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...

5 Major Categories of Abdominal Hernia

Infographic
3/17/2017
An abdominal hernia is an abnormal protrusion of an organ or tissue through a defect in the abdominal wall. This infographic provides information on incident diagnoses of the five types of abdominal hernia that were documented in health records of 72,404 active component service members from 1 January 2005 through 31 December 2014.  A total of 87,480 incident diagnoses of the five types of abdominal hernia were documented in health records of 72,404 active component service members. Here are highlights of the findings from this study: •	The give types of abdominal hernia categories used in this analysis were: inguinal, umbilical ventral/ incisional, femoral and “other.” •	 During the 10-year interval, incidence rates for most of the five types of hernia trended downward but increased for umbilical hernias in both males and females and ventral/ incisional hernias among females. •	Overall incidence rate of inguinal hernias among males was six times the rate among females. •	Incidence rates of femoral, ventral/ incisional and umbilical hernias were higher among females than males. •	For most types of hernia incidence rates tend to be higher among older age groups.  Abdominal hernias are diagnosed most frequently in the inguinal, umbilical, and femoral regions, but another category of relatively common hernias of the anterior abdominal wall includes ventral and incisional hernias. Health records contained documentation for 35,624 surgical procedures whose description corresponded to the types of hernia diagnoses in U.S. military service members. Learn more about the findings of the study at Health.mil/MSMR

An abdominal hernia is an abnormal protrusion of an organ or tissue through a defect in the abdominal wall. This infographic provides information on incident diagnoses of the five types of abdominal hernia that were documented in health records of 72,404 active component service members from 1 January 2005 through 31 December 2014.

Recommended Content:

Armed Forces Health Surveillance Branch | Men's Health

Chlamydia Trachomatis Infections

Infographic
3/17/2017
This report characterizes the rates of Chlamydia Trachomatis (CT) during the pre-deployment, deployment, and post-deployment phases for active component members of the U.S. Army, Navy, Air Force and Marine Corps. The surveillance period was 2008 through 2015.  For incidence rates of laboratory-confirmed Chlamydia Trachomatis diagnoses, by deployment cycle and sex, active component, U.S. Armed Forces, 2008-2015, there were 84,783 cases for men and 54,867 cases for women. The surveillance period findings show: •	Rates of CT were highest during the pre-deployment phase for both sexes •	Males tended to have similar rates of CT across pre-, post-, and non-deployed phases •	Women had substantial rate differences between phases  The results of these analyses underscore the need for better screening and documentation of STIs during deployment to assess the true burden of disease. Learn more about rates of CT among U.S. Armed Forces by visiting Health.mil/MSMR

This report characterizes the rates of Chlamydia Trachomatis (CT) during the pre-deployment, deployment, and post-deployment phases for active component members of the U.S. Army, Navy, Air Force and Marine Corps. The surveillance period was 2008 through 2015.

Recommended Content:

Armed Forces Health Surveillance Branch

Diabetes Mellitus

Infographic
3/17/2017
Diabetes Mellitus (DM) is a group of chronic metabolic conditions characterized by high blood glucose levels resulting from a decreased ability to produce and or use insulin. DM-related metabolic abnormalities are associated with damage to various organs and tissues. From 2008 - 2015, a total of 9,092 incident cases of DM were reported among active duty service members. This infographic provides details on the overall incidence rates of type 1 and 2 DM cases per 100,000 person-years. It also provides information about service members at higher risk of diabetes. Here are some key findings from the study: •	Type 1 DM (previously known as “insulin-dependent diabetes”) overall incidence rate was 3.0 cases per 100,000 p-yrs. •	Type 2 DM ( “non-insulin-dependent diabetes) was 74.5 cases per 100,000 p-yrs. And rates doubled within each successive age group.  Service members at higher risk of diabetes are male, black, non-Hispanic, unknown race/ ethnicity, Hispanic and enlisted in the Army and Navy. Learn more by visiting Health.mil/AFHSB

Diabetes Mellitus (DM) is a group of chronic metabolic conditions characterized by high blood glucose levels resulting from a decreased ability to produce and or use insulin. DM-related metabolic abnormalities are associated with damage to various organs and tissues. From 2008 - 2015, a total of 9,092 incident cases of DM were reported among active duty service members. This infographic provides details on the overall incidence rates of type 1 and 2 DM cases per 100,000 person-years. It also provides information about service members at higher risk of diabetes.

Recommended Content:

Conditions and Treatments | Armed Forces Health Surveillance Branch

Leishmaniasis

Infographic
3/17/2017
Leishmaniasis is a zoonotic disease caused by protozoan parasites of the genus Leishmania that are transmitted to humans by the bites of infected female sand flies. The disease remains a military medical surveillance interest because of deployments to endemic areas of the Middle East. It is also endemic in many other regions including Africa, Mexico, Southern Europe, Asia, and South and Central America. This report provides an update on the frequencies, rates, and demographic characteristics of U.S. service members who were diagnosed/ reported with leishmaniasis while expanding analysis to include information on the location of acquisition of leishmaniasis infection during a 2001-2016 surveillance period. Here are key findings from the surveillance period: •	There were 2,040 incident diagnoses/ reports of leishmaniasis among members of the U.S. Armed Forces. •	Cutaneous Leishmaniasis accounted for 61.0% of total diagnoses/ reports among active duty service members. •	71.1% of the total leishmaniasis case were diagnosed or reported during the 7 months from early autumn to spring (September – March) in the northern hemisphere. •	The majority of cases diagnosed or reported during this 7-month interval were acquired in the Middle East, South/Central America and other or unknown locations.  Learn more information at Health.mil/MSMR

Leishmaniasis is a zoonotic disease caused by protozoan parasites of the genus Leishmania that are transmitted to humans by the bites of infected female sand flies. This report provides an update on the frequencies, rates, and demographic characteristics of U.S. service members who were diagnosed/ reported with leishmaniasis while expanding analysis to include information on the location of acquisition of leishmaniasis infection during a 2001-2016 surveillance period.

Recommended Content:

Armed Forces Health Surveillance Branch

Global Influenza Summary: March 12, 2017

Report
3/12/2017

Recommended Content:

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

Global Influenza Summary: March 5, 2017

Report
3/5/2017

Recommended Content:

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

March 10 is National Women & Girls HIV/AIDS Awareness Day

Infographic
3/3/2017
This graphic shows the results of routine screening for antibodies to Human Immunodeficiency Virus (HIV) among both female civilian applicants for U.S. military service and female service members of the U.S. Armed Forces, active component - Army during  January 2015 through June 2016 surveillance period. 94,763 females out of 463,132 civilian applicants for U.S. military service were tested for antibodies to HIV. Out of 124 civilian applicants that were HIV positive, 10 were female. Throughout the period, seroprevalences were much higher among males than females.  During 2015 – 2016 seroprevalences dropped to zero among female applicants.  As for U.S. Armed Forces active component, 81,963 female service members out of 548,974 were tested for antibodies to HIV. Out of 120 soldiers that were HIV positive 3 were female. Annual seroprevalences for male active component Army members greatly exceed those of females. During the 2015, on average, one new HIV infection was detected among active duty army soldiers per 5,265 screening tests.  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. Of 515 active component soldiers diagnosed with HIV infections since 2011, a total of 291 (57%) were still in the military. Get tested and learn more by reading the Medical Surveillance Monthly Report at Health.Mil/MSMR.

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 information on routine screening for antibodies to HIV among female civilian applicants of the U.S. Military Service and U.S. Armed Forces, January 2011 – June 2016.

Recommended Content:

Armed Forces Health Surveillance Branch | HIV/AIDS Prevention and Treatment

Counts, Rates, & Trends of Incedent Diagnoses of Melanoma

Infographic
3/3/2017
Melanoma is a leading cause of cancer death. This graphic shows facts from an analysis for counts, rates, and trends of incident diagnoses of Melanoma among active component military members conducted during a 10-year surveillance period from 2005 through 2014.   Although melanoma is more common among males in the general U.S. population, in this analysis, females had a higher crude rate of malignant melanoma compared to males. From 2005 – 2014, there were 1,571 malignant melanoma cancers diagnosed in the U.S. Armed Forces. Here are other key facts from the analysis: •	Among male service members, malignant melanoma was one of the most frequent cancer diagnoses after testicular cancer. •	Among females, malignant melanoma was the 2nd most frequent cancer diagnoses after breast cancer. •	White, non-Hispanic service members had a much higher crude rate of malignant melanoma relative to their counterparts in other race/ ethnicity groups. •	In general, the strongest demographic correlate of increased risk of cancer diagnosis was older age. To learn more information, visit Health.mil/AFHSB

Melanoma is a leading cause of cancer death. This infographic provides information on an analysis for the counts, rates, and trends of incident diagnoses of melanoma among active component military members. The analysis was conducted during a 10-year surveillance period from 2005 through 2014.

Recommended Content:

Armed Forces Health Surveillance Branch

Global Influenza Summary: February 12, 2017

Report
2/12/2017

Recommended Content:

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

Global Influenza Summary: February 5, 2017

Report
2/5/2017

Recommended Content:

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

Cold injuries among active duty U.S. service members drop to lowest level since winter 2011–2012

Article
1/23/2017
U.S. service members often perform duties in cold weather climates where they may be exposed to frigid conditions and possible injury.

Cold injuries among active duty U.S. service members drop to the lowest level since winter 2011-2012, according to a study published in Defense Health Agency’s Armed Forces Health Surveillance Branch (AFHSB) peer-reviewed journal, the Medical Surveillance Monthly Report.

Recommended Content:

Armed Forces Health Surveillance Branch | Epidemiology and Analysis | Medical Surveillance Monthly Report | Winter Safety

Global Influenza Summary: January 22, 2017

Report
1/22/2017

Recommended Content:

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

Human Physiologic Responses to Cold Exposure

Infographic
1/9/2017
Human Physiologic responses to cold exposure preserve core body temperature, but those responses may not be sufficient to prevent hypothermia if heat loss is prolonged. This infographic offers helpful information on preserving core body temperature to counter the threat from cold environments. Physiologic responses include: •	Constriction of the peripheral (superficial) vascular system – may result in non-freezing injuries or hasten the onset of actual freezing of tissues (frostbite) •	Minimizing loss of body heat •	Protecting superficial tissues Protection includes:	 •	Nutrition •	Shelter •	Physical Activity •	Protective Clothing Learn more about preserving core body temperature by reading the Medical Surveillance Monthly Report at www.Health.mil/AFHSB

Human Physiologic responses to cold exposure preserve core body temperature, but those responses may not be sufficient to prevent hypothermia if heat loss is prolonged. This infographic offers helpful information on preserving core body temperature to counter the threat from cold environments.

Recommended Content:

Winter Safety | Armed Forces Health Surveillance Branch

Global Influenza Summary: January 1, 2017

Report
1/1/2017

Recommended Content:

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

Rift Valley Fever Virus Ecology

Infographic
12/5/2016
This infographic describes Rift Valley Fever (RVF) virus ecology and how RVF infects livestock and humans.   •	First the enzootic cycle begins. It is maintained via transfer from parent mosquito to offspring. This is a local, low-level transfer of disease to livestock and happens during periods of average rainfall. •	Next, high rainfall and flooding enable Aedes mosquito breeding environments to flourish. This is followed by epizootic outbreaks, which cause abortion storms in animals, with > 90% mortality in newborns and 10-20% mortality in adults. Secondary vectors, including other mosquito genera such as Culex, can pass on the virus to humans and animals.  Spillover to humans includes exposure to blood and tissue of infected livestock and occurs during slaughter or birthing activities. Humans can also be infected with RVF via bites of infected mosquitos.

This infographic describes Rift Valley Fever (RVF) virus ecology and how RVF infects livestock and humans.

Recommended Content:

Armed Forces Health Surveillance Branch | Mosquito-Borne Illnesses
<< < ... 36 37 38 39 40  ... > >> 
Showing results 586 - 600 Page 40 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.