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Article: Waning Vaccine Protection against Influenza among Department of Defense Adult Beneficiaries in the United States, 2016-2017 through 2019-2020 Influenza Seasons.

Hu, Wenping / Sjoberg, Paul A / Fries, Anthony C / DeMarcus, Laurie S / Robbins, Anthony S

2022 Volume 10, Issue 6

Abstract: The objective of this study was to assess inactivated influenza vaccine effectiveness (VE) by time since vaccination in adults aged ≥ 18 years using a test-negative design. All data were obtained from the US Department of Defense Global Respiratory ... ...

Abstract	The objective of this study was to assess inactivated influenza vaccine effectiveness (VE) by time since vaccination in adults aged ≥ 18 years using a test-negative design. All data were obtained from the US Department of Defense Global Respiratory Pathogen Surveillance Program over four influenza seasons, from 2016-2017 through 2019-2020. Analyses were performed to estimate VE using a generalized linear mixed model with logit link and binomial distribution. The adjusted overall VE against any medically attended, laboratory-confirmed influenza decreased from 50% (95% confidence interval (CI): 41-58%) in adults vaccinated 14 to 74 days prior to the onset of influenza-like illness (ILI), to 39% (95% CI: 31-47%) in adults vaccinated 75 to 134 days prior to the onset of ILI, then to 17% (95% CI: 0-32%) in adults vaccinated 135 to 194 days prior to the onset of ILI. The pattern and magnitude of VE change with increasing time since vaccination differed by influenza (sub)types. Compared to VE against influenza A(H1N1)pdm09 and influenza B, the decrease of VE against influenza A(H3N2) was more pronounced with increasing time since vaccination. In conclusion, based on the analysis of 2536 influenza-positive cases identified from 7058 adults over multiple influenza seasons, the effectiveness of inactivated influenza vaccine wanes within 180 days after 14 days of influenza vaccination.
Language	English
Publishing date	2022-06-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10060888
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sampling considerations for detecting genetic diversity of influenza viruses in the DoD Global Respiratory Pathogen Surveillance Program.

Fries, Anthony C / Gruner, William / Hanson, James

MSMR

2018 Volume 25, Issue 8, Page(s) 16–21

Abstract: The Department of Defense (DoD) Global Respiratory Pathogen Surveillance Program annually monitors the genetic diversity of influenza viruses circulating in DoD beneficiary populations. This program relies on a global network of partners across the DoD ... ...

Abstract	The Department of Defense (DoD) Global Respiratory Pathogen Surveillance Program annually monitors the genetic diversity of influenza viruses circulating in DoD beneficiary populations. This program relies on a global network of partners across the DoD to submit respiratory specimens throughout the influenza season. In previous seasons, representative specimens for sequencing were chosen because of cost and time restrictions associated with reliance on Sanger-based sequencing technology. The effect of this specimen prioritization for sequencing has not been previously examined in the respiratory surveillance program. Here, specimen prioritization was simulated by iteratively subsetting sequencing data sets from 1 October 2013 through 15 March 2017 to determine how prioritizing affects common metrics of genetic diversity. Prioritization of specimens did not meaningfully affect calculations of average influenza genetic diversity within seasons or subtypes. Because of the high genetic diversity of influenza, prioritizing resulted in fewer unique viruses and less accurate measures of geographic relationships although it still provided relevant estimates. Given the advent of cost-effective next-generation sequencing approaches, all programs should carefully consider how best to prioritize influenza sequencing to recover meaningful information on the evolutionary dynamics of the virus.
MeSH term(s)	Genes, Viral/genetics ; Genetic Variation ; Humans ; Influenza A virus/genetics ; Influenza, Human/virology ; Population Surveillance ; Seasons ; Sequence Analysis/methods ; United States ; United States Department of Defense
Keywords	covid19
Language	English
Publishing date	2018-08-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2623409-9
ISSN	2152-8217 ; 2158-0111
ISSN (online)	2152-8217
ISSN	2158-0111
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Article ; Online: SARS-CoV-2 Genome-Based Severity Predictions Correspond to Lower qPCR Values and Higher Viral Load.

Skarzynski, Martin / McAuley, Erin M / Maier, Ezekiel J / Fries, Anthony C / Voss, Jameson D / Chapleau, Richard R

Global health, epidemiology and genomics

2022 Volume 2022, Page(s) 6499217

Abstract: The 2019 coronavirus disease (COVID-19) pandemic has demonstrated the importance of predicting, identifying, and tracking mutations throughout a pandemic event. As the COVID-19 global pandemic surpassed one year, several variants had emerged resulting in ...

Abstract	The 2019 coronavirus disease (COVID-19) pandemic has demonstrated the importance of predicting, identifying, and tracking mutations throughout a pandemic event. As the COVID-19 global pandemic surpassed one year, several variants had emerged resulting in increased severity and transmissibility. Here, we used PCR as a surrogate for viral load and consequent severity to evaluate the real-world capabilities of a genome-based clinical severity predictive algorithm. Using a previously published algorithm, we compared the viral genome-based severity predictions to clinically derived PCR-based viral load of 716 viral genomes. For those samples predicted to be "severe" (probability of severe illness >0.5), we observed an average cycle threshold (Ct) of 18.3, whereas those in in the "mild" category (severity probability <0.5) had an average Ct of 20.4 (
MeSH term(s)	COVID-19/diagnosis ; COVID-19/genetics ; Humans ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/genetics ; Severity of Illness Index ; Viral Load/genetics
Language	English
Publishing date	2022-05-31
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2054-4200
ISSN (online)	2054-4200
DOI	10.1155/2022/6499217
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Article ; Online: Circulating Trends of Influenza and Other Seasonal Respiratory Viruses among the US Department of Defense Personnel in the United States: Impact of the COVID-19 Pandemic.

Hu, Wenping / Fries, Anthony C / DeMarcus, Laurie S / Thervil, Jeffery W / Kwaah, Bismark / Brown, Kayla N / Sjoberg, Paul A / Robbins, Anthony S

International journal of environmental research and public health

2022 Volume 19, Issue 10

Abstract: The objective of this study was to evaluate the impact of the COVID-19 pandemic on the circulation of influenza and other seasonal respiratory viruses in the United States. All data were obtained from the US Department of Defense Global Respiratory ... ...

Abstract	The objective of this study was to evaluate the impact of the COVID-19 pandemic on the circulation of influenza and other seasonal respiratory viruses in the United States. All data were obtained from the US Department of Defense Global Respiratory Pathogen Surveillance Program over five consecutive respiratory seasons from 2016-2017 through to 2020-2021. A total of 62,476 specimens were tested for seasonal respiratory viruses. The circulating patterns of seasonal respiratory viruses have been greatly altered during the pandemic. The 2019-2020 influenza season terminated earlier compared to the pre-pandemic seasons, and the 2020-2021 influenza season did not occur. Moreover, weekly test positivity rates dramatically decreased for most of the seasonal respiratory viruses from the start of the pandemic through spring 2021. After the easing of non-pharmaceutical interventions (NPIs), circulations of seasonal coronavirus, parainfluenza, and respiratory syncytial virus have returned since spring 2021. High rhinovirus/enterovirus activity was evident throughout the 2020-2021 respiratory season. The findings suggest a strong association between the remarkably changed activity of seasonal respiratory viruses and the implementation of NPIs during the COVID-19 pandemic. The NPIs may serve as an effective public health tool to reduce transmissions of seasonal respiratory viruses.
MeSH term(s)	COVID-19/epidemiology ; Humans ; Influenza, Human/epidemiology ; Pandemics ; Seasons ; United States/epidemiology ; Viruses
Language	English
Publishing date	2022-05-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph19105942
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Article ; Online: Respiratory pathogen surveillance trends and influenza vaccine effectiveness estimates for the 2018-2019 season among Department of Defense beneficiaries.

Kersellius, Geeta D / Gruner, William E / Fries, Anthony C / DeMarcus, Laurie S / Robbins, Anthony S

MSMR

2020 Volume 27, Issue 1, Page(s) 17–23

Abstract: This report primarily focuses on the data collected and analyzed from the worldwide network of sentinel military treatment facilities chosen to participate in the Department of Defense Global Respiratory Pathogen Surveillance (DoDGRS) program. Sites that ...

Abstract	This report primarily focuses on the data collected and analyzed from the worldwide network of sentinel military treatment facilities chosen to participate in the Department of Defense Global Respiratory Pathogen Surveillance (DoDGRS) program. Sites that participated in the 2018-2019 DoDGRS program submitted 24,320 respiratory specimens for diagnostic testing. Clinical results showed a total of 5,968 positive influenza cases. In the beginning of the season, starting in surveillance week 48, influenza A(H1N1)pdm09 was the predominant subtype. The predominant subtype switched to influenza A(H3N2) beginning in week 6 and continued through the end of the season. Influenza B virus detection was less common during the surveillance period (i.e., 1% of total submitted specimens and 5% of total influenza detected). In addition to routine surveillance, the DoDGRS program also conducts vaccine effectiveness (VE) studies twice per year to determine interim and end of season estimates. Overall, the adjusted end of season VE for all dependents regardless of influenza type was 30% (95% CI: 22%-38%).
MeSH term(s)	Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Infant, Newborn ; Influenza A Virus, H1N1 Subtype/immunology ; Influenza A Virus, H3N2 Subtype/immunology ; Influenza Vaccines/immunology ; Influenza Vaccines/therapeutic use ; Influenza, Human/epidemiology ; Influenza, Human/prevention & control ; Influenza, Human/virology ; Insurance Benefits/statistics & numerical data ; Male ; Middle Aged ; Military Health/statistics & numerical data ; Population Surveillance ; Seasons ; United States/epidemiology ; United States Department of Defense ; Young Adult
Chemical Substances	Influenza Vaccines
Language	English
Publishing date	2020-02-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2623409-9
ISSN	2152-8217 ; 2158-0111
ISSN (online)	2152-8217
ISSN	2158-0111
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Article ; Online: Clustered cases of human adenovirus types 4, 7, and 14 infections in US Department of Defense Beneficiaries during the 2018-2019 season.

Pollio, Adam R / Fries, Anthony C / Yang, Yu / Hughes, Jerry J / Fung, Christian K / Conte, Matthew A / Kuschner, Robert A / Collins, Natalie D / Macias, Elizabeth A / Hang, Jun

Journal of medical virology

2023 Volume 95, Issue 2, Page(s) e28571

Abstract: Human adenoviruses (HAdV) are genetically diverse and can infect a number of tissues with severities varied from mild to fatal. HAdV types 3, 4, 7, 11, 14, 21, and 55 were associated with acute respiratory illnesses outbreaks in the United States and in ... ...

Abstract	Human adenoviruses (HAdV) are genetically diverse and can infect a number of tissues with severities varied from mild to fatal. HAdV types 3, 4, 7, 11, 14, 21, and 55 were associated with acute respiratory illnesses outbreaks in the United States and in other countries. The risk of outbreaks can be effectively controlled by HAdV vaccination or mitigated by screening and preventive measures. During the influenza season 2018-2019, the DoD Global Respiratory Pathogen Surveillance Program (DoDGRS) received 24 300 respiratory specimens. HAdV samples that produced positive cytopathic effects in viral cultivation were subjected to next-generation sequencing for genome sequence assembly, genome typing, whole genome phylogeny, and sequence comparative analyses. A variety of HAdV types were identified in this study, including HAdV types 1-7, 14, 55, and 56. HAdV types 4, 7, and 14 were found in clustered cases in Colorado, Florida, New York, and South Carolina. Comparative sequence analyses of these isolates revealed the emergence of novel genetic mutations despite the stability of adenovirus genomes. Genomic surveillance of HAdV suggested possible undetected outbreaks and shed light on prevalence, genetic divergence, and viral evolution of HAdV. Continued surveillance will inform risk assessment and countermeasures.
MeSH term(s)	Humans ; United States ; Adenoviruses, Human ; Seasons ; Respiratory Tract Infections ; Adenovirus Infections, Human ; Genome, Viral ; New York ; Phylogeny
Language	English
Publishing date	2023-03-02
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28571
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Article ; Online: Influenza Surveillance Trends and Influenza Vaccine Effectiveness Among Department of Defense Beneficiaries During the 2019-2020 Influenza Season.

Hu, Wenping / Gruner, William E / DeMarcus, Laurie S / Thervil, Jeffrey W / Kwaah, Bismark / Fries, Anthony C / Sjoberg, Paul A / Robbins, Anthony S

MSMR

2021 Volume 28, Issue 3, Page(s) 2–8

Abstract: Laboratory-based influenza surveillance was conducted in the 2019-2020 influenza season among Department of Defense (DoD) beneficiaries through the DoD Global Respiratory Pathogen Surveillance Program (DoDGRS). Sentinel and participating sites submitted ... ...

Abstract	Laboratory-based influenza surveillance was conducted in the 2019-2020 influenza season among Department of Defense (DoD) beneficiaries through the DoD Global Respiratory Pathogen Surveillance Program (DoDGRS). Sentinel and participating sites submitted 28,176 specimens for clinical diagnostic testing. A total of 5,529 influenza-positive cases were identified. Starting at surveillance week 45 (3-9 November 2019), influenza B was the predominant influenza type, followed by high activity of influenza A(H1N1)pdm09 three weeks thereafter. Both influenza B and influenza A(H1N1)pdm09 were then highly co-circulated through surveillance week 13 (22-28 March 2020). End-of-season influenza vaccine effectiveness (VE) was estimated using a test-negative case-control study design. The adjusted end-of-season VE for all beneficiaries, regardless of influenza type or subtype, was 46% (95% confidence interval: 40%-52%). The influenza vaccine was moderately effective against influenza viruses during the 2019-2020 influenza season.
MeSH term(s)	Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Influenza Vaccines/therapeutic use ; Influenza, Human/epidemiology ; Influenza, Human/prevention & control ; Influenza, Human/virology ; Alphainfluenzavirus ; Male ; Middle Aged ; Military Health/statistics & numerical data ; Population Surveillance ; United States/epidemiology ; United States Department of Defense ; Vaccination Coverage/trends ; Young Adult
Chemical Substances	Influenza Vaccines
Language	English
Publishing date	2021-03-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2623409-9
ISSN	2152-8217 ; 2152-8217
ISSN (online)	2152-8217
ISSN	2152-8217
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Variants in SARS-CoV-2 associated with mild or severe outcome.

Voss, Jameson D / Skarzynski, Martin / McAuley, Erin M / Maier, Ezekiel J / Gibbons, Thomas / Fries, Anthony C / Chapleau, Richard R

Evolution, medicine, and public health

2021 Volume 9, Issue 1, Page(s) 267–275

Abstract: Introduction: The coronavirus disease 2019 (COVID-19) pandemic is a global public health emergency causing a disparate burden of death and disability around the world. The viral genetic variants associated with outcome severity are still being ... ...

Abstract	Introduction: The coronavirus disease 2019 (COVID-19) pandemic is a global public health emergency causing a disparate burden of death and disability around the world. The viral genetic variants associated with outcome severity are still being discovered. Methods: We downloaded 155 958 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from GISAID. Of these genomes, 3637 samples included useable metadata on patient outcomes. Using this subset, we evaluated whether SARS-CoV-2 viral genomic variants improved prediction of reported severity beyond age and region. First, we established whether including genomic variants as model features meaningfully increased the predictive power of our model. Next, we evaluated specific variants in order to determine the magnitude of association with severity and the frequency of these variants among SARS-CoV-2 genomes. Results: Logistic regression models that included viral genomic variants outperformed other models (area under the curve = 0.91 as compared with 0.68 for age and gender alone; Conclusion: Numerous SARS-CoV-2 variants have 2-fold or greater association with odds of mild or severe outcome and collectively, these variants are common. In addition to comprehensive mitigation efforts, public health measures should be prioritized to control the more severe manifestations of COVID-19 and the transmission chains linked to these severe cases.
Language	English
Publishing date	2021-06-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2684837-5
ISSN	2050-6201
ISSN	2050-6201
DOI	10.1093/emph/eoab019
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Article ; Online ; Research data: (with research data) AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data.

Sovic, Michael G / Fries, Anthony C / Gibbs, H Lisle

Molecular ecology resources

2015 Volume 15, Issue 5, Page(s) 1163–1171

Abstract: An increase in studies using restriction site-associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the ... ...

Abstract	An increase in studies using restriction site-associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the availability of AftrRAD, a bioinformatic pipeline that efficiently assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate AftrRAD's ability to perform accurate de novo assembly of loci, and we compare its performance with two other commonly used programs, stacks and pyrad. We demonstrate that AftrRAD is able to accurately assemble loci, while accounting for indel variation among alleles, in a more computationally efficient manner than currently available programs. AftrRAD run times are not strongly affected by the number of samples in the data set, making this program a useful tool when multicore systems are not available for parallel processing, or when data sets include large numbers of samples.
MeSH term(s)	Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2015-09
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.12378
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Article: Linking genetic structure, landscape genetics, and species distribution modeling for regional conservation of a threatened freshwater turtle

McCluskey, Eric M. / Lulla, Vijay / Peterman, William E. / Stryszowska-Hill, Kinga M. / Denton, Robert D. / Fries, Anthony C. / Langen, Tom A. / Johnson, Glenn / Mockford, Stephen W. / Gonser, Rusty A.

Landscape ecology. 2022 Apr., v. 37, no. 4

2022

Abstract: CONTEXT: Regional conservation efforts should incorporate fine scale landscape genetic and habitat suitability data for management decisions. This information permits conservation measures to be tailored to a specific landscape. OBJECTIVES: We ... ...

Abstract	CONTEXT: Regional conservation efforts should incorporate fine scale landscape genetic and habitat suitability data for management decisions. This information permits conservation measures to be tailored to a specific landscape. OBJECTIVES: We investigated the landscape determinants of gene flow and habitat suitability for the state-threatened Blanding’s turtle (Emydoidea blandingii) in northeastern New York (NNY). We applied the results from each to examine their complementary contributions to local connectivity and genetic structuring. METHODS: We conducted population and individual-based genetic analyses with microsatellite data to evaluate genetic structuring and landscape genetics in NNY. We coupled these genetic analyses with species distribution modeling (SDM) to estimate the extent of suitable habitat across this important region for species persistence in the state. RESULTS: Gene flow was strongly associated with open water and cultivated land, indicating the role open water channels play in connecting neighboring activity centers, and the propensity of females to select cultivated land to nest. Species distribution models based on Landsat-derived vegetation indices and percentage of scrub-shrub wetlands accurately identified Blanding’s turtle habitat. Connectivity estimates from our NNY focal area using landscape genetic and SDM resistance surfaces showed potential movement constraints between the two genetic clusters. CONCLUSIONS: Land cover better explained genetic distance data than geographic distance for Blanding’s turtles in our focal area. Accurate SDMs were developed for our focal area with a small number of occurrences (< 50). Using both gene flow and habitat-informed resistance surfaces revealed localized connectivity constraints associated with each, permitting more comprehensive landscape planning.
Keywords	Emydoidea blandingii ; agricultural land ; gene flow ; genetic distance ; genetic structure ; geographical distribution ; habitats ; land cover ; landscape genetics ; landscapes ; microsatellite repeats ; turtles ; vegetation ; New York
Language	English
Dates of publication	2022-04
Size	p. 1017-1034.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	1027798-5
ISSN	1572-9761 ; 0921-2973
ISSN (online)	1572-9761
ISSN	0921-2973
DOI	10.1007/s10980-022-01420-0
Database	NAL-Catalogue (AGRICOLA)

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