Back to Top Skip to main content Skip to sub-navigation

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.)

Recommended Content:

Armed Forces Health Surveillance Branch | Coronavirus | Global Emerging Infections Surveillance

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.”

You also may be interested in...

The Defense Medical Epidemiology Database System Overview Fact Sheet

Fact Sheet
5/12/2017

This fact sheet provides a system overview of the Defense Medical Epidemiology Database (DMED). DMED is a web-based tool to remotely query de-identified active component personnel and medical event data contained within the Defense Medical Surveillance System (DMSS). Learn about the newly released version of DMED and its key features in this document.

Recommended Content:

Armed Forces Health Surveillance Branch | Defense Medical Epidemiology Database

Global Influenza Summary: May 7, 2017

Report
5/7/2017

Recommended Content:

Health Readiness | Armed Forces Health Surveillance Branch | AFHSB Reports and Publications | Influenza Summary and Reports

Global Influenza Summary: April 30, 2017

Report
4/30/2017

Recommended Content:

Health Readiness | Armed Forces Health Surveillance Branch | AFHSB Reports and Publications | Influenza Summary and Reports

DoD Global, Laboratory-Based Influenza Surveillance Program, 2014- 2015 Season

Infographic
4/17/2017
The DoD Global, Laboratory-Based, Influenza Surveillance Program is a DoD-wide, year-round program that tests respiratory specimens from DoD beneficiaries presenting to military treatment facilities with influenza-like illness (ILI). ILI is defined as an illness characterized by a fever 100.5 degrees F or greater and cough or sore throat within 72 hours of seeking treatment. Sentinel sites submit 6-10 specimens per week from beneficiaries presenting with ILI. Each specimen is tested via reverse transcription-polymerase chain reaction (RT-PCR) and viral culture. The 2014-2015 influenza season was dominated by influenza A (H3N2) at the beginning; however by Week 10, identifications of influenza B viruses were more numerous than for influenza A. Out of a total of 6,432 specimens, 32.7% were positive for influenza. Additionally 19.6% of specimens were positive for other respiratory pathogens while 47.7% specimens were negative. The molecular characterization of specimens showed that the majority of influenza A (H3N2) viruses circulating had drifted from the vaccine strain by December 2014. This finding was in agreement with the Centers for Disease Control and Prevention and World Health Organization observations during the 2014-2015 influenza season. For more information visit Health.mil/AFHSB

The DoD Global, Laboratory-Based, Influenza Surveillance Program is a DoD-wide, year-round program that tests respiratory specimens from DoD beneficiaries presenting to military treatment facilities with influenza-like illness (ILI).

Recommended Content:

Armed Forces Health Surveillance Branch

Zika Virus Infections in Military Health System Beneficiaries

Infographic
4/17/2017
The introduction and rapid spread of the Zika virus (ZIKV), a Flavivrus of the Flaviviridae family, across the Western Hemisphere have posed a risk of infection to Military Health System (MHS) beneficiaries. This report documents: •	The impact of ZIKV transmission on MHS beneficiaries. •	ZIKV spread to nearly 50 countries and territories within a 17-month period. •	Among affected service members, the Army reported the most Zika cases. •	There have been 156 confirmed cases of Zika in MHS beneficiaries. •	A majority of cases reported exposure in Puerto Rico (n=91, 58.3%). Geographic regions of potential exposure to Zika cases in MHS beneficiaries between 01 Jan – 30 Nov 2016 included: •	Puerto Rico ( 91 cases) •	Caribbean ( 41 cases) •	Central America & Mexico (15 cases) •	South America (6 cases) •	Asia ( 3 cases) •	Unknown (3) •	U.S. Florida (1 case) Cases in Service Members Between 01 Jan – 30 Nov 2016 were: •	Army (48 cases) •	Coast Guard (29 cases) •	Air Force (16 cases) •	Navy (10 cases) •	Marine Corps (7 cases) Although most ZIKV infections are asymptomatic or have a relatively mild illness, the gravity of pregnancy and neurologic issues linked to infection remains a significant impetus for the continued surveillance of ZIKV in the MHS population. For more Zika surveillance and information on signs and symptoms, visit Health.mil/AFHSB

The introduction and rapid spread of the Zika virus (ZIKV), a Flavivrus of the Flaviviridae family, across the Western Hemisphere have posed a risk of infection to Military Health System (MHS) beneficiaries.

Recommended Content:

Armed Forces Health Surveillance Branch | Zika Virus | In the Spotlight

Findings from The Department of Defense Global, Laboratory-Based Influenza Surveillance Program, 2015-2016 Influenza Season

Infographic
4/17/2017
The Department of Defense (DoD) Global, Laboratory-Based, Influenza Surveillance Program monitors the circulation of influenza viruses throughout each influenza season. Each season runs from the beginning of October through end of the next September. During the 2015 – 2016 influenza season, a total of 4,591 specimens were tested from 80 locations. The predominant influenza strain was A (H1N1) pdm09. Additionally peak influenza activity occurred during weeks 7 – 13 (14 February – 2 April 2016). Of those submitted for routine surveillance, 1,182 (25.7%) tested positive for other respiratory pathogens, 377 (8.2%) tested positive for influenza B, 755 (16.5%) tested positive for influenza A, and 2,277 (49.6%) tested negative. For more information on the 2015-2016 influenza season and how to identify influenza-like illness (ILI), read the Medical Surveillance Monthly Report (MSMR) at Health.mil/AFHSB.

The Department of Defense (DoD) Global, Laboratory-Based, Influenza Surveillance Program monitors the circulation of influenza viruses throughout each influenza season. Each season runs from the beginning of October through end of the next September.

Recommended Content:

Armed Forces Health Surveillance Branch

Global Influenza Summary: April 16, 2017

Report
4/16/2017

Recommended Content:

Health Readiness | Armed Forces Health Surveillance Branch | AFHSB Reports and Publications | Influenza Summary and Reports

New and Improved Defense Medical Epidemiology Database

Infographic
4/4/2017
The new and improved Defense Medical Epidemiology Database (DMED), known as DMED 5.0, is now only available online.  DMED provides timely and efficient access to data of active component personnel and medical event data.  It contains a subset of data from the Defense Medical Surveillance System (DMSS), offering remote access to tri-service epidemiologic data. Moreover, it protects privacy using only de-identified data and updates monthly.  The new DMED features an enhanced user interface, query data using ICD-9 and ICD-10 diagnostic codes granting authorized users to search multiple databases simultaneously. These users are U.S. military personnel (DoD-CaC users) or Federal partners and civilian collaborators in military medical research and operations. Authorized U.S. military personnel with access to DMED include medical providers, epidemiologists, medical researchers, safety officers, and medical operations and clinical support staff. Sign up for a new account at www.health.mil/dmed

The new and improved Defense Medical Epidemiology Database (DMED), known as DMED 5.0, is now only available online. DMED provides timely and efficient access to data of active component personnel and medical event data.

Recommended Content:

Armed Forces Health Surveillance Branch | Defense Medical Epidemiology Database

Update: Exertional Hyponatremia U.S. Armed Forces, 2001-2016

Infographic
4/4/2017
Exertional Hyponatremia occurs during or up to 24 hours after prolonged physical activity. It is defined by a serum, plasma or blood sodium concentration below 135 millequivalents per liter. This infographic provides an update on Exertional Hyponatremia among U.S. Armed Forces, information on service members at high risk. Exertional hyponatremia can result from loss of sodium and/or potassium as well as relative excess of body water. There were 1,519 incident diagnoses of exertional hyponatremia among active component service members from 2001 through 2016. 86.8 percent were diagnosed and treated without having to be hospitalized. 2016 represented a decrease of 23.3 percent from 2015. In 2016, there were 85 incident diagnoses of exertional hyponatremia among active component service members and 77.6 percent of exertional hyponatremia cases affected males.  The annual rate was higher among females. Service members age 40 and over were most affected by exertional hyponatremia. High risk service members of exertional hyponatremia were: •	Females •	Service members aged 19 years or younger •	White, non-Hispanic and Asian/ Pacific Islander service members •	Recruit Trainees •	Marine Corps members Learn more at www.Health.mil/MSMR

Exertional Hyponatremia occurs during or up to 24 hours after prolonged physical activity. It is defined by a serum, plasma or blood sodium concentration below 135 millequivalents per liter. This infographic provides an update on Exertional Hyponatremia among U.S. Armed Forces, information on service members at high risk. Exertional hyponatremia can result from loss of sodium and/or potassium as well as relative excess of body water.

Recommended Content:

Armed Forces Health Surveillance Branch | Physical Fitness

Minority Health Heat Illness Active Component U.S. Armed Forces, 2016

Infographic
4/4/2017
Heat illness refers to a spectrum of disorders that occur when the body is unable to dissipate heat absorbed from the external environment and the heat generated by internal metabolic processes. As heat illness progresses, failure of one or more body systems can occur. This report summarizes reportable medical events of heat illnesses, heat-related hospitalizations and ambulatory visits among minority active component members (Black, non-Hispanic, Hispanic, and Asian/Pacific Islanders) during 2016. In 2016, incidence rates of heat stroke were highest among Asian/ Pacific Islanders than any other ethnicity. Crude incidence rate of “other heat illnesses” was higher among females than males.  Heat Incidence cases: •	Black, non-Hispanic heat illness incidence cases – 64 for heatstroke and 389 for other heat illnesses •	Hispanic heat illness incidence cases—  63 for heatstroke and 320 for other heat illnesses •	Asian/ Pacific Islander heat illness incidence cases – 32 for heatstroke and for  117 other heat illnesses Incidence rates: •	Black, non-Hispanic incidence rates – 0.30 for heatstroke and 1.84 for other heat illnesses •	Hispanic incidence rates – 0.33 for heatstroke and 1.67 for other heat illnesses •	Asian/Pacific Islander – 0.62 for heatstroke and 2.26 for other heat illnesses Of all military members, the youngest and most inexperienced marines and soldiers – particularly those training at installations in the south eastern U.S. – are at highest risk of heat illnesses including heat stroke, exertional hyponatremia, and exertional rhabdomyolysis. Learn more at www.Health.mil/MSMR

Heat illness refers to a spectrum of disorders that occur when the body is unable to dissipate heat absorbed from the external environment and the heat generated by internal metabolic processes. As heat illness progresses, failure of one or more body systems can occur. This report summarizes reportable medical events of heat illnesses, heat-related hospitalizations and ambulatory visits among minority active component members (Black, non-Hispanic, Hispanic, and Asian/Pacific Islanders) during 2016.

Recommended Content:

Armed Forces Health Surveillance Branch | Summer Safety

Global Influenza Summary: April 2, 2017

Report
4/2/2017

Recommended Content:

Health Readiness | Armed Forces Health Surveillance Branch | AFHSB Reports and Publications | Influenza Summary and Reports

Heat Illnesses by Location, Active Component, U.S. Armed Forces, 2012-2016 Fact Sheet

Fact Sheet
3/30/2017

This fact sheet provides details on heat illnesses by location during a five-year surveillance period from 2012 through 2016. 11,967 heat-related illnesses were diagnosed at more than 250 military installations and geographic locations worldwide. Three Army Installations accounted for close to one-third of all heat illnesses during the period.

Recommended Content:

Armed Forces Health Surveillance Branch | Medical Surveillance Monthly Report

Demographic and Military Traits of Service Members Diagnosed as Traumatic Brain Injury Cases

Fact Sheet
3/30/2017

This fact sheet provides details on the demographic and military traits of service members diagnosed as traumatic brain injury (TBI) cases during a 16-year surveillance period from 2001 through 2016, a total of 276,858 active component service members received first-time diagnoses of TBI - a structural alteration of the brain or physiological disruption of brain function caused by an external force.

Recommended Content:

Armed Forces Health Surveillance Branch | Medical Surveillance Monthly Report

Rhabdomyolysis by Location, Active Component, U.S. Armed Forces, 2012-2016 Fact Sheet

Fact Sheet
3/30/2017

This fact sheet provides details on Rhabdomyolysis by location for active component, U.S. Armed Forces during a five-year surveillance period from 2012 through 2016. The medical treatment facilities at nine installations diagnosed at least 50 cases each and, together approximately half (49.9%) of all diagnosed cases.

Recommended Content:

Armed Forces Health Surveillance Branch | Medical Surveillance Monthly Report

Routine Screening for Antibodies to Human Immunodeficiency Virus

Infographic
3/17/2017
The Human immunodeficiency virus type 1 (HIV-1) is the cause of Acquired immune deficiency syndrome (AIDS) and has had major impacts on the health of populations and on healthcare systems worldwide. This infographic provides an update on routine screening for antibodies to HIV among civilian applicants for the U.S. military service and U.S. Armed Forces during a January 2011 - June 2016 surveillance period.  Since October 1985, the U.S. military has conducted routine screening for antibodies to HIV-1 to enable adequate and timely medical evaluations, treatment and counseling; to prevent unwitting transmission; and protect the battlefield blood supply. From January 2015 through June 2016, 463,132 civilian applicants for U.S. military service were tested. 124 were identified as HIV antibody positive. During 2015, one was detected with antibodies to HIV per 3,267 screening tests. Annual seroprevalences peaked in 2015, up 29% from 2014. The seroprevalences were much higher among males than females and among black, non-Hispanics than other race/ethnicity groups. Seroprevalences decreased by approximately 26% among male applicants, dropped to zero among female applicants, and decreased by 43% among black, non-Hispanic applicants.  As for the active component of the U.S. Army, 548,974 soldiers were tested from January 2015 through June 2016. 120 were identified as HIV antibody positive. During 2015, one was detected with antibodies to HIV per 5,265 screening tests. Of the 515 active component soldiers diagnosed with HIV infections since 2011, a total of 291 (57%) were still in military service in 2016. Annual seroprevalences for male active component Army members greatly exceed those of females.  Among active and reserve component service members, seroprevalences continue to be higher among Army and Navy members and males than their respective counterparts. Service members who are infected with HIV receive clinical assessments, treatments, and counseling; they may remain in service as long as they are capable of performing their military duties. Learn more at Health.mil/AFHSB

The Human immunodeficiency virus type 1 (HIV-1) is the cause of Acquired immune deficiency syndrome (AIDS) and has had major impacts on the health of populations and on healthcare systems worldwide. This infographic provides an update on routine screening for antibodies to HIV among civilian applicants for the U.S. military service and U.S. Armed Forces during a January 2011 - June 2016 surveillance period.

Recommended Content:

Armed Forces Health Surveillance Branch | HIV/AIDS Prevention and Treatment
<< < ... 36 37 38 39 40  ... > >> 
Showing results 571 - 585 Page 39 of 42

DHA Address: 7700 Arlington Boulevard | Suite 5101 | Falls Church, VA | 22042-5101

Some documents are presented in Portable Document Format (PDF). A PDF reader is required for viewing. Download a PDF Reader or learn more about PDFs.