AWD ABD. Malaria. Measles. Others ARI ABD. Malaria AWD 100% 80% 60% 40% 20%

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1 Weekly Epidemiological Bulletin Integrated Disease Surveillance and Response (IDSR) Republic of South Sudan W49 3 Nov 6 Dec 215 Highlights Completeness for weekly reporting was 47% for the nonconflict affected states and 82% for the IDP sites. Four new suspect measles cases reported from Bentiu PoC (3) and UN House PoC (1) in the reporting week. trend in Warrap state and Bentiu PoC consistent with an epidemic nonetheless, there is a noticeable decline in malaria incidence in the two locations Special focus on malaria remains the major cause of morbidity in both nonconflict affected states (38%) and IDP sites (49%). This week, malaria cases declined as compared to week 48 of 215. Though the malaria incidence in Warrap state and Bentiu PoC is still consistent with malaria epidemic, there is a noticeable case decline Public Health Priorities Figure 1a IDSR Proportional morbidity W Early Warning, Alert and Response 1% 8% AWD Active responses 53% 38% ABD Measles Hepatitis E Virus Active alerts: Urgent Others Figure 1b Proportional morbidity in IDPs W Active alerts: Warning 27% 16% 1% ARI ABD Measles Meningitis 7% 49% Measles AWD System performance Completeness for weekly reporting was 47% for the nonconflict affected states and 82% for the IDP sites (Table 1). Warrap and Western Equatoria states attained the target completeness reporting rate of 8 (Figure 2). Timeliness for weekly reporting remains very low (38-39%) for both the non-conflict affected states and IDP sites (Table 1). Cumulative completeness reporting rate for 215 is 56% for the non-conflict affected states and 86% for the IDP sites (Table 1). Health Facilities reporting [%] Figure 2 IDSR weekly reporting by state W % 86% 72% 53% 42% 42% 5% 5% 3% 16% 72% 27% 62% 36% 44% 12% 23% 89% 86% CES EES Jonglei Lakes NBeG Unity UNS WBeG WES Warrap Timeleness Completeness Target Table 1 Surveillance performance in South Sudan as of W Number of Health Timelines Completeness Timeliness Completeness System Facilities in week 49 of 215 Cumulative for 215 IDSR (38%) 653 (47%) 57(41%) 773(56%) EWARN (39%) 54 (82%) 27 (51%) 45 (86%)

2 Silent counties and facilities Table 2 Silent counties and facilities in W No. IDSR EWARN Silent Counties W Silent Facilities W Yei Goah mobile (UNIDO) 2 Juba Machar PHCU (IRC) 3 Budi Kol PHCU (IRC) 4 Kapoeta North Mayendit mobile (UNIDO) 5 Kapoeta South Yuai (MSF OCA) 6 Lopa Jiech PHCU (UNKEA) 7 Ikotos Makal West PHCU (IMA) 8 Magwi Liang IDP mobile (MSF OCB) 9 Torit Mangatain IDP 1 Rumbek East 11 Jur River 12 Raja Though 17 (33%) hospitals, 146 (45%) PHCCs, and 49 (48%) PHCUs in 47 counties of the non-conflict affected states submitted their reports, a total of 12 counties did not submit any report in the reporting week (Table 2). Nine partner-supported health facilities in the conflictaffected states did not submit their reports in the reporting week (Table 2). Low reporting rates are partly attributed to long distances to the next reporting levels, insecurity, hardware and software failure of computerized database, and lack of investment in mhealth applications to enhance reporting. Consultations Table 3 Consultations in South Sudan as of W Surveillance System Consultations in week 49 of 215 Cumulative consultations for 215 <5 years 5 years Total <5 years 5 years Total IDSR 31,548 51,94 82,642 2,4,18 3,234,13 5,238,211 EWARN 31,23 1,11,873 Total 113,665 6,349,84 Number of consultations Figure 3 EWARN consultations by IDP camp W Awerial Bentiu Bor Lankien Malakal Melut Nasir UN HOUSE Renk CCM IMC IOM IRC MSF- E MSF- OCA Medair HealthL ink GOAL IMA SMC UNKEA The total consultations were 113,665 for the reporting week and a cumulative of 6,349,84 consultations for 215 (Table 3). A total of 31, 23 consultations were reported from IDP clinics in the reporting week (Table 3). Figure 3 shows consultations in the partner-supported health facilities serving displaced populations;; Kodok Lul Ogod Akobo Wau Shilluk Twic East DU K Manyo Panyijiar Leer Bentiu State Hospital Rubkona Trends for top causes of Morbidity Table 4 Top causes of morbidity in 214 and 215 System Disease New cases W49 Cumulative cases W1 to W ,63 31,47 1,434,5 2,99,63 AWD 5,566 6,19 27, ,76 IDSR Meningitis ABD 1,351 1,37 56,555 94,43 Measles 18 1, AJS ,757 3,162 15,39 144,31 341,438 AWD 1,611 2,216 64,73 91,479 ARI 3,173 5,32 11,826 21,5 EWARN ABD ,59 11,317 Measles 5 4 1, AJS ,367 Meningitis is the top cause of morbidity in both non-conflict affected states and IDP sites where it currently constitutes 38% and 49% of the total consultations respectively (Figures 1a, 1b, 6a, 6b, Table 4). Acute respiratory infections (ARI) and acute watery diarrhoea (AWD) are the second and third commonest causes of morbidity in the IDP sites (Figures 1a, 1b, 6a, 6b, Table 4). Overall morbidity trends in 215 Figure 6a IDSR priority disease morbidity trends W1 to W Figure 6b EWARN Priority Disease Proportionate Morbidity W1 to W cases per, population Epidemiological week of reporting in 215 Completeness ABD Measles AWD Completeness (%) Percent of all consultations Epidemiologic Week Completeness ARI Bloody Diarrhea Suspected Measles Watery Diarrhoea Completeness

3 is the commonest cause of morbidity and accounts for 38% and 49% of the consultations in the non-conflict affected states and IDP sites respectively (Figures 7, 9). During the current reporting week, malaria trend in Warrap state and Bentiu PoC are consistent with an epidemic nonetheless, there is a noticeable decline in malaria incidence in the two locations (Figures 8, 1a, 1b) The malaria incidence in Malakal PoC has returned to preepidemic levels while interpretation of malaria trends in Northern Bahr el Ghazal and Western Bahr el Ghazal is negated by the low reporting rates (Figure 1b). cases per, Population Status: Urgent Figure 7 IDSR trends for malaria by week, Epidemiological Week of reporting Figure 8 IDSR trends for in Warrap, W1 to W Figure 9 trends in IDPs W to W Third quartile Epide miologic W e e k cases per 1, Figure 1a trend for IDPs in Bentiu PoC 214 to Week of reporting incidence 214 incidence 215 Third quartile cases per 1, Figure 5 Trend in proportional morbidity due to malaria W to W Figure 1b trend for IDPs in Malakal PoC 214 to Week of reporting incidence 214 incidence 215 Third quartile 252 Acute Respiratory Infection (ARI) ARI registered the second highest proportionate morbidity of 16.2% as compared to 16.3% in week 49 of 214 and 13.8% in week 48 of 215 (Figure 11). UN House PoC registered the highest ARI incidence (cases per 1,) of 237 followed by Kodok (27), and Malakal PoC (161). ARI incidence was 414 in Malakal PoC, 357 in UN house PoC, and 264 in Bentiu PoC in week 49 of Figure 11 ARI trends in IDPs W to W Epidemiologic Week

4 Acute watery diarrhoea (AWD) AWD is a common cause of morbidity that currently accounts for 8% and 7% consultations in the non-conflict affected states and IDP sites respectively (Figures 1a, 1b). The overall AWD incidence [cases per,] in the reporting week was 53 in the non-conflict affected states with Upper Nile (11), Warrap (98), and Lakes (93) being the most affected (Figure 12). Among the IDPs, the current AWD burden is lower when compared to 214 (Figures 13 and 14). cases per, population Figure 12 IDSR AWD trends by week, Epidemiological Week of reporting Acute watery diarrhoea (AWD) Figure 13 AWD trends in IDPs W to W Figure 14 AWD Incidence by IDP Site in W and Cases per 1, Epidemiologic Week Awerial Bentiu Bor Lankien Malakal Melut UN House Yuai Tongping Nasir Man- Anguei Akoka Renk Wau Shiluk Kodok Lul Ogod Man- Awan Akobo Twic East Duk Ayod Manyo Panyijiar Mayom Leer Mayendit Bentiu State Hospital Robkona Mangatain wk 49 of 214 wk 49 of 215 Acute bloody diarrhoea (ABD) ABD is a common cause of morbidity that currently accounts for 1% of consultations in the non-conflict affected states and IDP sites (Figures 1a, 1b). The overall ABD incidence [cases per,] in the reporting week was 9 in the non-conflict affected states with Upper Nile (16), Warrap (17), and Lakes (14) being the most affected (Figure 12). Among the IDPs, the current ABD burden is lower when compared to 214 (Figures 16 and 17). cases per, Population Figure 15 IDSR ABD trend by week, Epidemiological Week of reporting Acute bloody diarrhoea (ABD) Figure 16 ABD trends in IDPs W to W Figure 17 ABD Incidence by IDP Site in W and Epidemiologic Week Cases per 1, Awerial Bentiu Bor Lankien Malakal Melut UN House Yuai Tongping Nasir Man- Anguei Akoka Renk Wau Shiluk Kodok Lul Ogod Man- Awan Akobo Twic East Duk Ayod Manyo Panyijiar Mayom Leer Payinjiar Mayendit Bentiu State Robkona Mangatain wk 49 of 214 wk 49 of 215

5 Nutrition Rubkona county In weeks 48 and 49, Nutrition Cluster reported a total of 1,517 children aged between 6-59 months screened for acute malnutrition in Bentiu PoC, Rubkona, and Bentiu Town. Among them, 417 (3.9%) were SAM;; whilst 944 (9.) were MAM. This gives a proxy GAM rate of approximately 14%. A total of 66 children were admitted into the stabilization center to manage SAM cases with medical complications in the weeks under review, of which 24 in week 48 and 42 in week 49 (Figure 17a). New cases admitted in outpatient programs were 616, across the PoC, Rubkona and Bentiu town (Figure 17b). The total number of children with SAM admitted in OTP at the end of week 49 was Admissions to OTP and SC in week 49 mark a significant increase compared to the previous weeks. Nutrition Figure 17a Admissions into the Stabilisation Centre in Bentiu PoC W1 to W Nutrition Source: nutrition cluster Figure 17b Admissions into outpatient nutrition programs in Rubkona County 214 and 215 Admissions Admissions 214 Admissions Epide miological W e e k 452 Source: nutrition cluster Awerial county (Mingkaman) Due to the significant influx of new arrivals in Mingkaman, that reached 29,659 on December 4th (Source IRNA Assessment) a rapid nutrition assessment was conducted in week 49, by IMC, CCM and CHD, to appraise the nutritional status of IDPs. A total of 886 under five children were screened: proxy GAM rate resulted 17.3%, with associated SAM of 4.3%. Severe Acute Malnutrition for U5 is on average for Mingkaman, however the situation is evolving and might rapidly worsen, due to lack of food and difficult conditions of living. Pregnant and lactating women are particularly vulnerable;; 468 pregnant and lactating mothers were screened;; among them, 11% of pregnant and 22% of lactating mothers resulted to be affected and at risk of acute malnutrition, with MUAC between cm. (source of info: Nutrition Sub cluster IMC, CCM and CHD)

6 Measles Measles is a common cause of morbidity especially in children under fives years living in the conflict-affected states. 2.5 Figure 18 Suspect measles trends W to W Of the 1, suspect measles cases reported countrywide in 215, a total of have been investigated with 49 being confirmed as measles IgM positive, another 79 were confirmed by epidemiological linkage, and 26 being clinically compatible. Four new suspect measles cases reported from Bentiu PoC (3) and UN House PoC (1) in the reporting week. These are part of declining outbreaks for which reactive measles vaccination campaigns have been conducted Epidemiologic Week Current measles burden lower when compared to 214 (Figure 18) Hepatitis E Virus (HEV) HEV is the commonest cause of acute jaundice syndrome 1 with cases confirmed in Mingkaman, Bentiu, Lankien, Guit, and Leer. Bentiu PoC reported 36 new HEV cases including one death in the reporting week. A cumulative of 2,172 HEV cases including 18 deaths (CFR.83%) reported in Bentiu;; 158 cases including seven deaths (CFR 4.4%) in Mingkaman;; 37 cases including one death (CFR 2.7%) in Lankien;; 3 confirmed HEV cases in Melut;; 3 HEV confirmed cases in Guit;; and 1 HEV confirmed case in Leer. No, cases in other sites Figure 19 HEV trends in Mingkaman, Bentiu & Lankien W1 214 to W No. cases in Bentiu Active transmission is ongoing in Bentiu PoC where despite the health and WASH cluster response, the ever increasing population continues to constrain access to safe drinking water and sanitation facilities (Figure 19). Epidemiological week Awerial Lankien Bentiu 1 This only applies to the current context of South Sudan Other diseases of public health importance Acute Flaccid Paralysis Suspected Polio Since the beginning of 215, a cumulative of 31 AFP cases have been reported countrywide. The annualized non-polio AFP (NPAFP) rate (cases per, population children -14 years) is 3.9 per, population of children -14 years (target 2 per, children -14 years). All but two states (Unity and Upper Nile) have attained the targeted NPAFP rate of 2 per, children -14 years. The non-polio Enterovirus (NPEV) isolation rate (a measure of the quality of the specimen cold chain) is 15% (target 1). Stool adequacy stands at 95%, a rate that is higher than the target of 8. The cumulative for circulating Vaccine Derived Poliovirus type 2 (cvdpv2) cases now stands at three cases with only one case reported in 215. Guinea Worm Dracunculiasis No reported cases. Meningitis Two meningitis cases were reported in Bentiu with one of the cases involving a 3 year old boy testing positive for Streptococcus ssp. Visceral Leishmaniasis Kala-azar Since the beginning of 215, a total of 3,99 cases [2,53 (8.8%) new and 596 (19.2 %) relapses/pkdl] including 12 deaths (CFR 3.3%) and 143 (4.6%) defaulters have been reported from 23 treatment centers. During the corresponding period in 214, a total of 7,385 cases including 21 deaths (CFR 2.7%) and 23 (3.1%) defaulters were reported from 21 treatment centers. Of the 3,99 cases reported, majority was from Lankien (1,386) followed by Walgak (338), Pagil (187), Narus MOH/ARC (173), Ulang (22), Melut IDP (156), Akobo (133), Chuil (126), Kapoeta Civil Hospital (71) and Rom (64) The most affected groups included male [1,747 cases (56.4%)], those aged 15years [1,336 cases (43.1%]) and those aged 5-14years [1,263 (4.8%). Children under five years were less affected [492 cases (15.9%)]. Viral Haemorrhagic Fever No reported cases. Animal bites Suspected rabies No reported cases.

7 Mortality Table 5 Trend in mortality cases W to W Counties AWD U5 years AWD 5 & above U5 years Others Total deaths U5 years A total of nine deaths were reported from the nonconflict affected counties including 3 (33%) in children <5 years and 4 (44%) attributed to AWD (Table 5). Among the IDPs, Bentiu PoC, Juba 3 PoC, Melut, and Malakal PoCs submitted mortality data (Table 6). This week, 21 deaths were reported including 14 (67%) in Bentiu PoC and 11 (52%) in children <5 years (Table 6). This week, malaria and AWD had the highest proportionate mortality of 23.8% and 14.3% respectively (Table 6). Total deaths 5 & above Kajo- Keji 1 1 Rumbek North Mayom 1 1 Renk The U5MR in all the IDP sites that submitted mortality data in week 49 of 215 were below the emergency threshold of 2 deaths per 1, per day (Figure 2). Table 6 Proportional mortality by age W to W Cause of Death by Bentiu Juba 3 Malakal Melut Total Proportionate IDP site <5yrs 5yrs <5yrs 5yrs 5yrs 5yrs deaths mortality [%] Acute watery diarrhoea Chronic cough Hepatitis E Pneumonia SAM TB/HIV/AIDS Trauma Unknown Drowned Liver Failure Hepatic failure Intestinal obstruction Total deaths The Crude Mortality Rates [CMR] in all the IDP sites that submitted mortality data in week 49 of 215 were below the emergency threshold of 1 death per 1, per day (Figure 21). The other causes of mortality in the week included AWD [two deaths in UN House PoC and one death in Bentiu PoC];; Hepatitis E [one death reported in Bentiu PoC];; pneumonia [one death in Juba 3];; and medical complications of malnutrition [one death reported in Bentiu PoC]. Note: Mortality rates are calculated for PoC sites only and are based on the latest available population data from OCHA. They are reported from line lists and should include community and facility-based deaths. However, due to rapid in/out migration from the PoC sites, and possible under-reporting of community-level deaths, they should be interpreted carefully. Crude and under five mortality rates in IDPs deaths per 1, per day Figure 2 EWARN U5MR by Site - weeks 1 to 49 of Epidemiological week 215 deaths per 1, per day Figure 21 EWARN Crude Mortality Rate for week 1 to 49 of Epidemiological week 215 Juba 3 Malakal Mingkaman Melut Bentiu Juba 3 Malakal Mingkaman Overall mortality in 215 Table 7 Mortality by IDP site and cause of death W1 to W IDP site Acute Jaundice Syndrome Acute watery diarrhoea Cancer Gunshot wound Heart disease Hepatitis E Hypertension Kala- Azar Bentiu Bor Juba Malakal Melut Mingkaman Akobo Wau Shiluk Grand Total Proportionate mortality [%] Mate rnal de ath Me asle s Perinatal death Pneumonia SAM Se ptice mia TB/HIV/AIDS Trauma Othe r Grand Total Since the beginning of 215, a total 1,485 deaths have been reported from the IDP sites of which 79 (48%) were children under-5 years (Table 7). Most of deaths occurred in Bentiu, Malakal, Juba 3 PoC and, Wau Shiluk (Table 7). Since the beginning of 215, malaria has registered the highest proportionate mortality of 18% (Table 7). During 215, commonest causes of death in U5s were severe malaria, medical complications of malnutrition, and severe pneumonia.

8 Data sources This bulletin presents disease trends from the Integrated Disease Surveillance and Response (IDSR) System and the Early Warning Alert and Disease Network (EWARN). The respective data is submitted by public health facilities serving host communities (non-conflict affected states or non IDP sites) and partner-supported facilities serving internally displaced persons (IDP) in the Republic of South Sudan. Editorial Editorial: Dr. Thomas A. Ujjiga, John M. Juma, Sheila Baya, Dr. Alice L. Igale, Dr. George W. Worri, Korsuk Scopus, Robert M. Lasu, Rose A. Dagama, Jane Pita, Marina Adrianopoli, Morris Gargar, Dr. Asta Kone Coulibaly, Dr. Lincoln Charimari, Dr. Allan M. Mpairwe, Dr. Joseph F. Wamala Founders: Dr. John P. Rumunu, Dr. John Lagu, Dr. Abdinasir Abubakar Acknowledgements MoH and WHO gratefully acknowledge the support of all MoH staff in the states, WHO Field Officers, and implementing-healt h cluster partners in collecting and reporting the data used in this bulletin. Contact For more information, please contact: Department of Epidemics, Preparedness and Response MoH Republic of South Sudan outbreak_22_21@yahoo.com Outbreak toll-free line:1144 This bulletin is produced by the Ministry of Health with technical support from the WHO