Johns Hopkins APL and Armed Forces Health Surveillance Center Release Open Source Electronic Disease Surveillance Software

For Immediate Release

July 1, 2013

 

Media Contact:

Gina Ellrich (240) 228-7796 or (443) 778-7796

gina.ellrich@jhuapl.edu

 

Judith Evans

(301)319-2255 or (301) 222-7905

Judith.l.evans8.ctr@mail.mil

 

Tools now available for customization, analysis and widespread distribution

 

The Johns Hopkins University Applied Physics Laboratory (APL) and the Armed Forces Health

Surveillance Center (AFHSC) have released the Suite for Automated Global Electronic bioSurveillance (SAGES), a collection of flexible, open -source software products developed for electronic disease surveillance in all settings.

 

Public health officials around the world, especially those with limited capabilities or resources to

meet World Health OrganizationInternational Health Regulations requirements for outbreak surveillance and reporting, can use a SAGES system that is both effective and secure

(http://www.jhuapl.edu/sages/).

Through this initial open source code release, users can download and customize the various software to fit their needs, as well as contribute to the continued development of SAGES.

 

Developed by APL in collaboration with the Global Emerging Infections Surveillance and Response

System (GEIS), a division of AFHSC, the free software suite is designed to collect, analyze, visualize and share information within a national disease surveillance system. Individual SAGES tools may be used to complement existing disease surveillance systems, or used all together to create an end - to - end disease surveillance capability.  

 

“Having the ability to quickly detect disease cases is critical for global health security,” says U.S.

Public Health Service Lt. Cmdr. Christopher Perdue, the GEIS project manager. SAGES analysis and visualization tools are modeled after the successful U.S. civilian and military surveillance systems known as the Electronic Surveillance System for the Early Notification of Community-

based Epidemics (ESSENCE), developed more than a decade ago by APL and the U.S. Department of Defense.

 

SAGES-based systems can use any combination of radios, simple cell phones, Android-based

smartphones, tablets, and computers to collect data. In Central and South America, Southeast Asia, and Africa, public health collaborators have used SAGES tools to develop sustainable, customized electronic disease surveillance systems and provide vital end-user feedback to APL during development. “Resource-limited countries have traditionally lagged behind the information technology revolution in public health because of the challenges they face with IT infrastructure, resources and cost of proprietary software,” says Sheri Lewis, APL’s Global Disease Surveillance program manager. “SAGES is designed to fit the needs of the local environment and uses the existing infrastructure and technology available, requiring minimal investment.”

 

Those who modify the computer code may share their innovations with other users. APL and GEIS

will continue to monitor the SAGES website and update the downloadable version as new components are tested and validated. “SAGES will promote fast and effective public health responses, and we want users to be involved in its ongoing development,” says Perdue. “We have designed it to be highly adaptable and easily sustainable, while allowing each national authority to maintain control over its own data systems.”

 

 

 

 

The Applied Physics Laboratory, a not-for-profit division of The Johns Hopkins University, meets criticalnational challenges through the innovative application of science and technology. For more information, visit www.jhuapl.edu

.

The AFHSC provides timely, relevant, actionable and comprehensive health surveillance information in order to promote, maintain and enhance the health of military and military-associated populations. For more information, visit www.afhsc.mil

http://afhsc.mil/viewDocument?file=AFHSC%20Sages%20Press%20Release.pdf

 

 

 

Press Conference: Audio File - WHO update on Middle East respiratory syndrome coronavirus (MERS-CoV) Dr. Keiji Fukuda, Assistant Director- General, Health Security &Environment, WHO

Download - Press Conferences (audio)
5 July 2013
WHO update on Middle East respiratory syndrome coronavirus (MERS-CoV)
Dr. Keiji Fukuda, Assistant Director- General, Health Security and Environment, WHO 

ftp://unis-ftp.unog.ch/PCWHO20130705.mp3

CDC: Interim Guidance on Case Definitions to be Used For Investigations of Influenza A (H3N2)v Virus Cases

[This will be filed on the right side-bar under H3N2v Information List for future reference]

Posted on July 3, 2013

This document provides updated interim guidance for state and local health departments conducting investigations of infections with influenza A (H3N2) variant (H3N2v) viruses. Influenza viruses that typically infect swine are referred to as “variant” when they infect humans. The following definitions are for the purpose of investigations of confirmed cases and cases of influenza A (H3N2)v virus infection under investigation. CDC is requesting notification of all confirmed cases of influenza A (H3N2)v virus infection within 24 hours of identification. When possible, state health departments are encouraged to investigate all potential cases of influenza A (H3N2)v virus infection further to determine case status.

Case Definitions for Infection with Influenza A (H3N2)v Virus

Confirmed: Influenza A (H3N2)v virus infection in a patient with laboratory confirmation by:

• Reverse-transcription polymerase chain reaction (RT-PCR) testing or genetic sequencing results positive for influenza A (H3N2)v virus at the CDC Influenza Division Laboratory

OR

• RT-PCR testing results at a public health laboratory consistent with influenza A (H3N2)v virus using a CDC-approved assay (for example, InfA, H3, and pdmInfA positive results, and H1 and pdmH1 negative results using the CDC Flu rRT-PCR Dx Panel)¹. Please see Interim Guidance on Specimen Collection, Processing, and Testing for Patients with Suspect Influenza A (H3N2)v Virus Infection for additional guidance on testing for H3N2v viruses.

Continued:  http://www.cdc.gov/flu/swineflu/case-definitions.htm

CDC: Interim Guidance for Enhanced Influenza Surveillance: Additional Specimen Collection for Detection of Influenza A (H3N2) Variant Virus Infections

[This has been posted on the right side-bar, under H3N2v Information list for future reference]

Posted on July 3, 2013

Summary

This document is an update to interim enhanced surveillance guidance posted in 2012. In anticipation of the 2013 agricultural fair season, states should consider expanding surveillance to include reverse-transcription polymerase chain reaction (RT-PCR) testing of specimens from ILINet providers statewide, of specimens collected from people with ILI reporting recent swine contact or agricultural fair attendance, and of specimens collected from people with unusual or severe presentations of ILI. States should also consider collection of specimens from outbreaks of ILI among children in child-care and school settings, since these settings have been associated with person-to-person H3N2v virus transmission in 2011. CDC will continue to evaluate new information as it becomes available and will update this guidance as needed.

Continued:  http://www.cdc.gov/flu/swineflu/h3n2v-surveillance.htm

WHO sets up emergency committee on #MERS virus

hat-tip @makoto_au_japon

GENEVA, July 5 | Fri Jul 5, 2013 4:26pm IST

(Reuters) - The World Health Organization is forming an emergency committee of international experts to prepare for a possible worsening of the Middle East coronavirus, which has killed 40 people, WHO flu expert Keiji Fukuda said on Friday.

Fukuda said there was currently no emergency or pandemic but the experts would advise on how to tackle the disease if the number of cases suddenly grows.

"We want to make sure we can move as quickly as possible if we need to," Fukuda told a news conference in Geneva. (Reporting by Tom Miles; Editing by Kevin Liffey)

 http://in.reuters.com/article/2013/07/05/health-coronavirus-emergency-committee-u-idINL5N0FB1EQ20130705

WHO: Human infection with avian influenza A(H7N9) virus – update July 3, 2013

4 July 2013 - The National Health and Family Planning Commission, China notified WHO of an additional retrospectively detected laboratory-confirmed case of human infection with avian influenza A(H7N9) virus.

The patient is a 15-year-old boy reported from Jiangsu who became ill on 25 April 2013 and hospitalized on 26 April 2013. He recovered and was discharged on 2 May 2013. The results of molecular diagnostics were positive for H3N2 seasonal influenza virus and H7N9 avian influenza virus. On 1 July, Jiangsu Provincial Health Department consulted national and provincial experts for diagnosis.

To date, WHO has been informed of a total of 133 laboratory-confirmed cases, including 43 deaths.

continued:  http://www.who.int/csr/don/2013_07_04/en/index.html

Chile: #H1N1 Outbreak Kills at least 11, Health Minister to travel there today, Cancelling Fiesta de la Tirana...

July 5, 2013

SANTIAGO – At least 11 people have been killed in an outbreak of H1N1 flu virus in northern Chile, where the rate of infection is more than six times higher than the rest of the country, authorities said Thursday.

“The average across the country is 24 patients per 100,000 residents, but in Tarapaca, in the past week, the rate was 148 patients per 100,000 residents,” Medical Association president Enrique Paris said.

Citing fears of aggravating the outbreak, Paris recommended postponing or cancelling the upcoming Fiesta de la Tirana, a religious celebration planned for July 15-17 where 200,000 people are expected.

Meanwhile, Health Minister Jaime Manalich announced he will travel Friday to the region 1,900 kilometers (1,180 miles) north of Santiago near the border with Bolivia.

The minister also said some 115,000 vaccines will be sent to immunize the population, which numbers around 300,000.

http://newsinfo.inquirer.net/438895/h1n1-flu-outbreak-in-northern-chile-kills-11

MERS virus doesn’t yet have pandemic potential, but that could change: study

Helen Branswell
July 4, 2013

TORONTO – The new MERS coronavirus currently doesn’t spread well enough among people to trigger a pandemic, says a new study that calculates the rate at which the virus is transmitting person to person.

But the senior author says the pattern of how the virus is spreading now cannot be used to predict whether MERS will become a bigger threat in the future.
“There is absolutely no guarantee that this virus will stay as it is. It could very well follow the same path as SARS did 10 years ago,” Dr. Arnaud Fontanet, who heads the emerging diseases epidemiology unit at the Institut Pasteur in Paris, said in an interview.

Others too say the study should not be used to write off the new virus.

“The virus has shown a potential for human-to-human transmission. And whether such transmission is sustained depends on the intensity of control measures as well as the characteristics of the people involved in transmission,” said Marc Lipsitch, an infectious diseases specialist who teaches at Harvard University.
“For that reason, I think it’s premature to say that this virus does not present a pandemic threat.”

  -snip-

Using the publicly available data on MERS cases, Fontanet and his co-authors set out to figure out what the basic reproduction number for the new coronavirus has been to date.

There are many holes in the available data. For instance, Saudi Arabia, which is responsible for 63 of the 77 confirmed MERS cases, often does not disclose if new infections have links to previous ones – which might mean they caught the virus from another person – or are what are called sporadic cases, people thought to have been infected by an animal or exposure to the virus in the environment.
The authors tried to work around the gaps by calculating best- and worst-case scenarios. Both, it turns out, came up with a reproductive number of less than one, which suggests the virus doesn’t yet have pandemic potential, they said. Those rates were 0.60 and 0.69 respectively.

Complete article:  http://globalnews.ca/news/694212/mers-virus-doesnt-yet-have-pandemic-potential-but-that-could-change-study/

#H1N1 Vietnam Case List 2013

Vietnam H1N1 2013

Name—From—Adm--Condition

46M—Yen Bai—3/28—DOD: 3/30

27(M)—Yen Binh Dist., Yen Bai—4/14—DOD: 4/18

12(F)—Thanh Hoe—DOD 4/23

72M--HCMC Dist. 11—Cho Ray Hosp--DOD early May

56M—Hau Giang—April—DOD 5/21

61M—An Long, Dist. Tam Nong, Dong Thap-Cho Ray Hosp--DOD 6/3

3yo—Dong Thap—Childrens Hosp HCMC—contact of 61M--recovered 

24F—HCMC Dist. 9—6/1 Cho Ray Hosp-- DOD 6/5

49M—HCMC Dist. 3—5/24 Gia Dinh Hosp HCMC--DOD 6/3 

48M—Ben Tre—6/9—DOD 6/12

Nurse—Ben Tre—6/?—Stable

47F—My Thanh, Ben Tre—6/2—DOD 6/12

50M—HCMC Dist. 3—Nhan Gia Dinh Hosp.

Justice Dept Empl.—Tien Giang—6/3—discharged 6/21

Justice Dept Empl—Tien Giang—6/3—discharged 6/21

Justice Dept Empl—Tien Giang—6/3—discharged 6/21

Justice Dept Empl—Tien Giang—6/3—discharged 6/21

Woman—Mang Thit Dist, Long Tan Comm.,Vinh Long—6/15—DOD 6/17

55—Ward 8, Vinh Long—Gia Dinh Hosp—DOD 6/14

69(M)—Nguyen Phich, U Minh, Ca Mau—5/21

no name—Hoa Hiep, H. Tam Binh Vinh Long—6/21—

no name—Hoa Hiep, H. Tam Binh Vinh Long—6/21

30(M)—Binh Thanh Dist , HCMC—6/23

Le Hoang Be—Ca Mau—6/19—Pham Ngoc Thach Hospital

67M—U Minh, Ca Mau--6/26—U Minh Hospital

30F—Cai Doi Vam, H.Phu, Ca Mau—6/27—

58M-- Vĩnh Viễn, Hau Giang Prov.—6/18—DOD 6/27

30M-- Đầm Dơi (Cà Mau)

Detailed Listing:

Yen Bai Province

Name:  46(M)

From:  Yen Bai

Adm:   3/28  Central Hosp. for Tropical Diseases [was transferred]

Sym’s on adm: severe respiratory distress

Note: 7 days cough fever, 4 more days difficult to breath, sought dr.  No comorbidities.

DOD:  3/30

Yen Bai Province

Name:  27(M)

From:  Yen Binh dist., Yen Bai Province

Adm:  4/14 Bach Mai Hospital

Sym’s on adm.: respiratory failure, hypoxemia have ventilation, coagulopathy, multiple organ failure.

DOD:  4/18

Thanh Hoe Province

Name:  12(F)

From:  Thanh Hoe Province

DOD:  4/23

Ho Chi Minh City

Name:  72(M)

From:  HCMC – District 11

Adm:  Cho Ray Hospital

Sym’s on Adm:  Breathlessness

DOD:  Early May

Ha Giang Province

Name:  56(M)

From:  Lung Sinh, Lam Commune, Xuyen Dist. Ha Giang Province

DOD:  5/21

Hau Giang Province

Name:  56(M)

From:  Hau Giang Province

Adm:  April

DOD:  4/21

Dong Thap Province

Name:  Ly Kim Sen (61M)

From:  An Long, Tam Nong District, Dong Thap, Farmer

Adm:  6/1  Cho Ray Hospital

Adm:  5/24 Dong Thap General Hospital

Sym’s on Adm:  Abdominal pain, cough fever, shortness of breath

Note:  patient sellf-medicated, condition worsened.  According to relatives, infected with duck meat cooked.

DOD:  6/1 a few hours after admission

Dong Thap Province

Name:  Hiện 3yo (contact of 61M above)

From:  Tam Nong District, Dong Thap

Adm:  Children’s Hospital 1,  HCMC

Note:  Granddaughter of Ly Kim Sen (61M) above. 

Confirmed:  Positive, PCR Test

Ho Chi Minh City

Name:  Le Thi Cam Van  (24F)

From:  HCMC – District 9 (worked)

From:  Native of Kom Tum Province.

Adm:   6/1 Cho Ray Hospital

Syms on Adm:  respiratory failure

Adm:   5/31 Tu Du Obstetric Hospital, delivered baby, lived.

Note:  Husband had flu 3 days prior to onset of wife.  She worked at TPHCM (Tech Park, HCM)

DOD:  6/5

Ho Chi Minh City

Name:  Nguyen Xuan Thien  (49M)

From:  HCMC – District 3

Adm:  5/24 Nhan Gia Dinh People’s Hospital

Sym’s on Adm:  fever, diarrhea, entered gastroenterology

DOD:  6/3

Ben Tre Province

Name:  Nurse

From:  Ben Tre. Province

Onset:  5/28

Adm:  Cho Ray Hospital, Saigon

Confirmed:  Positive.

Note:  Out of danger. Worked at Gen. Hosp. Binh Dai district

Ben Tre Province

Name:  Phan (47F)

From:  Thuan An Village, Mỹ Thạnh An

 Commune, Ben Tre City.  Ben Tre Province

Onset:  6/2

Adm:  Trans. to Pham Ngoc Thach Hosp, HCMC

Adm:  6/10 Cho Ray Hospital, HCMC

Note:  Sold Rice.

DOD:  6/12

Ho Chi Minh City

Name:  50M

From:  HCMC – District 3

Adm:  Nhan Gia Dinh People’s Hospital

Sym’s on adm:  Breathless, lung damage

Tien Giang Province

Name:  Employee Justice Department

From:  Tien Giang

Onset:  5/31

Adm:  6/3:  L'Hôpital Français de Hanoi, HCMC

Note:  Tested positive.  Stable condition

Note:  Discharged 6/21

Tien Giang Province

Name:  employees Justice Department

From:  Tien Giang

Onset:  6/6 Headache, dizziness.  Private Treatment.

Adm:  6/8 French Hospital HCMC.

Note:  Discharged 6/21

Vinh Long Province

Name: Phan Thị Lài

From:  Mang Thit District, Long Tan Commune, Vinh Long Prov.

Onset:  6/11

Adm:  6/15

Note:  Bought chicken at market in commune on 6/8.

DOD:  6/17

Tien Giang Province

Name:  employees Justice Department

From:  Tien Giang

Adm:  No.  Monitored only at Tien Giang Gen. Hosp.

Note:  Discharged 6/21

Tien Giang Province

Name:  employee Justice Department

From:  Tien Giang

Adm:  No.  Monitored only at Tien Giang General Hosp.

Note:  Discharged 6/21

Vinh Long Province

Name:  55yo

From:  16B Dinh Tien Hoang St., Ward 8, Vinh Long

Adm:  Gia Dinh Hospital, Vinh Long

Note:  Was in Cancer Treatment 12.6 days (12 ½).  Showed signs of illness and went to Gia Dinh Hospital.

DOD:  6/14

Ca Mau Province

Name:  69M

From: Nguyễn Phích, huyện U Minh, Ca Mau

Adm:  5/21

Sym’s:  breathless

Conf.  Positive

Vinh Long Province

Name:  Reported on 6/24/13 

From: Thuận, H.Vũng Liêm và xã Hòa Hiệp, H.Tam Bình Vĩnh Long province

Adm:  6/21 Vinh Long Hospital

Sym’s on Adm: high fever, sore throat, nasal pharynx. 

Note:  X-ray normal.  Treated w/tamiflu.  Pay special attention to patients receiving treatment Hoa Hiep Commune in HCMC Tropical Hospital.

Good Condition.

Confirmation:  Positive 6/24.  Recovered.  Discharged 3/7/13.

  

Vinh Long Province

Name:  Reported on 6/24/13

From: Thuận, H.Vũng Liêm và xã Hòa Hiệp, H.Tam Bình Vĩnh Long province

Adm:  6/21 Vinh Long Hospital

Sym’s on Adm: high fever, sore throat, nasal pharynx. 

Note:  X-ray normal.  Treated w/tamiflu.  Pay special attention to patients receiving treatment Hoa Hiep Commune in HCMC Tropical Hospital.

Confirmation:  Positive 6/24.  Recovered.  Discharged 7/3/13.

Ho Chi Minh City

Name:  30(M)

From:  Binh Thanh District, HCMC

Adm:  6/23 Nhan Dan Gia Dinh Hosp.

Sym’s at hosp: high fever, breathless

Adm:  6/26 Tropical Disease Hospital

Sym’s at adm: respiratory failure, serious pneumonia

Note:  hepatitus C

Ca Mau Province

Name:  Lê Hoàng Bé,  Dir. of Interior

From:  Ca Mau

Onset:  6/18, while traveling in Ha Noi

Adm:  6/19 Gen. Hosp. Cau Mau, Trans. to HCMC

Adm:  6/26 trans. to Pham Ngoc Thach Hosp (HCMC)

Syms on 6/26: high fever, shortness breath

Confirmed:  6/27

Ca Mau Province

Name:  67(F) Lương Văn Đua

From:  Nguyen Phich Commune, U Minh District, Ca Mau

Adm:  6/19 U Minh Hospital

Note:  10 days of treatment, recovered.  discharged.

Ca Mau Province

Name:  30(F) Trần Thị Mùa

From:  Cái Đôi Vàm town,  Phu Tan District, Ca Mau

Onset:  6/24

Adm:  6/27  Cai Nuoc Hospital

Sym’s on adm:  shortness of breath, fever, cough

Hau Giang Province

Name:  Ly Van Thanh (55/58)M

From: Vĩnh Viễn, Hau Giang Province

Adm:  6/18 Private Hospitals, fever, cough

Adm:  6/24 Hospital Long My district

Adm:  6/26 Military Hospital 121, Can Tho City

DOD:  6/27

Ca Mau Province

Name: 30(M) Trần Hoàng Thám

From: Bến Bàu, xã Quách Phẩm Bắc, H. Đầm Dơi Dist., Ca Mau

Adm:  4/7

#H7N9 Flu Virus’ Ability to Replicate Deep in Lung Triggers Dangerous Immune Response

[This article is much easier to understand, than the one I posted out of China.]

by Kathy Jones on  July 04, 2013

Editing is mine - Excerpt:
A new study revealed that the H7N9 bird flu virus has the ability to replicate deep in the lungs from where it can trigger a dangerous response from the immune system.

In addition, no one is likely to have pre-existing immunity to H7N9 and so-called seasonal vaccines cannot protect against it, the study said, confirming suspicions among many virologists. 

And while lab tests show that leading anti-flu drugs are effective, there are concerns the virus may acquire gene mutations to blunt these weapons, it added. 

The study, published in Nature by the Chinese Centre for Disease Control and Prevention (CDC) in Beijing, delved into the genetic ID of the virus which emerged in China in February. 

The virus has been characterised by severe symptoms of pneumonia and respiratory distress, with a high fatality rate, especially among the elderly. 
-snip-

The paper said "the first epidemic has subsided" but a potent threat remains. 

"Together with the challenges in the available treatments for H7N9 infection caused by its clinical severity and emerging antiviral resistance, further unpredictable evolution and adaptation of the H7N9 virus and the lack of pre-existing immunity leave the human population at high risk," it said. 

"The threats of the H7N9 virus with pandemic potential should not be underestimated and intensive surveillance must be undertaken." 

H7N9 kills more than a third of hospitalised patients, The Lancet reported last month. 



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