HEPATITIS A: PULLING A MOLECULAR RABBIT FROM SAN DIEGOS HAT Tracy - PDF document

6/28/2019 1 HEPATITIS A: PULLING A MOLECULAR RABBIT FROM SAN DIEGO’S HAT Tracy Basler June 28, 2019 PUBLIC HEALTH SERVICES 1

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A OBJECTIVES  Participants will be able to:  Describe the strategies and tactics used by San Diego County to combat the Hepatitis A outbreak.  Discuss how Next Generation Sequencing (NGS) technologies aided in characterizing the Hepatitis A virus outbreak and provided cluster detection. SAN DIEGO COUNTY – HEPATITIS A SAN DIEGO COUNTY IS… 2

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A SAN DIEGO HAS…  3.3 million residents  18 federally recognized Indian reservations  16 naval and military installations  18 municipalities; 36 unincorporated towns  42 school districts  21 hospitals SAN DIEGO COUNTY – HEPATITIS A OUTLINE  Hepatitis A Background  Hepatitis A in San Diego  Public Health Response  Laboratory Response 3

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A  Hepatitis A Background  Hepatitis A in San Diego  Public Health Response  Laboratory Response SAN DIEGO COUNTY – HEPATITIS A OVERVIEW  Hepatitis A can be easily spread from person to person Can cause liver disease lasting a few weeks to a  serious illness lasting several months  Can cause death in some cases  Average incubation period for the Hepatitis A virus is 28 days ( range:15-50 days) Hepatitis A virus can live outside the body for  months, depending on the environmental conditions 4

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A WHAT ARE THE SYMPTOMS OF HEPATITIS A? SAN DIEGO COUNTY – HEPATITIS A WHO IS AT RISK FOR HEPATITIS A?  Travelers to certain countries  Men who have sex with men  Injection and non-injection drug users  Persons with clotting factor disorders  Persons with chronic liver disease  Persons experiencing homelessness &/or those with unstable living conditions  Household members, and other close personal contacts with high or intermediate Hepatitis A occurrences  Persons with close ongoing contact with persons experiencing homelessness and/or illicit drug users or their environment via employment or volunteer activities (during this outbreak) 5

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A  Hepatitis A Background  Hepatitis A in San Diego  Public Health Response  Laboratory Response SAN DIEGO COUNTY – HEPATITIS A  Reportable in California within one working day of identification by laboratory & provider (CCR Title 17 Sections 2500, 2505)  Surveillance noted increase in cases above baseline in early March 2017  11/16 to 2/17: 7- 9 cases expected, 19 cases reported  Health alert on outbreak on March 10, 2017 6

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A  592 confirmed outbreak cases from 11/22/16 – 10/18/18  407 (68%) hospitalizations, 20 (3.4%) deaths  404 (68%) male (14 MSM), 188 (32%) female  Age range 5-87 (median 43.0)  Suspected Exposure Type  201 (34%) homeless and illicit drug use  91(15%) homeless only  79 (13%) illicit drug use only  167 (28%) neither  54 (9%) unknown Outbreak-associated Hepatitis A Cases by Onset Week San Diego County Residents, 11/1/2016 – 10/18/2018*, N = 592 40 9/1/17 Public Health Emergency Declared 35 Confirmed and Probable Cases Reported 30 3/8/17 10/13/17 State Outbreak Emergency 25 Determined Declared 1/23/18 Public Health Emergency 20 Undeclared 10/18/18 Outbreak Declared Over 15 10 5 0 11/6/16 12/4/16 1/1/17 1/29/17 2/26/17 3/26/17 4/23/17 5/21/17 6/18/17 7/16/17 8/13/17 9/10/17 10/8/17 11/5/17 12/3/17 12/31/17 1/28/18 2/25/18 3/25/18 4/22/18 5/20/18 6/24/18 7/22/18 8/19/18 9/16/18 10/14/18 | 2018 2016 | 2017 N = 571 N = 15 N = 6 Onset Week Data as of 10/18/18 7

6/28/2019 Hepatitis A Cases, San Diego County HEPATITIS A, SAN DIEGO 1994 – 2019* 700 Vaccine introduced 600 Routine vaccination for children in high‐incidence states (including California) 500 400 300 Routine vaccination for all U.S. children 200 100 0 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 . *Year to date as of 05/31/2019. New CSTE case definition effective 01/01/2019 may affect case numbers and trends. Prepared by County of San Diego, Health & Human Services Agency, Public Health Services, Epidemiology & Immunization Services, 05/31/2019 SAN DIEGO COUNTY – HEPATITIS A Rate of HAV Infection by Age, San Diego County 1996‐2019* 35 0‐14 years 30 15‐24 years 25 Rate per 100,000 25‐44 years 45‐64 years 20 65+ years 15 10 5 0 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 *2019 *Year to date as of 05/31/2019. New CSTE case definition effective 01/01/2019 may affect case numbers and trends. Prepared by County of San Diego, Health & Human Services Agency, Public Health Services, Epidemiology & Immunization Services, 05/31/2019 8

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A OUTBREAK SUMMARY n = 538 Cases (% of 592) Homelessness Dark urine 413 (70%) 17% Jaundice 394 (67%) Sex (male) 404 (68%) 37% Age (years) Minimum 5 Median 43 15% Maximum 87 Hospitalized 407 (69%) Illicit drug use Died 20 (3.4%) Data as of 10/18/18 SAN DIEGO COUNTY – HEPATITIS A  Hepatitis A Background  Hepatitis A in San Diego  Public Health Response  Laboratory Response  Summary 9

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A PUBLIC HEALTH INTERVENTIONS ~203,858 vaccinations ~85% targeting risk groups  Vaccinate - Handwashing  Sanitize/hygiene stations - Street sanitation - Hygiene kits - Food inspections  Educate - Presentations - Outreach - Posters - 2-1-1 San Diego Calls SAN DIEGO COUNTY – HEPATITIS A Mass Vaccination at St. Vincent de Paul 4/10/17 10

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A Mobile Vaccination in Rosecrans Parking Lot 5/15/17 with outreach workers from Family Health Centers San Diego SAN DIEGO COUNTY – HEPATITIS A “Foot team” in downtown San Diego 6/8/17 with volunteers from Friend to Friend, Episcopal Community Services Photo credit: County of San Diego 11

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A Source: COSD. Downloaded 10/19/18 from: https://www.sandiegocounty.gov/content/dam/sdc/hhsa/programs/phs/Epidemiology/HepA_ZipCodes.pdf SAN DIEGO COUNTY – HEPATITIS A Source: COSD. Downloaded 10/19/18 from: https://www.sandiegocounty.gov/content/dam/sdc/hhsa/programs/phs/Epidemiology/HepA_ZipCodes.pdf 12

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A PHS staff member with “Hepatitis A prevention kits” for distribution to raise awareness among homeless about hepatitis. They contain water, non-alcohol hand sanitizer, cleaning wipes, clinic location information, and plastic bags. SAN DIEGO COUNTY – HEPATITIS A Handwashing station being installed in downtown San Diego on 9/2 (Photo: San Diego Union Tribune) 13

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A City contractor cleaning a street in downtown San Diego on 9/11/2017 (Photo: San Diego Union Tribune) SAN DIEGO COUNTY – HEPATITIS A Photo of “tent city” set up in September 2017 by the City of San Diego January 2018 Photo credit: San Diego Union Tribune Interior photo of one of three homeless tents set up by the City of San Diego January 2018 Photo credit: San Diego Union Tribune 14

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A  Hepatitis A Background  Hepatitis A in San Diego  Public Health Response  Laboratory Response SAN DIEGO COUNTY – HEPATITIS A LABORATORY APPROACH  Phase 1  Acquire funding and equipment  Phase 2  Laboratory assay implementation  Phase 3  Analysis and Genotyping 15

6/28/2019 SAN DIEGO COUNTY – HEPATITIS A LABORATORY TIMELINE Phase 2 October 2017 August 2017 January March 2017 Begin testing 2018 Order MiSeq specimens in- First instrument Begin testing house by specimen and research specimens in- NAAT October 18, sent to CDC screening house for screening 2018 for methods to genotyping method. genotyping perform by NGS Outbreak by Sanger testing in- MiSeq method using Declared sequencing house Installed. GHOST Over May 2017 September 1, November January 23, 2017 2017 2018 Research sequencing Emergency Molecular Emergency methods to Outbreak scientist hired Declaration perform Declared by Ended testing in- San Diego house County Health Officer Phase 1 Phase 3 SAN DIEGO COUNTY – HEPATITIS A LABORATORY CHALLENGES  Staffing  Training  Capacity strained due to high volume  PCR screening of Zika specimens  Sequencing  Shipping specimens to the CDC and  Instrumentation California Department of Public Health (CDPH)- Viral and Rickettsial Disease  Purchasing NGS equipment Laboratory (VRDL)  IT and Bioinformatics  Implementing PCR screening assay  Software and networking approvals  Implementing NGS methods through County IT  Novice experience in bioinformatics 16