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DoD Establishes Collaborative Virus Genetic Sequencing Capability for COVID-19

Image of two scientists in masks looking at a computer monitor Research associate Lindsay Glang and senior bioinformatics analyst Gregory Rice sequencing SARS-CoV-2 genomes on Oxford Nanopore MinION platform at NMRC BDRD. (Photo Courtesy of Naval Medical Research Center, Genomics & Bioinformatics Department.)

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As the pandemic continues to unfold, genetic sequence data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Coronavirus Disease 2019 (COVID-19), has played a critical role in the public health response, including in the design of diagnostics and vaccines. Within the Department of Defense, SARS-CoV-2 genetic sequence data plays a vital role in force health protection efforts.

To jumpstart the DoD’s SARS-CoV-2 sequencing efforts, Armed Forces Health Surveillance Branch’s Global Emerging Infections Surveillance (GEIS) section used its existing partnerships with Army, Navy, and Air Force public health and medical research laboratories. This connection helped to establish a collaborative approach to the sequencing capabilities. Sequence data from this collaboration will provide critical information about transmission patterns, track diagnostic effectiveness, and guide the development and evaluation of medical countermeasures for the 1.4 million active duty and 331,000 reserve personnel.

“GEIS-funded surveillance provides near-real time understanding of how the SARS-CoV-2 virus is evolving. This information is critical for the development of a vaccine and treatment,” stated Navy Capt. Guillermo Pimentel, GEIS chief. “Previous investments by GEIS in this technology have given our partners the capability to respond and sequence SARS-CoV-2 genomes isolated from DoD Service members around the world.”

In 2017, GEIS established a Next Generation Sequencing and Bioinformatics Consortium to work with GEIS partner DoD laboratories to coordinate and improve pathogen sequencing and analysis efforts around the world. Consortium partners can rapidly detect and characterize known, emerging, and novel infectious disease agents using data from pathogen sequencing. This helps to inform force health protection decision making. The core Consortium partners include: the Naval Medical Research Center (NMRC), U.S. Army Medical Research Institute of Infectious Diseases, Walter Reed Army Institute of Research, U.S. Air Force School of Aerospace Medicine, and the Naval Health Research Center.

“We have used virus sequence data in numerous studies to track virus transmission [such as dengue and influenza],” said Irina Maljkovic Berry, chief of Viral Genetics and Emerging Diseases for the WRAIR Viral Diseases Branch in Silver Spring, Maryland. “We estimate outbreak origins to detect and track vaccine escape and other important mutations throughout the world to aid in vaccine design.”

Consortium partners played a key role in analyzing previous viral outbreaks, such as Ebola in West Africa and Zika in South America, and in seasonal influenza vaccine selection. "Each year we generate thousands of influenza genomes that we use to determine how influenza is evolving or evading our vaccines which directly impact our forces," said Clarise Starr, deputy chief of Pathogen Detection and Therapeutics Portfolio Applied Technology and Genomics Division, U.S. Air Force School of Aerospace Medicine. "These efforts will be the same essential practices that we'll need to deploy in response to SARS-CoV-2."

This open partnership and investment proved extremely helpful in response to the COVID-19 pandemic. DoD laboratories quickly established the ability to isolate the virus, share samples, and compare laboratory methods to improve their sequencing capabilities. “We have been evaluating a few different laboratory sequencing protocols to determine which one works best for samples with certain attributes, in order help increase the efficiency of SARS-CoV-2 sequencing from swabs,” according to Kimberly Bishop-Lilly, head of Genomics & Bioinformatics Department at NMRC in Fort Detrick, Maryland.

The sequence data that's being collected is a valuable source of information to better understand virus transmission patterns among DoD personnel, particularly when combined with other clinical and epidemiological data. These data are also compared to global virus sequence data.

“The goal is to have data and information that could help answer how local outbreaks may have started, how SARS-CoV-2 may have spread in a community or geographic area, and how we can better contain spread or improve interventions,” said Lindsay Morton, GEIS’s senior molecular epidemiologist. Thus far, SARS-CoV-2 sequence data has been gathered from infected personnel at more than 25 locations across the globe.

Additionally, GEIS partners are leveraging this technology to improve understanding of global circulation of SARS-CoV-2 through surveillance programs at DoD overseas labs, such as in Thailand, Peru, Kenya, and Cambodia.

“The OCONUS (Outside Continental United States) labs are starting to stand up SARS-CoV-2 sequencing capabilities and the core labs of the Consortium are providing them reach-back support for sequencing protocols and for bioinformatics analyses,” said Bishop-Lilly. “Consensus viral genomes are being produced at some of the OCONUS labs and we are comparing to viral genomes obtained from samples in other regions such as the U.S., to identify what lineage is predominant in a given geographic region and what key genetic variations may be predominant in a certain area.”

These data will provide a better understanding of transmission in these locations and result in a better understanding of risk to U.S. forces deployed around the world as the COVID-19 pandemic continues. GEIS leaders hope that increased collaboration across the agencies will propel the research and production of an effective vaccine.

“The key to fully utilizing SARS-CoV-2 sequence data is collaboration,” said Morton, “Consortium partners are ready and willing to engage with organizations involved with clinical studies and outbreak investigations across the DoD to better guide the Department’s response to COVID-19 and reduce the impact to readiness and operations around the world.”

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Insomnia is the most common sleep disorder in adults and its incidence in the U.S. Armed Forces is increasing. A potential consequence of inadequate sleep is increased risk of motor vehicle accidents (MVAs). MVAs are the leading cause of peacetime deaths and a major cause of non-fatal injuries in the U.S. military members. To examine the relationship between insomnia and motor vehicle accident-related injuries (MVAs) in the U.S. military, this retrospective cohort study compared 2007 – 2016 incidence rates of MVA-related injuries between service members with diagnosed insomnia and service members without a diagnosis of insomnia. After adjustment for multiple covariates, during 2007 – 2016, active component service members with insomnia had more than double the rate of MVA-related injuries, compared to service members without insomnia. Findings:  •	Line graph shows the annual rates of motor vehicle accident-related injuries, active component service members with and without diagnoses of insomnia, U.S. Armed Forces, 2007 – 2016  •	Annual rates of MVA-related injuries were highest in the insomnia cohort in 2007 and 2008, and lowest in 2016 •	There were 5,587 cases of MVA-related injuries in the two cohorts during the surveillance period. •	Pie chart displays the following data: 1,738 (31.1%) in the unexposed cohort and 3,849 (68.9%) in the insomnia cohort The highest overall crude rates of MVA-related injuries were seen in service members who were: •	Less than 25 years old •	Junior enlisted rank/grade •	Armor/transport occupation •	 •	With a history of mental health diagnosis •	With a history of alcohol-related disorders Access the full report in the December 2017 (Vol. 24, No. 12). Go to www.Health.mil/MSMR Image displays a motor vehicle accident.

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This retrospective study estimated the rates of seizures diagnosed among deployed and non-deployed service members to identify factors associated with seizures and determine if seizure rates differed in deployment settings. It also attempted to evaluate the associations between seizures, traumatic brain injury (TBI), and post-traumatic stress disorder (PTSD) by assessing correlations between the incidence rates of seizures and prior diagnoses of TBI and PTSD. Seizures have been defined as paroxysmal neurologic episodes caused by abnormal neuronal activity in the brain. Approximately one in 10 individuals will experience a seizure in their lifetime. Line graph 1: Annual crude incidence rates of seizures among non-deployed service members, active component, U.S. Armed Forces data •	A total of 16,257 seizure events of all types were identified among non-deployed service members during the 10-year surveillance period. •	The overall incidence rate was 12.9 seizures per 10,000 person-years (p-yrs.) •	There was a decrease in the rate of seizures diagnosed in the active component of the military during the 10-year period. Rates reached their lowest point in 2015 – 9.0 seizures per 10,000 p-yrs. •	Annual rates were markedly higher among service members with recent PTSD and TBI diagnoses, and among those with prior seizure diagnoses. Line graph 2: Annual crude incidence rates of seizures by traumatic brain injury (TBI) and recent post-traumatic stress disorder (PTSD) diagnosis among non-deployed active component service members, U.S. Armed Forces •	For service members who had received both TBI and PTSD diagnoses, seizure rates among the deployed and the non-deployed were two and three times the rates among those with only one of those diagnoses, respectively. •	Rates of seizures tended to be higher among service members who were: in the Army or Marine Corps, Female, African American, Younger than age 30, Veterans of no more than one previous deployment, and in the occupations of combat arms, armor, or healthcare Line graph 3: Annual crude incidence rates of seizures diagnosed among service members deployed to Operation Enduring Freedom, Operation Iraqi Freedom, or Operation New Dawn, U.S. Armed Forces, 2008 – 2016  •	A total of 814 cases of seizures were identified during deployment to operations in Iraq and Afghanistan during the 9-year surveillance period (2008 – 2016). •	For deployed service members, the overall incidence rate was 9.1 seizures per 10,000 p-yrs. •	Having either a TBI or recent PTSD diagnosis alone was associated with a 3-to 4-fold increase in the rate of seizures. •	Only 19 cases of seizures were diagnosed among deployed individuals with a recent PTSD diagnosis during the 9-year surveillance period. •	Overall incidence rates among deployed service members were highest for those in the Army, females, those younger than age 25, junior enlisted, and in healthcare occupations. Access the full report in the December 2017 MSMR (Vol. 24, No. 12). Go to www.Health.mil/MSMR

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