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Article ; Online: Functional Features of the Respiratory Syncytial Virus G Protein.

Anderson, Larry J / Jadhao, Samadhan J / Paden, Clinton R / Tong, Suxiang

2021 Volume 13, Issue 7

Abstract: Respiratory syncytial virus (RSV) is a major cause of serious lower respiratory tract infections in children <5 years of age worldwide and repeated infections throughout life leading to serious disease in the elderly and persons with compromised immune, ... ...

Abstract	Respiratory syncytial virus (RSV) is a major cause of serious lower respiratory tract infections in children <5 years of age worldwide and repeated infections throughout life leading to serious disease in the elderly and persons with compromised immune, cardiac, and pulmonary systems. The disease burden has made it a high priority for vaccine and antiviral drug development but without success except for immune prophylaxis for certain young infants. Two RSV proteins are associated with protection, F and G, and F is most often pursued for vaccine and antiviral drug development. Several features of the G protein suggest it could also be an important to vaccine or antiviral drug target design. We review features of G that effect biology of infection, the host immune response, and disease associated with infection. Though it is not clear how to fit these together into an integrated picture, it is clear that G mediates cell surface binding and facilitates cellular infection, modulates host responses that affect both immunity and disease, and its CX3C aa motif contributes to many of these effects. These features of G and the ability to block the effects with antibody, suggest G has substantial potential in vaccine and antiviral drug design.
MeSH term(s)	Animals ; Antibodies, Viral/immunology ; GTP-Binding Proteins/genetics ; GTP-Binding Proteins/metabolism ; Humans ; Mice ; Respiratory Syncytial Virus Infections/virology ; Respiratory Syncytial Virus, Human/chemistry ; Respiratory Syncytial Virus, Human/genetics ; Respiratory Syncytial Virus, Human/metabolism ; Viral Fusion Proteins/genetics ; Viral Fusion Proteins/immunology ; Viral Fusion Proteins/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Antibodies, Viral ; Viral Fusion Proteins ; Viral Proteins ; GTP-Binding Proteins (EC 3.6.1.-)
Language	English
Publishing date	2021-07-01
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13071214
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Early Estimates of Updated 2023-2024 (Monovalent XBB.1.5) COVID-19 Vaccine Effectiveness Against Symptomatic SARS-CoV-2 Infection Attributable to Co-Circulating Omicron Variants Among Immunocompetent Adults - Increasing Community Access to Testing Program, United States, September 2023-January 2024.

Link-Gelles, Ruth / Ciesla, Allison Avrich / Mak, Josephine / Miller, Joseph D / Silk, Benjamin J / Lambrou, Anastasia S / Paden, Clinton R / Shirk, Philip / Britton, Amadea / Smith, Zachary R / Fleming-Dutra, Katherine E

MMWR. Morbidity and mortality weekly report

2024 Volume 73, Issue 4, Page(s) 77–83

Abstract: On September 12, 2023, CDC's Advisory Committee on Immunization Practices recommended updated 2023-2024 (updated) COVID-19 vaccination with a monovalent XBB.1.5-derived vaccine for all persons aged ≥6 months to prevent COVID-19, including severe disease. ...

Abstract	On September 12, 2023, CDC's Advisory Committee on Immunization Practices recommended updated 2023-2024 (updated) COVID-19 vaccination with a monovalent XBB.1.5-derived vaccine for all persons aged ≥6 months to prevent COVID-19, including severe disease. During fall 2023, XBB lineages co-circulated with JN.1, an Omicron BA.2.86 lineage that emerged in September 2023. These variants have amino acid substitutions that might increase escape from neutralizing antibodies. XBB lineages predominated through December 2023, when JN.1 became predominant in the United States. Reduction or failure of spike gene (S-gene) amplification (i.e., S-gene target failure [SGTF]) in real-time reverse transcription-polymerase chain reaction testing is a time-dependent, proxy indicator of JN.1 infection. Data from the Increasing Community Access to Testing SARS-CoV-2 pharmacy testing program were analyzed to estimate updated COVID-19 vaccine effectiveness (VE) (i.e., receipt versus no receipt of updated vaccination) against symptomatic SARS-CoV-2 infection, including by SGTF result. Among 9,222 total eligible tests, overall VE among adults aged ≥18 years was 54% (95% CI = 46%-60%) at a median of 52 days after vaccination. Among 2,199 tests performed at a laboratory with SGTF testing, VE 60-119 days after vaccination was 49% (95% CI = 19%-68%) among tests exhibiting SGTF and 60% (95% CI = 35%-75%) among tests without SGTF. Updated COVID-19 vaccines provide protection against symptomatic infection, including against currently circulating lineages. CDC will continue monitoring VE, including for expected waning and against severe disease. All persons aged ≥6 months should receive an updated COVID-19 vaccine dose.
MeSH term(s)	United States/epidemiology ; Adult ; Humans ; Adolescent ; COVID-19 Vaccines ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; Vaccine Efficacy ; SARS-CoV-2
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7304a2
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Article: Functional Features of the Respiratory Syncytial Virus G Protein

Anderson, Larry J. / Jadhao, Samadhan J. / Paden, Clinton R. / Tong, Suxiang

Viruses. 2021 July 01, v. 13, no. 7

2021

Abstract	Respiratory syncytial virus (RSV) is a major cause of serious lower respiratory tract infections in children <5 years of age worldwide and repeated infections throughout life leading to serious disease in the elderly and persons with compromised immune, cardiac, and pulmonary systems. The disease burden has made it a high priority for vaccine and antiviral drug development but without success except for immune prophylaxis for certain young infants. Two RSV proteins are associated with protection, F and G, and F is most often pursued for vaccine and antiviral drug development. Several features of the G protein suggest it could also be an important to vaccine or antiviral drug target design. We review features of G that effect biology of infection, the host immune response, and disease associated with infection. Though it is not clear how to fit these together into an integrated picture, it is clear that G mediates cell surface binding and facilitates cellular infection, modulates host responses that affect both immunity and disease, and its CX3C aa motif contributes to many of these effects. These features of G and the ability to block the effects with antibody, suggest G has substantial potential in vaccine and antiviral drug design.
Keywords	Respiratory syncytial virus ; antibodies ; antiviral agents ; burden of disease ; disease prevention ; drug design ; elderly ; immune response ; respiratory system ; vaccines
Language	English
Dates of publication	2021-0701
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13071214
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants - United States, November 2021-January 2023.

Scobie, Heather M / Ali, Akilah R / Shirk, Philip / Smith, Zachary R / Paul, Prabasaj / Paden, Clinton R / Hassell, Norman / Zheng, Xiao-Yu / Lambrou, Anastasia S / Kondor, Rebecca / MacCannell, Duncan / Thornburg, Natalie J / Miller, Joseph / Wentworth, Dave / Silk, Benjamin J

MMWR. Morbidity and mortality weekly report

2023 Volume 72, Issue 5, Page(s) 125–127

Abstract: Monitoring emerging SARS-CoV-2 lineages and their epidemiologic characteristics helps to inform public health decisions regarding vaccine policy, the use of therapeutics, and health care capacity. When the SARS-CoV-2 Alpha variant emerged in late 2020, a ...

Abstract	Monitoring emerging SARS-CoV-2 lineages and their epidemiologic characteristics helps to inform public health decisions regarding vaccine policy, the use of therapeutics, and health care capacity. When the SARS-CoV-2 Alpha variant emerged in late 2020, a spike gene (S-gene) deletion (Δ69-70) in the N-terminal region, which might compensate for immune escape mutations that impair infectivity (1), resulted in reduced or failed S-gene target amplification in certain multitarget reverse transcription-polymerase chain reaction (RT-PCR) assays, a pattern referred to as S-gene target failure (SGTF) (2). The predominant U.S. SARS-CoV-2 lineages have generally alternated between SGTF and S-gene target presence (SGTP), which alongside genomic sequencing, has facilitated early monitoring of emerging variants. During a period when Omicron BA.5-related sublineages (which exhibit SGTF) predominated, an XBB.1.5 sublineage with SGTP has rapidly expanded in the northeastern United States and other regions.
MeSH term(s)	United States/epidemiology ; Humans ; Public Health ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Mutation ; COVID-19 Testing
Language	English
Publishing date	2023-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7205e2
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Article ; Online: Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2.

Paden, Clinton R / Tao, Ying / Queen, Krista / Zhang, Jing / Li, Yan / Uehara, Anna / Tong, Suxiang

Emerging infectious diseases

2020 Volume 26, Issue 10, Page(s) 2401–2405

Abstract: We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the ... ...

Abstract	We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the other uses singleplex, nested reverse transcription PCR and Sanger sequencing. These protocols enable sensitive virus sequencing in different laboratory environments.
MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/virology ; Multiplex Polymerase Chain Reaction ; Pandemics ; Pneumonia, Viral/virology ; RNA, Viral/analysis ; SARS-CoV-2 ; Sequence Analysis, RNA/methods ; Whole Genome Sequencing/methods
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2610.201800
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Zs.A 4778: Show issues

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Article ; Online: Early Detection and Surveillance of the SARS-CoV-2 Variant BA.2.86 - Worldwide, July-October 2023.

MMWR. Morbidity and mortality weekly report

2023 Volume 72, Issue 43, Page(s) 1162–1167

Abstract: Early detection of emerging SARS-CoV-2 variants is critical to guiding rapid risk assessments, providing clear and timely communication messages, and coordinating public health action. CDC identifies and monitors novel SARS-CoV-2 variants through diverse ...

Abstract	Early detection of emerging SARS-CoV-2 variants is critical to guiding rapid risk assessments, providing clear and timely communication messages, and coordinating public health action. CDC identifies and monitors novel SARS-CoV-2 variants through diverse surveillance approaches, including genomic, wastewater, traveler-based, and digital public health surveillance (e.g., global data repositories, news, and social media). The SARS-CoV-2 variant BA.2.86 was first sequenced in Israel and reported on August 13, 2023. The first U.S. COVID-19 case caused by this variant was reported on August 17, 2023, after a patient received testing for SARS-CoV-2 at a health care facility on August 3. In the following month, eight additional U.S. states detected BA.2.86 across various surveillance systems, including specimens from health care settings, wastewater surveillance, and traveler-based genomic surveillance. As of October 23, 2023, sequences have been reported from at least 32 countries. Continued variant tracking and further evidence are needed to evaluate the full public health impact of BA.2.86. Timely genomic sequence submissions to global public databases aided early detection of BA.2.86 despite the decline in the number of specimens being sequenced during the past year. This report describes how multicomponent surveillance and genomic sequencing were used in real time to track the emergence and transmission of the BA.2.86 variant. This surveillance approach provides valuable information regarding implementing and sustaining comprehensive surveillance not only for novel SARS-CoV-2 variants but also for future pathogen threats.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2/genetics ; Wastewater ; Wastewater-Based Epidemiological Monitoring
Chemical Substances	Wastewater
Language	English
Publishing date	2023-10-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7243a2
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Article ; Online: Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2

Clinton R. Paden / Ying Tao / Krista Queen / Jing Zhang / Yan Li / Anna Uehara / Suxiang Tong

Emerging Infectious Diseases, Vol 26, Iss 10, Pp 2401-

2020 Volume 2405

Abstract	We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the other uses singleplex, nested reverse transcription PCR and Sanger sequencing. These protocols enable sensitive virus sequencing in different laboratory environments.
Keywords	coronavirus disease ; COVID-19 ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; coronavirus ; viruses ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216 ; covid19
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: COVID-19 on the Nile: a cross-sectional investigation of COVID-19 among Nile River cruise travellers returning to the United States, February-March 2020.

Guagliardo, Sarah Anne J / Quilter, Laura A S / Uehara, Anna / White, Stefanie B / Talarico, Sarah / Tong, Suxiang / Paden, Clinton R / Zhang, Jing / Li, Yan / Pray, Ian / Novak, Ryan T / Fukunaga, Rena / Rodriguez, Andrea / Medley, Alexandra M / Wagner, Riley / Weinberg, Michelle / Brown, Clive M / Friedman, Cindy R

Journal of travel medicine

2022 Volume 30, Issue 4

Abstract: Background: Early in the pandemic, cruise travel exacerbated the global spread of SARS-CoV-2. We report epidemiologic and molecular findings from an investigation of a cluster of travellers with confirmed COVID-19 returning to the USA from Nile River ... ...

Abstract	Background: Early in the pandemic, cruise travel exacerbated the global spread of SARS-CoV-2. We report epidemiologic and molecular findings from an investigation of a cluster of travellers with confirmed COVID-19 returning to the USA from Nile River cruises in Egypt. Methods: State health departments reported data on real-time reverse transcription-polymerase chain reaction-confirmed COVID-19 cases with a history of Nile River cruise travel during February-March 2020 to the Centers for Disease Control and Prevention (CDC). Demographic and epidemiologic data were collected through routine surveillance channels. Sequences were obtained either from state health departments or from the Global Initiative on Sharing Avian Flu Data (GISAID). We conducted descriptive analyses of epidemiologic data and explored phylogenetic relationships between sequences. Results: We identified 149 Nile River cruise travellers with confirmed COVID-19 who returned to 67 different US counties in 27 states: among those with complete data, 4.7% (6/128) died and 28.1% (38/135) were hospitalized. These individuals travelled on 20 different Nile River cruise voyages (12 unique vessels). Fifteen community transmission events were identified in four states, with 73.3% (11/15) of these occurring in Wisconsin (as the result of a more detailed contact investigation in that state). Phylogenetic analyses supported the hypothesis that travellers were most likely infected in Egypt, with most sequences in Nextstrain clade 20A 93% (87/94). We observed genetic clustering by Nile River cruise voyage and vessel. Conclusions: Nile River cruise travellers with COVID-19 introduced SARS-CoV-2 over a very large geographic range, facilitating transmission across the USA early in the pandemic. Travellers who participate in cruises, even on small river vessels as investigated in this study, are at increased risk of SARS-CoV-2 exposure. Therefore, history of river cruise travel should be considered in contact tracing and outbreak investigations.
MeSH term(s)	Humans ; United States/epidemiology ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Phylogeny ; Cross-Sectional Studies ; Rivers
Language	English
Publishing date	2022-12-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1212504-0
ISSN	1708-8305 ; 1195-1982
ISSN (online)	1708-8305
ISSN	1195-1982
DOI	10.1093/jtm/taac153
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Article: Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic.

Babiker, Ahmed / Martin, Michael A / Marvil, Charles / Bellman, Stephanie / Petit Iii, Robert A / Bradley, Heath L / Stittleburg, Victoria D / Ingersoll, Jessica / Kraft, Colleen S / Li, Yan / Zhang, Jing / Paden, Clinton R / Read, Timothy D / Waggoner, Jesse J / Koelle, Katia / Piantadosi, Anne

Virus evolution

2022 Volume 8, Issue 1, Page(s) veac011

Abstract: In early 2020, as diagnostic and surveillance responses for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early ... ...

Abstract	In early 2020, as diagnostic and surveillance responses for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early patterns of SARS-CoV-2 spread within the USA by analyzing detailed clinical, molecular, and viral genomic data from the state of Georgia through March 2020. We find evidence for multiple early introductions into Georgia, despite relatively sparse sampling. Most sampled sequences likely stemmed from a single or small number of introductions from Asia three weeks prior to the state's first detected infection. Our analysis of sequences from domestic travelers demonstrates widespread circulation of closely related viruses in multiple US states by the end of March 2020. Our findings indicate that the exclusive focus on identifying SARS-CoV-2 in returning international travelers early in the pandemic may have led to a failure to recognize locally circulating infections for several weeks and point toward a critical need for implementing rapid, broadly targeted surveillance efforts for future pandemics.
Language	English
Publishing date	2022-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veac011
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2

Paden, Clinton R. / Tao, Ying / Queen, Krista / Zhang, Jing / Yan, Li / Uehara, Anna / Tong, Suxiang

Emerg Infect Dis

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #712837
Database	COVID19

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