Walter Q Betancourt
- Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W. Calle Agua Nueva, Tucson, AZ 85745, USA
| | - Erin Buttery
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89106, USA
| | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV 89597, USA
| | - Michael A Picker
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89106, USA
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV, 89193, USA.
| | - Edwin C Oh
- Laboratory of Neurogenetics and Precision Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Department of Internal Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
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6
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Li L, Uppal T, Hartley PD, Gorzalski A, Pandori M, Picker MA, Verma SC, Pagilla K. Detecting SARS-CoV-2 Variants in Wastewater and Their Correlation With Circulating Variants in the Communities.. [PMID: 35313589 PMCID: PMC8936115 DOI: 10.21203/rs.3.rs-1435729/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
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 2021 to June 2021 were analyzed for SARS-CoV-2 variants and were compared with the variants detected in the clinical specimens (nasal/nasopharyngeal swabs) of infected individuals during the same period. The comparison was found to be conclusively in agreement. Therefore, wastewater monitoring for SARS-CoV-2 variants in the community is a feasible strategy both as a complementary tool to clinical specimen testing and in the latter’s absence.
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Affiliation(s)
| | - Timsy Uppal
- University of Nevada, Reno School of Medicine
| | | | | | | | - Michael A. Picker
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District
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7
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Hartley PD, Tillett RL, AuCoin DP, Sevinsky JR, Xu Y, Gorzalski A, Pandori M, Buttery E, Hansen H, Picker MA, Rossetto CC, Verma SC. Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. J Genet Genomics 2021; 48:40-51. [PMID: 33820739 PMCID: PMC7891100 DOI: 10.1016/j.jgg.2021.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Received: 10/11/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/28/2022]
Abstract
Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the variants of SARS-CoV-2 circulating in the state of Nevada, specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform, which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads, without the need of culture-based amplification. High genome coverage allowed the identification of single and multi-nucleotide variants in SARS-CoV-2 in the community and their phylogenetic relationships with other variants present during the same period of the outbreak. We report the occurrence of a novel mutation at 323aa (314aa of orf1b) of nsp12 (RNA-dependent RNA polymerase) changed to phenylalanine (F) from proline (P), in the first reported isolate of SARS-CoV-2, Wuhan-Hu-1. This 323F variant was present at a very high frequency in Northern Nevada. Structural modeling determined this mutation in the interface domain, which is important for the association of accessory proteins required for the polymerase. In conclusion, we report the introduction of specific SARS-CoV-2 variants at very high frequency in distinct geographic locations, which is important for understanding the evolution and circulation of SARS-CoV-2 variants of public health importance, while it circulates in humans.
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Affiliation(s)
- Paul D Hartley
- Nevada Genomics Center, Reno, NV 89557, USA; University of Nevada, Reno, Reno, NV 89557, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
| | - David P AuCoin
- University of Nevada, Reno, Reno, NV 89557, USA; Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | | | - Yanji Xu
- University of Nevada, Reno, Reno, NV 89557, USA; Nevada Center for Bioinformatics, Reno, NV 89557, USA
| | - Andrew Gorzalski
- University of Nevada, Reno, Reno, NV 89557, USA; Nevada State Public Health Laboratory, Reno, NV 89503, USA
| | - Mark Pandori
- University of Nevada, Reno, Reno, NV 89557, USA; Nevada State Public Health Laboratory, Reno, NV 89503, USA
| | - Erin Buttery
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89107, USA
| | - Holly Hansen
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89107, USA
| | - Michael A Picker
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89107, USA
| | - Cyprian C Rossetto
- University of Nevada, Reno, Reno, NV 89557, USA; Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| | - Subhash C Verma
- University of Nevada, Reno, Reno, NV 89557, USA; Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
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Picker MA, Knoblock RJ, Hansen H, Bautista I, Griego R, Barber L, Bendik W, Lam K, Adelman E, Qiu-Shultz Z, Raphael BH, Pham CD, Kersh EN, Weinstock H, St. Cyr SB. Notes from the Field: First Case in the United States of Neisseria gonorrhoeae Harboring Emerging Mosaic penA60 Allele, Conferring Reduced Susceptibility to Cefixime and Ceftriaxone. MMWR Morb Mortal Wkly Rep 2020; 69:1876-1877. [PMID: 33301430 PMCID: PMC7737691 DOI: 10.15585/mmwr.mm6949a5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Hartley PD, Tillett RL, Aucoin DP, Sevinsky JR, Xu Y, Gorzalski A, Pandori M, Buttery E, Hansen H, Picker MA, Rossetto CC, Verma SC. Genomic surveillance revealed prevalence of unique SARS-CoV- 2 variants bearing mutation in the RdRp gene among Nevada patients.. [PMID: 32869037 PMCID: PMC7457609 DOI: 10.1101/2020.08.21.20178863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Patients with signs of COVID-19 were tested with CDC approved diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from nasopharyngeal/nasal swabs. In order to determine the variants of SARS-CoV-2 circulating in the state of Nevada, 200 patient specimens from COVID-19 patients were sequenced through our robust protocol for sequencing SARS-CoV-2 genomes. Our protocol enabled sequencing of SARS-CoV-2 genome directly from the specimens, with even very low viral loads, without the need of culture-based amplification. This allowed the identification of specific nucleotide variants including those coding for D614G and clades defining mutations. These sequences were further analyzed for determining SARS-CoV-2 variants circulating in the state of Nevada and their phylogenetic relationships with other variants present in the united states and the world during the same period of the outbreak. Our study reports the occurrence of a novel variant in the nsp12 (RNA dependent RNA Polymerase) protein at residue 323 (314aa of orf1b) to Phenylalanine (F) from Proline (P), present in the original isolate of SARS-CoV-2 (Wuhan-Hu-1). This 323F variant is found at a very high frequency (46% of the tested specimen) in Northern Nevada. Functional significance of this unique and highly prevalent variant of SARS-CoV-2 with RdRp mutation is currently under investigation but structural modeling showed this 323aa residue in the interface domain of RdRp, which is required for association with accessory proteins. In conclusion, we report the introduction of specific SARS-CoV-2 variants at a very high frequency within a distinct geographic location, which is important for clinical and public health perspectives in understanding the evolution of SARS-CoV-2 while in circulation.
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10
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Weatherspoon-Griffin N, Picker MA, Pew KL, Park HS, Ginete DR, Karney MM, Usufzy P, Castellanos MI, Duhart JC, Harrison DJ, Socea JN, Karabachev AD, Hensley CT, Howerton AJ, Ojeda-Daulo R, Immak JA, Wing HJ. Insights into transcriptional silencing and anti-silencing in Shigella flexneri: a detailed molecular analysis of the icsP virulence locus. Mol Microbiol 2018; 108:505-518. [PMID: 29453862 DOI: 10.1111/mmi.13932] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2018] [Indexed: 11/28/2022]
Abstract
Transcriptional silencing and anti-silencing mechanisms modulate bacterial physiology and virulence in many human pathogens. In Shigella species, many virulence plasmid genes are silenced by the histone-like nucleoid structuring protein H-NS and anti-silenced by the virulence gene regulator VirB. Despite the key role that these regulatory proteins play in Shigella virulence, their mechanisms of transcriptional control remain poorly understood. Here, we characterize the regulatory elements and their relative spacing requirements needed for the transcriptional silencing and anti-silencing of icsP, a locus that requires remotely located regulatory elements for both types of transcriptional control. Our findings highlight the flexibility of the regulatory elements' positions with respect to each other, and yet, a molecular roadblock docked between the VirB binding site and the upstream H-NS binding region abolishes transcriptional anti-silencing by VirB, providing insight into transcriptional anti-silencing. Our study also raises the need to re-evaluate the currently proposed VirB binding site. Models of transcriptional silencing and anti-silencing at this genetic locus are presented, and the implications for understanding these regulatory mechanisms in bacteria are discussed.
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Affiliation(s)
| | - Michael A Picker
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Krystle L Pew
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Hiromichi S Park
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Daren R Ginete
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Monika Ma Karney
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Pashtana Usufzy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Maria I Castellanos
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Juan Carlos Duhart
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Dustin J Harrison
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Jillian N Socea
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | | | - Christopher T Hensley
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Amber J Howerton
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Rosa Ojeda-Daulo
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Joy A Immak
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Helen J Wing
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
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