Situation Report #99 on Cholera in South Sudan As at 23:59 Hours, 15 December 2016

Situation Update Cholera outbreaks were confirmed in 9 (32%) of 28 states countrywide. The affected states include Imatong, Eastern Lakes, Jubek, Terekeka, Jonglei, Western Bieh, Northern Liech, Southern Liech; and Eastern Nile (Table 1 and Figure 1.0). Suspect cholera cases were reported in Mayendit, Panyijiar, and Ayod (Table 4). Cumulatively 133 (34.2 %) of the samples tested positive for Vibrio Cholerae inaba in the National Public Health Laboratory as of 15 December 2016 (Table 3). Jubek state has recorded 2,006 cholera cases including 27 deaths (CFR 1.35 %). No new cholera case was reported in Jubek State during week 48 of 2016 (Table 1 and Figure 1.1).

Active transmission is ongoing in Bentiu PoC where 118 new cases were reported in week 49 of 2016 (Annex 1). Ongoing transmission in the PoC is suspected to be associated with exposure to unsecured water reservoirs that are used for washing, bathing and swimming - largely in sectors 1, 2, and 3. The other factors include open defecation in the buffer zone around the water bodies; poor latrine use & poor inappropriate handing of child feces; and poor solid waste management.

Table 1: Summary of cholera cases reported in South Sudan as of 15 December 2016

New New Total cases Total Reporting New deaths Total facility Total Total cases admission discharges currently community Total cases Sites WK 49 deaths deaths discharged s WK 49 WK 49 admitted deaths

Jubek – - - - - 8 19 27 1,979 2,006 Juba Jonglei- - - - - 5 3 8 84 92 Duk

Terekeka - - - - - 8 8 14 22

Eastern Lakes - - - - 2 1 3 4 345 351 Awerial Imatong ------1 1 28 29 Pageri Western Bieh - 2 7 - - 4 - 4 266 270 Fangak Northern Liech - 118 56 - 10 5 1 6 529 545 Rubkona Southern Liech - - - - - 1 - 1 41 42 Leer Eastern 5 168 Nile - Pigi 5 163

Total 120 63 - 12 29 35 64 3,449 3,525

In Southern Liech (Leer and Mayendit), the response is led by UNIDO although implementation of sustained and comprehensive investigation and response activities continues to be constrained by security concerns. In

1 Pigi, Eastern Nile state, transmission has been contained with the last four cases discharged from Kurwai PHCC on 15 November 2016. Cholera was confirmed in Pigi after two cases tested positive by culture on 2 November 2016. A least 163 cases including 6 deaths (5 health facility and one community) (CFR 2.98%) were reported since 10 October 2016. Health and WASH activities in Pigi are led by NHDF supported by WHO, UNICEF, and MSF-F.

Figure 1.0: Cholera incidence (cases per 10,000) and case fatality rate (%) as of 15 December 2016

World Health Organization Cholera Fatality Density Map for cases per population and CFR Weeks 24-49 2016

Map Date: 16 December, 2016 Manyo

Renk The boundaries and names shown and the designations used on this map do not imply ofcial endorsement or acceptance by the United Nations.

Sudan 0 50 100 200 Melut Kilometers Fashoda Maban Abyei Pariang Malakal Abiemnhom Baliet Aweil East Panyikang Aweil North Rubkona Fangak Guit Longochuk Twic Mayom Pigi Aweil West 1.10 2.98 1.48 Luakpiny/NasirMaiwut Aweil South Raga Gogrial East Koch Nyirol Ulang Aweil Centre Gogrial West Tonj North Leer Ayod Mayendit 2.38 Ethiopia Tonj East Duk Uror Akobo Jur River Rumbek NorthPanyijiar 8.7 Wau Twic East Pochalla Central African Republic Tonj SouthCueibetRumbek Centre Yirol East Rumbek East Nagero Bor South Yirol West Awerial Pibor Wulu Tambura 1.14 Mvolo Legend Terekeka xx Case fatality rate (CFR) 36.4 Counties with Cholera alert Mundri WestMundri East Lafon Kapoeta North Cases per 10,000 population Ezo Ibba Maridi Kapoeta East Juba 40.1 - 50 Yambio Nzara 1.35 20.1 - 40 Kapoeta South 10.1 - 20 Torit Budi Yei Lainya 5.1 - 10 Magwi Ikotos 0.1 - 5 Kajo-Keji 3.45 Kenya No case reported Morobo Pageri River Democratic Republic of Congo Uganda

Figure 1.1: New cholera cases admitted by location in week 48 of 2016

140 118 120 100 80 60 40 Number of Cases 20 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 Puluk Dongchak Kator Juba Rejaf Munuki Northern Nimule Terekeka New Fangak Old Fangak Toch Thonyor Yang Bentiu PoC Bentiu Town Piliny Bari

Eastern Jonglei Jubek Imatong Terekeka Western Bieh Southern Liech Northern Liech Lakes

In Eastern Lakes state, cholera cases were reported in Mingkaman IDP settlement. The initial cases were confirmed on 24 August 2016, after two of four samples tested postive for Vibrio cholerae Inaba. The cumulative cases are 351 cholera cases including 17 confirmed cases and 4 deaths (one facility and three community) (CFR 1.14 %). This outbreak has been controlled with only sporadic cases being reported – the most recent being admitted on 26 November 2016.

In Jonglei state, 92 suspected cholera cases including 8 deaths (CFR 8.7 %) were reported from Duk County involving mainly the three Islands of Kawer, Long, and Moldova. The index case was reported on 3rd July 2016 from Moldova Island. Of the five samples from Duk Islands that underwent culturing, one sample from Moldova

2 Island, also the most affected, was confirmed as cholera on 29 July 2016. The most recent cases reported in Duk originated from Koyom Island on 10 Nov 2016. No additional cases were reported since then. Figure 1.2: Cumulative cholera cases by payam of residence as at 15 December 2016

700 606 600 536

500 470

400 351 358 320 300 Number of Cases 210 219 200 167

90 100 42 22 37 25 7 1 1 3 2 4 2 1 15 1 1 5 1 1 7 1 1 2 15 1 0 Yang Toch Buko Rejaf Piliny Kator Puluk Lwoki Leer Padiat Paguir Lokiliri fangak kurwai Pageet Nimule Munuki Uganda Nyarjwa Thonyor Dhorbor Mareang Terekeka Mangalla Dongchak Kolanyang Juba Town Leer Town Gondokoro Bentiu PoC Old Fangak Bentiu Town New Fangak Northern Bari Eastern Imatong Jonglei Jubek Terekeka Western Bieh Northern Liech Southern Liech Eastern Nile Lakes

Terekeka state has reported 22 cases of cholera including 8 deaths (CFR 36.4%) with 2 samples confirmed by the laboratory to be cholera. All the deaths were reported at the onset of the outbreak from Islands on River Nile where access to health services is poor. No additional deaths occurred after the rapid response team was deployed. The most of the recent cases originated from Kuda village, Lwoki payam, Nyori county on 22 September 2016. No additional cases were reported since then.

In Nimule, Imatong state, a cumulative of 29 cholera cases including four laboratory confirmed cases and one death (CFR 3.45%) were reported from 15 August 2016.The afffected locations in Imatong state included Abila, Malakia, and Motoyo. The last cholera case in Nimule was admitted in Nimule hospital on 29 Sept 2016 and discharged on 2 Oct 2016. No additional cases were reported since then.

Table 1.1: Cholera cases and deaths by state and county as of 15 December 2016 Week 49 Weeks 24-49 Cases per Cases per Population New cases 10,000 10,000 State County at risk W49 population No. cases population CFR [%]

Northern Western Bieh Fangak 139,509 2 0.14 270 19.4 1.48 Southern Liech Rubkona 126,976 118 9.29 545 42.9 1.10 Liech Leer 67,167 0 - 42 6.3 2.38 Eastern Lakes Awerial 114,837 0 - 351 30.6 1.14 Imatong Pageri 215,130 0 - 29 1.3 3.45 Jonglei Duk 26,180 0 - 92 35.1 8.7 Jubek Juba 471,762 0 - 2,006 42.5 1.35 Terekeka Terekeka 177,849 0 - 22 1.2 36.4 Eastern Nile Pigi 125,496 0 - 168 13.4 2.98 Total 1,464,906 120 0.82 3,525 24.1 1.82

The cholera outbreak in Western Bieh state was confirmed on 22 September 2016 after two of four samples tested positive for Vibrio cholerae inaba. The initial cases were reported on 10 August 2016 in Old Fangak. The cumulative cases are 270 cholera cases including 13 confirmed cases and 4 deaths (4 facility and zero community) (CFR 1.48%). As of 15 December 2016, the affected areas included Old Fangak (217 cases); New Fangak (42 cases); Mareang (1 case); Paguir (1 cases); Toch (3 cases); and Kolanyang (1 case) (Figure 1.2). Three cases were reported from Old Fangak in week 48 of 2016.

In Northern Liech state, 545 cholera cases including 16 confirmed cases and three deaths (CFR 1.1%) were reported in Bentiu Town/PoC since 29 September 2016. The cholera taskforce, chaired by MoH and constituted by Health and WASH cluster partners is coordinating the response. The new cases in Bentiu are largely reported among children under two years and in individuals that arrived from Leer, Mayendit, Koch, Panyijiar, and Guit after the 2015 oral cholera vaccine campaign in Bentiu PoC. Over 90% of cholera cases in Bentiu PoC did not receive oral cholera vaccine (Annex 1). Ongoing transmission is suspected to be associated with exposure to unsecured water reservoirs that are used for washing, bathing and swimming.

In Southern Liech, two cholera cases originating from Leer Town tested positive for Vibrio cholerae Inaba on 11 October 2016. Cumulatively, 42 cholera cases were reported from Leer in Southern Liech state. Since 7 October 2016, at least 57 suspect cholera cases including three deaths were reported by UNIDO response team in Mayendit. The implementation of sustained and comprehensive response activities in Leer and Mayendit has been constrained by security concerns.

To improve access to timely rehydration, at least twenty of twenty-three (90%) oral rehydration points (ORPs) were set up and are submitting case line list data countrywide. Cholera cases were reported in seven special populations: Bentiu PoC, UN House PoC, Tongping UNMISS transit site, Gorom Refugee camp, Mahad IDPs, Mangatain IDPs, and among IDPs in Gumbo. The Tongping UNMISS transit site reported 50 cholera cases with one confirmed case and no death, while the UN House PoC has recorded 96 cholera cases with 6 confirmed cases and no death.

Cumulatively, 3,525 cholera cases including 64 deaths (29 facilities and 35 community) (CFR 1.82%) were reported in South Sudan involving 9 states since the initial case was reported on 18 June 2016 for Jubek state; 3rd July 2016 in Jonglei state; 14 July 2016 for Terekeka state, 15 August 2016 for Eastern Lakes and Imatong states; 10 August 2016 for Fangak in Western Bieh and state; 29 September 2016 for Rubkona in Northern Liech state; October 2016 for Leer in Southern Liech state; and 10 October 2016 for Pigi in Eastern Nile state (Figure 2.1 and Table 1.1).

As seen from Figure 2.1 there was a spike in cholera transmission in weeks 43-49 that was attributed to transmission in Bentiu PoC where most cases were <2 years of age and did not receive oral cholera vaccine.

Figure 2:1 Epidemic curve for cholera cases in South Sudan, from 18 June - 15 December 2016

350

21.1% 300 20%

250 16.9% 15% 200 316 316 150 10% CFR %

Number of cases 217 100 181 185 168 189 5% 3.3% 3.6% 50 35 2.8% 101 97 2.1% 1 1.9% 1.4% 1.6% 1.434% 1.6% 31 1.8% 1.7% 0.6% 0.9% 0.228% 22 12 28 1.180% 13 0.9% 0.9% 0 0.01% 0.0% 0.04% 0.4% 0.0% 0.0% 0.0% 5 1 0% 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Epidemiological week of onset Jonglei Jubek Terekeka Imatong Eastern Lakes Western Bieh Northern Liech CFR[%] Southern Liech Eastern Nile

Figure 3:1 Cholera case distribution by gender and age in Jubek State 15 December 2016

300 Cholera - age and sex distribution Jubek up to 15 Dec 2016 250

200 161 154 135 150 141 118 76 100 92 59 59 Number of Cases 110 48 50 81 100 80 107 102 39 46 58 64 35 16 22 0 21 10 17 104 138 57 3

Female Male

Out of the 2006 cholera cases in Jubek State, 851 (42.4%) were female, while 1155 (57.6%) were male

Figure 3:2 Cholera case distribution by gender and age in Jonglei State 15 December 2016 20 Cholera - age and sex distribution Jonglei up to 15 Dec 2016

10 10 1 12

Number of Cases 2 5 8 1 2 2 7 5 7 3 4 2 4 7 2 1 1 3 3 1 1 0 Under 2 3-5 6-10 11-15 16-20 21-25 26-30 31-35 36-40 41-45 46-50 51-55 56-60 61-65 66-70 70+ Adult Female Male

Data on Age missing for 11 cases

Out of the 92 cholera cases, in Jonglei State 40 (43.5 %) were female, while 52 (56.5%) were male

Figure 3:3 Cholera case distribution by gender and age in Eastern Lake State 15 December 2016

100 Cholera - age and sex distribution Eastern Lakes up to 15 Dec 2016 80

40 39 50 27 15 Number of Cases 9 12 20 13 17 7 6 7 17 23 30 14 20 15 9 14 31 1 34 0 Under 2 3-5 6-10 11-15 16-20 21-25 26-30 31-35 36-40 41-45 46-50 51-55 56-60

Female Male

Out of the 351 cholera cases, in Eastern Lake State 151 (43%) were female, while 200 (57 %) were male.

Figure 3:4 Cholera case distribution by gender and age in Western Bieh State 15 December 2016

60 Cholera - age and sex distribution Western Bieh up to 15 Dec 2016 50 40 29 30 9 10 5 5 20 11 5 Number of Cases 10 22 24 22 23 5 24 14 8 12 2 10 0 6 0 0 4 5 1 21 1 21 3 1

Female Male

Out of the 268 cholera cases, in Western Bieh State 174 (65 %) were female, while 94 (35 %) were male.

Figure 3:5 Cholera case distribution by gender and age in Southern Liech State 15 December 2016

12 Cholera - age and sex distribution Southern Liech up to 15 Dec 2016 10

8 2 6 2 4

Number of Cases 8 2 2 0 2 6 01 01 03 4 2 03 0 01 01 02 01 0 01 0 Under 2 3-5 6-10 11-15 16-20 21-25 26-30 31-35 36-40 41-45 46-50 51-55 56-60 61-65 66-70 70+

Female Male

Out of the 42 cholera cases, in Southern Liech State 14 (33 %) were female, while 28 (67 %) were male.

Figure 3:6 Cholera case distribution by gender and age in Northern Liech State 15 December 2016

80 Cholera - age and sex distribution Northern Liech up to 15 Dec 2016 41 64 63 50

31 2 5 2 2 20 12 3 Number of Cases 4 1 57 54 51 26 25 15 19 13 18 4 6 20 10 1 21 01

Under 2 -10 3-5 6-10 11-15 16-20 21-25 26-30 31-35 36-40 41-45 46-50 51-55 56-60 61-65 66-70 70+

Female Male

Out of the 545 cholera cases, in Northern Liech State 309 (56.7 %) were female, while 236 (43.3 %) were male.

Figure 3:7 Cholera case distribution by gender and age in Eastern Nile State 15 December 2016

45 Cholera - age and sex distribution Eastern Nile up to 15 Dec 2016 40 35 30 25 23 20 6 10 15 14 4 10 7 3 Number of Cases 5 14 13 11 16 5 6 10 13 23 25 12 21 1 0 1 0 0

Female Male

6 Out of the 168 line listed cholera cases, in Eastern Nile State 85 (50.6 %) were female, while 83 (49.4 %) were male.

Table 2: Case distribution by gender in South Sudan 15 December 2016 States Female Male Total cases Eastern Lakes 151 200 351 Imatong 13 16 29 Jonglei 40 52 92 Jubek 851 1,155 2,006 Terekeka 13 9 22 Western Bieh 176 94 270 Northern Liech 309 236 545 Southern Liech 14 28 42 Eastern Nile 85 83 168 Total cases 1,652 1,873 3,525

The probable risk factors fueling transmission include: using untreated water from the River Nile and water tankers; lack of household chlorination of drinking water; eating food from unregulated roadside food vendors or makeshift markets; open defecation/poor latrine use especially following the conflict.

Laboratory updates

Table 3: Cholera laboratory test results for Juba by 15 December 2016

Culture results State New positives in Cumulative Cumulative Total tested week 49 Positive Negative Eastern Nile 0 0 5 5 Jonglei 0 1 4 5 Jubek 0 73 126 199 Terekeka 0 2 0 2 Eastern Lakes 0 17 38 55 Imatong 0 7 1 8 Fangak 0 13 29 39 Wau 0 0 6 6 Boma 0 0 2 2 Northern Liech 2 16 40 49 Southern Liech 0 2 0 2 Eastern Nile (Pigi) 0 2 5 7 Total tested 02 133 256 389

7 Table 4: Cholera Alerts – Date of Details of the alert Area Action notification No alerts 13-Sept- From 14-17 Nov, the MedAir Wiechdeng, Ayok MedAir responded to suspect cholera 2016 team responded to 78 suspect county, Southern cases in Wiechdeng by setting up a 10 cholera cases including 15 Bieh state bed CTU. deaths in Wiechdeng, Ayod. One case tested positive on cholera RDT. 8- Oct-2016 UNIDO reported 57 suspect Thaker, Tutnyang, UNIDO is the healthcare partner cholera cases including three & Leah Payams, responding to suspect cases in deaths Mayendit North, Mayendit. Security concerns have Southern Liech constrained comprehensive and state sustained interventions. 26-Oct-16 In Panyijiar 128 suspect cholera Ganyliel, Tayar, Facility and community based response cases including 3 deaths were Nyal, Panyijiar, is ongoing with cases being managed in reported in Ganyliel; Nyal; Southern Liech Ganyliel PHCC with support from IRC Tayar. Of these, 58 cases and Nyal PHCC. Laboratory including three deaths reported confirmation of cases is still pending. by Ganyliel PHCC. The initial case seen on 22 Oct 2016 involving a trader from Duk. Cases have also been reported in Nyal PHCC (70 cases in total since 27 Oct 2016). 3 Dec 2016 Yirol East County Health Nyluel, Yirol East Yirol East RRT to investigate these Director reported three suspect cases and search for additional cases in cholera cases including two this area including sample collection deaths in Nyluel. from suspect cases and close contacts to suspect cases.

Cholera Response Activities Overall coordination of the cholera response at the national level is coordinated by the National cholera taskforce to review outbreak trends and progress of implementation activities. Security concerns have remained a major impediment to the implementation of sustained and comprehensive cholera investigation and response activities in Leer and Mayendit.

Cholera case management is ongoing at the designated cholera treatment facilities in the nine affected states. As cases decline in the affected areas, laboratory surveillance has been strengthened to ensure that all suspect cholera cases undergo rapid diagnostic testing and stool culturing to confirm cholera. WHO has therefore supported the partners operating cholera treatment facilities with ample supplies for sample collection, onsite rapid diagnostic testing, and shipment to the National Public Health Laboratory for culturing.

WHO is supporting the cholera investigation and response activities in all the nine affected states and the two states with alert suspect cases. Core to WHO’s support to the current cholera response is technical support to the taskforce committees by providing updated situation reports; supporting the investigation and testing of suspect cases; support towards case management activities through trainings on cholera case management protocols; recommending tailored strategies in response to emerging trends; and support for the outbreak evaluation process that is already underway. WHO technical officers are currently deployed in Mingkaman; Bentiu, Bor, Malakal, Imatong, and Juba to support the ongoing response activities.

UNICEF continues to support the Cholera response at the community level across all relevant sectors of Health, WASH, and communication through active partnerships with following implementing partners: Health Link South Sudan (HLSS), LiveWell, ACROSS, CAPIAD, THESO, BEDN, IMC, RUWASSA, SMC, NHDF, UNIDO, World Relief, and ARUDA.

In Bentiu, the weekly cholera taskforce meetings take place weekly on Wednesdays to coordinate preparedness and response activities. The implementation of the integrated case-centered approach is ongoing with at least 2,300 doses oral cholera vaccines deployed to augment the response. Ongoing transmission is suspected to be associated with exposure to unsecured water reservoirs that are used for washing, bathing and swimming.

Security concerns continue to be the main impediment for a sustained and comprehensive response in Leer and Mayendit. In Panyijiar; at least 57 suspect cases including three deaths were reported in Ganyliel; Nyal; and Tayar. WHO and UNICEF have supported IRC, UNIDO, and Sign of Hope to respond to the suspect cases.

In Fangak, MSF France is running a CTC in Fangak town where cholera cases are being managed. The health and WASH clusters have mobilized additional partners – Hold the Child and ACF to support the community interventions including establishment of ORPs, community health education, hygiene promotion and support for personal hygiene and chlorination of water at water collection points.

In Pigi; cases were managed in Kurwai PHCC by Nile Hope with support from WHO, UNICEF, and MSF-F. At least 168 cases including six deaths of cholera were reported. The cases declined and by 15 December 2016, there were no cholera cases admitted in the treatment center. The last four cases were discharged from Kurwai PHCC on 15 November 2016.

Planned Activities 1. The next weekly EPR/cholera taskforce meeting is scheduled for 4 January 2017 starting 2:00pm in the WHO Conference Hall. 2. Continue social mobilization activities, active case surveillance, and street announcements with open van, house to house awareness and distribution of WASH supplies by HHPs in affected and at risk areas.

Many thanks to the staff at CTCs, MoH at national level and state levels, especially the Department of IDSR, who have helped to gather the information presented here. Situation Reports are posted on the WHO website: http://www.who.int/hac/crises/ssd/en/ as well as on the Humanitarian Info webpage: http://southsudan.humanitarianresponse.info/clusters/health.

The MoH/WHO surveillance team welcomes feedback and data provided by individual agencies. Given the fast evolving nature of this epidemic, errors and omissions are inevitable: we will be grateful for any information that helps to rectify these. Send any comments and feedback to: E-mail: [email protected], The Toll free number for Vivacell calls is: 1144.

Contacts For more information, please contact

Dr. John Rumunu Dr. Alice Igale Director General - Preventive Health Services Ag. Director - IDSR MoH, Republic of South Sudan MoH, Republic of South Sudan Tel: +211955668178 Tel: +211956420189

9 Annex 1: Cholera distribution in Bentiu PoC as of 15 December 2016

Annex 1.1: Cholera case distribution by time in Bentiu PoC 15 December 2016

Epidemic Curve for cholera in Bentiu PoC as of 15 Dec 2016

30 25 20 15 10 No. cases 5

0 11/1/16 11/3/16 11/5/16 11/7/16 11/9/16 12/1/16 12/3/16 12/5/16 12/7/16 12/9/16 10/16/16 10/18/16 10/20/16 10/22/16 10/24/16 10/26/16 10/28/16 10/30/16 11/11/16 11/13/16 11/15/16 11/17/16 11/19/16 11/21/16 11/23/16 11/25/16 11/27/16 11/29/16 12/11/16 Date of onset

Annex 1.2: Cholera age and sex distribution in Bentiu PoC as of 15 December 2016

150 Cholera - age and sex distribution Northern Liech up to 15 Dec 2016 120

41 64 60 62

Number of Cases 30 1 30 2 5 11 2 1 3 57 54 51 26 24 15 18 13 18 4 51 20 10 1 21 1 0 6 0 Under 3-5 6-10 11-1516 -2021 -2526 -3031 -3536 -4041 -4546 -5051 -5556 -6061 -6566 -70 70+ Adult Blank 2 Female Male

Annex 1.3: Cholera case distribution by sector in Bentiu PoC as of 15 December 2016

140 128 130 115 120

100 87 83 80

Number of cases 40 15 20 10 1 0 Sector 1 Sector 2 Sector 3 Sector 4 Sector 5 (blank) New arrival Referral Area of residence