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Abstract
Superinfection exclusion (SIE) is a phenomenon in which a primary viral infection interferes with secondary viral infections within that same cell. Although SIE has been observed across many viruses, it has remained relatively understudied. A recently characterized glycoprotein D (gD)-independent SIE of alphaherpesviruses presents a novel mechanism of coinfection restriction for herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV). In this study, we evaluated the role of multiplicity of infection (MOI), receptor expression, and trafficking of virions to gain greater insight into potential mechanisms of alphaherpesvirus SIE. We observed that high-MOI secondary viral infections were able to overcome SIE in a manner that was independent of receptor availability. We next assessed virion localization during SIE through live microscopy of fluorescently labeled virions and capsid assemblies. Analysis of these fluorescent assemblies identified changes in the distribution of capsids during SIE. These results indicate that SIE during PRV infection inhibits viral entry or fusion while HSV-1 SIE inhibits infection through a postentry mechanism. Although the timing and phenotype of SIE are similar between alphaherpesviruses, the related viruses implement different mechanisms to restrict coinfection. IMPORTANCE Most viruses utilize a form of superinfection exclusion to conserve resources and control population dynamics. gD-dependent superinfection exclusion in alphaherpesviruses is well documented. However, the undercharacterized gD-independent SIE provides new insight into how alphaherpesviruses limit sequential infection. The observations described here demonstrate that gD-independent SIE differs between PRV and HSV-1. Comparing these differences provides new insights into the underlying mechanisms of SIE implemented by two related viruses.
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Chang W, Jiao X, Sui H, Goswami S, Sherman BT, Fromont C, Caravaca JM, Tran B, Imamichi T. Complete Genome Sequence of Herpes Simplex Virus 2 Strain G. Viruses 2022; 14:v14030536. [PMID: 35336943 PMCID: PMC8954253 DOI: 10.3390/v14030536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Herpes simplex virus type 2 (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD90e, and MS). Strain G is commonly used for HSV-2 research, but only a partial genome sequence has been assembled with Illumina sequencing reads. In the current study, we de novo assembled and annotated the complete genome of strain G using PacBio long sequencing reads, which can span the repetitive regions, analyzed the ‘α’ sequence, which plays key roles in HSV-2 genome circulation, replication, cleavage, and packaging of progeny viral DNA, identified the packaging signals homologous to HSV-1 within the ‘α’ sequence, and determined both termini of the linear genome and cleavage site for the process of concatemeric HSV-2 DNA produced via rolling-circle replication. In addition, using Oxford Nanopore Technology sequencing reads, we visualized four HSV-2 genome isomers at the nucleotide level for the first time. Furthermore, the coding sequences of HSV-2 strain G have been compared with those of HG52, 333, and MS. Moreover, phylogenetic analysis of strain G and other diverse HSV-2 strains has been conducted to determine their evolutionary relationship. The results will aid clinical research and treatment development of HSV-2.
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Affiliation(s)
- Weizhong Chang
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
- Correspondence: (W.C.); (T.I.); Tel.: +1-(301)-846-6295 (W.C.); +1-(301)-846-5450 (T.I.)
| | - Xiaoli Jiao
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Hongyan Sui
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Suranjana Goswami
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Brad T. Sherman
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Caroline Fromont
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.F.); (J.M.C.); (B.T.)
| | - Juan Manuel Caravaca
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.F.); (J.M.C.); (B.T.)
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.F.); (J.M.C.); (B.T.)
| | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
- Correspondence: (W.C.); (T.I.); Tel.: +1-(301)-846-6295 (W.C.); +1-(301)-846-5450 (T.I.)
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Hadi AM, Mohammed Al-Alwany SH, Al-Khafaji ZA, Sharaf M, Mofed D, Khan TU. Molecular diagnosis of Herpes virus type 1 by glycoprotein receptor primers. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Bourassa L, Perchetti GA, Phung Q, Lin MJ, Mills MG, Roychoudhury P, Harmon KG, Reed JC, Greninger AL. A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. J Clin Virol 2021; 141:104900. [PMID: 34171548 DOI: 10.1101/2021.05.05.21256527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 05/27/2023]
Abstract
More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.
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Affiliation(s)
- Lori Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly G Harmon
- Department of Family Medicine, for Stanley Herring Department of Physical Medicine and Rehabilitation, University of Washington, Seattle, Washington, USA
| | - Jonathan C Reed
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Bourassa L, Perchetti GA, Phung Q, Lin MJ, Mills MG, Roychoudhury P, Harmon KG, Reed JC, Greninger AL. A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. J Clin Virol 2021; 141:104900. [PMID: 34171548 PMCID: PMC8219478 DOI: 10.1016/j.jcv.2021.104900] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.
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Affiliation(s)
- Lori Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly G Harmon
- Department of Family Medicine, for Stanley Herring Department of Physical Medicine and Rehabilitation, University of Washington, Seattle, Washington, USA
| | - Jonathan C Reed
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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