Measles. Gogrial West. Duk. Rubkona. Tonj North. Pariang. Wau. National. Bor South. Manyo. Fashoda. Renk. Kajo-keji. Yirol West. Mundri East.

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1 Weekly Epidemiological Bulletin Integrated Disease Surveillance and Response (IDSR) Republic of South Sudan W 6 Dec 6 Jan 7 Highlights Completeness for weekly reporting was % for the nonconflict states and 66% for the IDP sites. Overall completeness for weekly reporting in 6 was % in the nonconflict areas and 69% in the IDP sites. Malaria is a leading cause of morbidity in nonconflict areas and IDPs. Transmission has returned to normal in most counties. Cholera case confirmed in Panyijiar and another six cases confirmed in UN House PoC. Active transmission is ongoing in Northern and Southern Liech states. Measles transmission is ongoing in Wau PoC where at least 7 cases were reported in week of 6 as compared to cases in week of 6. Special focus on malaria Malaria accounted for 6% and 9% of consultations in nonconflict-affected and IDP areas (Figs. a and b). Analysis of malaria trends at state level showed that malaria cases were within expected levels in all the states (Fig. 8af). In the 6 (%) affected counties; malaria cases have continued to decline to expected transmission levels (Fig. 9a). Early Warning, Alert and Response Active responses Four suspect meningitis cases reported from Bentiu PoC. Complications related to Gun Shot Wounds were the leading cause of death in IDPs during the week. Overall, TB/HIV/AIDS were the leading cause of death in IDPs in 6. Public Health Priorities System performance Completeness for weekly reporting was % for the nonconflict states and 66% for the IDP sites (Table ). Five counties attained % completeness in reporting. Overall, 6 counties attained completeness of at least 8% (Figures c). Timeliness for weekly reporting remains very low (-%) for both the non-conflict affected states and IDP sites (Table ). Cumulative completeness reporting rate for 6 is % for the non-conflict affected states and 69% for the IDP sites (Table ). Table Surveillance performance in South Sudan as of W 6 System Figure a IDSR Proportional morbidity WK, 6 Total Facilities 6% % Timelines Completeness Timeliness Completeness in week of 6 Cumulative for 6 IDSR 9 6 (%) (%) 7 (7%) 68 (%) EWARN 7() (66) (9%) (69%) % 6%.7% Figure b Proportional morbidity in IDPs W 6 6% % 9% % % % Measles Malaria ARI AWD ABD Other AWD ABD Malaria Measles Others Gogrial West Cholera Malaria Measles Kala azar Hepatitis E virus Guinea worm Active alerts: Meningitis Event based surveillance W of 6 Two states - Imatong and Wau submitted event log data with no events reported during the reporting period. Figure c IDSR Completeness by county in W 6 Duk Rubkona Tonj North Pariang Wau National Bor South Manyo Fashoda Renk Kajo-keji Yirol West Mundri East Ulang Raga Rumbek North Rumbek Centre Abyei Maridi Ibba Mundri West Longochuk Nzara Nagero Maban Ezo Tambura Yambio Tonj South Mvolo Abiemnhom Mayendit Wulu % 7% % % % % % 8% % % % 9% % 7% 7% 7% 7% 7% 8% 8% 8% 8% 8% 8% 88% 88% 89% 9% 9% % % % % % % % % 6% 8% % % Completeness

2 IDSR and EWARN Reporting Performance by Partner and County in 6 Table Reporting Performance [Timeliness and Completeness] by Partner and County as of W 6 Partner Number of health facilities Completeness W 6 Timeliness # # % # % COSV % % GOAL % % HLSS % % IMA % % IMC 6 6 % 6 % IOM % 9% IRC % % Medair 67% 67% MSF-E % % MSF-H % % SMC % % UNIDO % % UNKEA % % World Relief % % Total 66% 7 % No. IDSR Silent Counties W 6 Juba* Lainya Morobo Terekeka Yei Budi Ikotos Kapoeta East Kapoeta North Kapoeta South Lofan Magwi Torit Akobo* Ayod Canal/Pigi Fangak Nyirol* Pibor Pochalla Twic East *Counties with EWARS reporting sites uror Awerial* Yirol East Guit Mayom Cueibet Aweil East Koch Leer* Payinjiar* Akoka Baliet Luakpiny/Nasir* Aweil South Melut Panyikang Malakal* Gogrial East Tonj East Twic Mayardit (%) hospitals, (%) PHCCs, and 7 (%) PHCUs in 9 counties of the nonconflict-affected states submitted their IDSR reports (Table ). A total of counties did not submit any IDSR report in the reporting week (Table ).However eight of these counties submit their data through EWARS (Table ). 7 partner-supported health facilities in the conflict-affected states did not submit their reports in the reporting week (Table ). Trends for top causes of Morbidity Table Top causes of morbidity in and 6 System Disease New cases W Cumulative cases as at W 6 6 Malaria,79 6,8,887,,8, 68 AWD, 7,8 9,66 6, IDSR Meningitis ABD 8, 79,6 6,87 Measles AJS 6 7 Malaria,7,776 8,7 6,8 AWD,97,9 9,68 6,6 ARI,88,8 6,88, EWARN ABD 7,76 7,6 Measles 6 969,89 AJS 7,67 8, Meningitis 777 Malaria is the top cause of morbidity in the nonconflict states and the second highest cause of morbidity in IDP areas (Figures a, b, 6a, 6b, Table ). The 7 health facilities in the IDPs that did not submit their reports in week are supported by IMA, MSF-E, MSF-H, MedAir, UNKEA, World Relief, and SMC (Table ). The best performing partner-supported facilities during the week were GOAL, HLSS, IMC, IOM, IMA, IRC, and UNIDO. Consultations Table Consultations in South Sudan as of W 6 Surveillance System Consultations in week of 6 Cumulative consultations for 6 < years years Total < years years Total IDSR 7, 6,,9,67,99,6,77,,76 EWARN 9,87,6, Total 66,98,88,8 Table shows the total consultations in 6. Overall morbidity trends for -6 Figure 6a IDSR priority disease morbidity trends W 6 to W 6 Figure 6b EWARN Priority Disease Proportionate Morbidity W to W 6 cases per, population IDSR Priority Disease Morbidity trends from week to of of reporting in Completeness ABD Malaria Measles AWD Completeness (%) Percentage of all consultations 8% 7% 6% % % % % % % %_Malaria %_ARI %_Measles %_AJS %_AWD %_ABD

3 Malaria Malaria is the top cause of morbidity and accounted for 6% and 9% of the consultations in the nonconflict-affected states and IDP sites respectively (Fig. a, b). As seen from Figs. 8a-f, analysis of malaria trends at state level showed that malaria cases were within expected levels in all the states*. In the 6 (%) affected counties; the malaria trends have continued to decline. (Fig 9a). The malaria incidence in the IDP sites are within expected levels (Figs. a-d). In the week, three malaria deaths were reported from Aweil North (); and UN House Poc () (Tables, 6). Cases per, Population 6 Status: Urgent Figure 7 IDSR malaria trends by week, of reporting 6 Malaria trend by state Figure 8a Malaria Incidence for Wau state, week to, 6 Figure 8b IDSR trends for malaria Gogrial, Tonj, Twic, Wk to Wk, 6 cases per, 8 6 cases per, Third quartile Epidemiological Week 6 Third quartile - Malaria cases per, Figure 8c IDSR trends for Malaria Aweil, Aweil East, Lol from week to, Third quartile - cases per, 8 6 Figure 8d IDSR trends for malaria in Western Lakes, Eastern Lakes, and Gok states, Wk to Wk, Third quartile - 6 Malaria 8 Figure 8e IDSR Malaria trends for Imatong and Lomurnyang, week -, 8 Figure 8f IDSR trends for Malaria in Gbudwe, Maridi, and Amadi states from week to, 6 cases per, 6 cases per, Third quartile Third quartile - *Actual disease trends may be masked by low reporting rates

4 Status: Urgent Malaria trends by county () Figure 9a IDSR trends for Malaria in Bor county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Week Figure 9a IDSR trends for Malaria in Awerial county from week to, 6 Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Figure 9a IDSR trends for Malaria in Rumbek Centre county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile Week Figure 9a IDSR trends for Malaria in Rumbek North county from week to, 6 Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile Figure 9a IDSR trends for Malaria in Wulu county from week to,6 Figure 9a IDSR trends for Malaria in Yirol East county from week to, 6 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile - 6 Figure 9a IDSR trends for Malaria in Yirol West county from week to, 6 Figure 9a IDSR trends for Malaria in Awiel Centre county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Figure 9a IDSR trends for Malaria in Awiel East county from week to, 6 6 Figure 9a IDSR trends for Malaria in Awiel North county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile - 6

5 Malaria trends by county () Status: Urgent Figure 9a IDSR trends for Malaria in Awiel South county from week to, 6 8 Figure 9a IDSR trends for Malaria in Awiel West county from week to,6 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile Figure 9a IDSR trends for Malaria in Abiemnhom county from week to, 6 Figure 9a IDSR trends for Malaria in Guit county from week to, 6 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile Figure 9a IDSR trends for Malaria in Mayendit county from week to, 6 Figure 9a IDSR trends for Malaria in Mayom county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile - 6 Figure 9a IDSR trends for Malaria in Pariang county from week to, 6 Figure 9a IDSR trends for Malaria in Longochuk county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile - 6 Figure 9a IDSR trends for Malaria in Maban county from week to, 6 Figure 9a IDSR trends for Malaria in Melut county from week to, Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6

6 Malaria trends by county () Status: Urgent Figure 9a IDSR trends for Malaria in Raga county from week to, 6 Figure 9a IDSR trends for Malaria in Abyei county from week to, Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile - 6 Figure 9a IDSR trends for Malaria in Gogrial East county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Figure 9a IDSR trends for Malaria in Tonj South county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile - 6 Figure 9a IDSR trends for Malaria in Payinjiar county from week to, 6 Figure 9a IDSR trends for Malaria in Nzara county from week to, 6 Week Week Week 7 Week Week Week 6 Week 9 Week Week Week Week Week 7 Week Week Week 6 Week 9 Week Week Third quartile - 6 Third quartile - 6

7 Malaria in IDPs, Figure a Malaria trend for IDPs in Bentiu PoC to 6 8 Figure b Malaria trend for IDPs in Malakal PoC to 6 cases per, 8 6 cases per, Week of reporting incidence incidence Third quartile incidence Week of reporting incidence incidence Third quartile incidence 6 6 Figure c EWARN trends for Malaria in UN House PoC to Figure d EWARN trends for Malaria in Mingkaman, to cases per, cases per, Week of reporting incidence incidence Third quartile incidence 6 Week of reporting incidence incidence Third quartile incidence 6 Acute Respiratory Infection (ARI) Percent of total consultations % Figure ARI trends in IDPs W to W 6 % % % % % % % of reporting 6 Percent of all consultations 8% 7% 6% % % % % % % Figure b ARI Incidence by IDP Site in W 6 UNIDO Majak PHCU Medair Wonthow Clinic Medair Abayok Clinic UNIDO Meer Mobile Clinic MSF-H Bentiu PoC Hospital UNIDO Bow PHCU IOM Wonthow Mobile GOAL Dethoma Camp IOM Gerger Clinic IOM Abayok Clinic IOM Halaka Clinic IMC Akobo Hospital IOM Bentiu Sector PHCC HLSS Mingkaman Hospital IOM Payer Clinic IMC UN House Clinic UNIDO Gandor PHCU IOM Sector Clinic IMC Malakal PoC Clinic IOM Bentiu Sector PHCC IRC Sector Clinic IOM Malakal PoC Clinic IOM Wau PoC PHCU IMC Malakal PoC Clinic IOM Ramela Clinic IOM Nazareth Mobile Clinic GOAL Koradar IDP clinic IMC UNMISS PoC Clinic HLSS Bor Clinic In the IDPs, ARI registered the second highest proportionate morbidity of.8% as compared to 7.8% in week of and.6% in week of 6 (Fig. ). Figure b shows ARI morbidity by IDP site in week of 6. Meningitis (suspected) During the week, four suspect meningitis cases were reported from Bentiu PoC. Case-based investigations are ongoing. A total of 7 samples have been tested in the National Public Health Laboratory in 6 - none of these has been confirmed to be due to epidemic meningitis. Since week 7, a total of suspect meningitis cases have been reported with the most recent being suspect cases reported from Bentiu PoC in week. A total of suspect meningitis cases have been reported in Bentiu PoC. The initial suspect in Bentiu PoC was reported on 6 Nov 6. Seven out of suspect cases have been tested using rapid pastorex with testing positive for Streptococcus pneumoniae; two samples involving two-month-old children tested positive for Neisseria meningitidis Y/W; one case was positive for Hemophilus influenza type b; one case tested negative; and the one from Wau Teaching Hospital was not tested. A meningitis alert has been issued and surveillance has been enhanced countrywide.

8 Acute watery diarrhoea (AWD) AWD is a common cause of morbidity that currently accounts for % consultations in the nonconflict-affected states and IDP sites respectively (Fig. a, b). The overall AWD incidence [cases per,] in the reporting week was 6 in the nonconflict-affected areas with Gbudwe, Amadi, and Maridi () and Aweil, Aweil East, and Lol states (6) states being the most affected (Fig. ). In the IDP sites, AWD morbidity is higher when compared to the same period of and (Fig. ). Figure shows AWD morbidity by IDP site in week of 6. Cases per, Population 8 6 Figure IDSR AWD trends by week, of reporting 6 Acute watery diarrhoea (AWD) Percent of all consultations Figure AWD trends in IDPs W to W 6 % % % % % % Percent of all consultations % % % % % % % % Figure b AWD Incidence by IDP Site in W 6 UNIDO Bow PHCU UNIDO Gandor PHCU MSF-H Bentiu PoC Hospital IRC Sector Clinic GOAL Dethoma Camp IMC Malakal PoC Clinic HLSS Mingkaman Hospital IMC UNMISS PoC Clinic IOM Ramela Clinic UNIDO Meer Mobile Clinic IMC Akobo Hospital IMC ER PoC IOM Bentiu Sector PHCC IOM Sector Clinic IOM Gerger Clinic GOAL Koradar IDP clinic IOM Wonthow Mobile UNIDO Majak PHCU IOM Wau PoC PHCU IOM Abayok Clinic IOM Bentiu Sector PHCC IOM Cathedral Church IDP HLSS Bor Clinic Medair Wonthow Clinic IMC UN House Clinic IMC Malakal PoC Clinic IOM Nazareth Mobile Clinic IOM Malakal PoC Clinic Medair Abayok Clinic Acute bloody diarrhoea (ABD) ABD is a common cause of morbidity that currently accounts for % and % of consultations in both the non-conflict affected states and IDP sites respectively (Fig. a, b). The overall ABD incidence [cases per,] in the reporting week was in the non-conflict affected areas with Gbudwe, Amadi, and Maridi states (87) and Ruweng, Northern Liech and Southern Liech states () states being the most affected (Fig. ). Among the IDPs, the current ABD burden is lower when compared to and (Fig. 6 and 7). Figure 7 shows the number of ABD cases by IDP clinic in week of 6. Cases per, Population Figure IDSR ABD trend by week, of reporting 6 Acute bloody diarrhoea (ABD) Percent of all consultations 6% % % % % % % Figure 6 ABD trends in IDPs W to W Percent of all consultations % % % % % % Figure 7 ABD Incidence by IDP Site in W 6 Medair Abayok Clinic UNIDO Meer Mobile Clinic Medair Wonthow Clinic UNIDO Majak PHCU IOM Payer Clinic GOAL Koradar IDP clinic IOM Halaka Clinic IOM Gerger Clinic HLSS Mingkaman Hospital UNIDO Bow PHCU IMC Malakal PoC Clinic IOM Abayok Clinic IMC UN House Clinic IOM Bentiu Sector PHCC GOAL Dethoma Camp IRC Sector Clinic IMC Malakal PoC Clinic IOM Malakal PoC Clinic IOM Sector Clinic IOM Wonthow Mobile IOM Cathedral Church IDP IOM Bentiu Sector PHCC IMC Akobo Hospital IOM Wau PoC PHCU HLSS Bor Clinic MSF-H Lankien PHCC IOM Ramela Clinic MSF-H Bentiu PoC Hospital IMC UNMISS PoC Clinic IOM Nazareth Mobile Clinic HLSS Mingkaman IDP Site UNIDO Gandor PHCU IMC ER PoC

9 Measles At least 7 new measles cases reported from Wau PoC in the week (Table.). One suspect case reported from Gogrial West. Since the beginning of 6, a total of,9 suspected measles cases including at least 8 deaths (CFR.%) have been reported countrywide (Table.). Investigations and response to cases in Wau are underway. County Table. Measles cases by location and status as at W of 6 Measles Cases[No] % 8% 6% % % % New suspect cases W, 6 Table. Trend of measles cases by age-group and week in Gogrial West, W-W, 6 Suspect cases in 6 Confirmed Cases in 6 Samples tested in 6 Outbreak status in 6 Mangatain IDP Confirmed & controlled UN House PoC Confirmed & controlled Juba 9 6 Alert Yei 7 7 Alert Kajo keji Alert Lainya Alert Magwi 7 Alert Kapoeta South 9 Alert Mingkaman Alert Awerial 8 Alert Rumbek Center Alert Rumbek East Alert Yirol East Alert Yirol West Confirmed & controlled Aweil West 79 Confirmed & controlled Aweil Center 9 Confirmed & controlled Aweil East 9 6 Confirmed & controlled Aweil South 7 Alert Aweil North Confirmed & controlled Abiemnhom 6 Alert Guit Alert Mayendit 7 Confirmed & controlled Mayom 88 Confirmed & controlled Leer (Adok) 7 6 Confirmed & controlled Rubkona 6 Confirmed & controlled Renk Alert Koch Alert Pariang Alert Maban Alert Abyei 97 Confirmed Gogrial East Alert Gogrial West 89 6 Confirmed Twic 7 6 Confirmed & controlled Tonj North Alert Torit Alert Tonj South 8 Alert Wau Confirmed & controlled Jur river 7 Alert Ibba Alert Tambura Alert Yambio 9 Alert Nagero Alert Nzara Alert Malakal PoC 7 Confirmed & controlled Wau Shiluk Alert Pibor Alert Bor South 7 Alert Bor PoC 7 Alert 7, of rash onset in 6 <yrs -yrs -9yrs -years +yrs Cases[No] % 8% 6% % % % Number of cases Number of cases Number of cases 6 Figure 8. Measles cases, Wau, W to WK Week of rash onset Figure 8. Measles cases, Gogrial West, W to W Week of rash onset Alive Deaths Figure 8. Measles cases, Mayom, W to W Week of rash onset 6 Aive Alive 6 7 Deaths Died Table. Trend of measles cases by age-group and week in Wau, W-W, of rash onset in 6 <yrs -yrs -9yrs -yrs +yrs Cases [No] Table. Trend of measles cases by age-group and week in Abyei, W to W9, 6 % % % of rash onset in 6 <yr -yrs -9yrs -yrs +yrs Cases [No] % % % Table. Trend of measles cases by age-group and week in Mayom, W to W, of rash onset in 6 <yr. -yrs. -yrs.. -9 years +yrs.. Measles outbreaks confirmed in counties (Table.) Fig. to. show the trend of measles cases by age-group in Gogrial West, Abyei, Wau, and Mayom.

10 Visceral Leishmaniasis Kala-azar In 6, a total of, cases [,7 (9.8%) new; 7 (. %) relapses; and 7 (.8%) PKDL] including 9 deaths (CFR.%) and 7 (.8%) defaulter were reported from treatment centers. During the corresponding period in, a total of,67 cases including 8 deaths (CFR.%) and 7 (.8%) defaulters were reported from treatment centers. Of the, cases reported in 6, the majority were from Lankien (8), Old Fangak (9), Kurwai (66), Ulang (6), Walgak (), Chuil (7), Kodok (), and Melut (7). The most affected groups included male [,99 cases (.9%)], those aged - years [6 cases (8.%]) and those aged years [78 (.8%). Children under five years were less affected [8 cases (8.%)]. Since week 7, 6, the number of weekly cases were higher than the those reported during the corresponding period of. Hepatitis E Virus (HEV) Two clusters of AJS reported in Mayom [9 cases including deaths since 9//6] and Abyei [involving 8 cases including deaths [since Oct 6]. Seven of samples tested positive for HEV by PCR. Co-infection with malaria has been common in the children that died. Three suspect AJS cases were reported from Wau PoC from October 6; all tested negative for HEV by PCR. In Bentiu PoC, 6 new HEV cases were reported in week (Fig. 9). Since the beginning of 6, a total of 99 HEV cases have been reported from Bentiu. Since the beginning of the crisis,, HEV cases including deaths (CFR.77%) reported in Bentiu; 8 cases including seven deaths (CFR.%) in Mingkaman; 8 cases including one death (CFR.6%) in Lankien; confirmed HEV cases in Melut; HEV confirmed cases in Guit; and HEV confirmed case in Leer. HEV transmission is currently reported in Bentiu PoC and Bentiu Town and is largely propagated by the sub-optimal access to safe water and sanitation. No, cases in other sites Figure 9 HEV trends in Mingkaman, Bentiu & Lankien W to W Awerial Lankien Bentiu No. cases in Bentiu Other diseases of public health importance Acute Flaccid Paralysis Suspected Polio Table.. Non Polio AFP rate by county as of week 6 of 6 6 During 6, a cumulative of AFP cases have been reported countrywide ( new AFP cases in week 9 of 6). In 6, the annualized non-polio AFP (NPAFP) rate (cases per, population children - years) is.9 per, population of children - years (target per, children - years). All state hubs except Unity have attained the targeted NPAFP rate of per, children - years in 6 (Fig. 9.). The non-polio Enterovirus (NPEV) isolation rate (a measure of the quality of the specimen cold chain) is % in 6 (target %). Stool adequacy was 9% in 6, a rate that is higher than the target of 8%. Guinea Worm Dracunculiasis South Sudan has reported its sixth CDC-confirmed Guinea worm case. The case is an 8-year-old female detected on th November 6 in Khor William village, Roc-roc-dong Payam, Jur river County, Wau state. The case is uncontained but is being followed by field teams. The cumulative in 6 now rises to six (6) confirmed Guinea worm cases compared to Four () cases in. During the week two suspect cases were reported from Gogrial West and Yirol West. The cash reward for reporting a Guinea worm case is now, SSP. Animal bites Suspected rabies There were no new suspect rabies cases in the week. Viral Haemorrhagic Fever No new suspect hemorrhagic fever cases reported from Aweil North. The cumulative remains suspect VHF cases including deaths (CFR 8.%) reportd since December. Children were most afffected and accounted for most cases and deaths. There are no new deaths reported since 8 February 6. Most common case symptoms include: unexplained bleeding (epistaxis), fever, fatigue, vomiting, jaundice. There is no evidence of person-to-person transmission. Mixed vectorborne VHF suspected. A total of 8 blood samples were initially obtained from suspect cases and shipped for testing. Test results (PCR, PRNT, ELISA) from WHO CC laboratories in Uganda (UVRI), South Africa (NICD) and Senegal (IPD) were negative for Ebola, Marburg, CCHF, Rift Valley Fever, Yellow Fever, Zika, West Nile, and Arenaviruses; samples tested positive for Onyong-nyong virus by PRNT; samples were IgM positive for Chikungunya; and IgM positive for Dengue at NICD. An additional 66 samples were collected during the follow up investigations (- June 6) have been shipped to NICD, South Africa and Netherlands for testing.

11 Cholera Cholera outbreaks have been confirmed in nine states [Jubek, Terekeka, Jonglei, Imatong, Eastern Lakes, Western Bieh, Northern Liech, Southern Liech; and Eastern Nile] (Figs 9. & 9.). On Jan 7; a cholera case was confirmed from Panyijiar and an additional six cases were confirmed from UN House PoC. As of Jan 7, a cumulative of,96 cholera cases including 7 deaths (7 facilities and 8 community) (CFR.89%) had been reported in South Sudan (Table.). National and state level cholera taskforce committees are coordinating preparedness and response activities. Current trends highlight the need to enhance the cholera response in Northern and Southern Liech states. Table. Cholera cases and deaths by county as of Jan 7 Figure 9. Cholera Epidemic curve in South Sudan as of Jan 7 Readers are referred to the cholera situation report for details on the ongoing cholera response in South Sudan Reporting sites Total cases Total Facility deaths Total community deaths Total deaths Juba County, Duk County 9 8 Terekeka County 8 8 Awerial County Pageri 9 Fangak 7 Rubkona Leer 9 Panyijiar 9 6 Pigi 68 Total, Number of cases.% 6.9% 66 % %.%.7%.8% 97.%.9%.6%.9%.%.6% 8.%.%.%.%.%.8%.6%.%.7%.% 8.%.%.8%.6%.6%.%.%.% % of onset Jonglei Jubek Terekeka Imatong Eastern Lakes Western Bieh Northern Liech CFR[%] Southern Liech Eastern Nile % % CFR % Figure 9. Cholera incidence (cases per,) and case fatality rate (%) as of Jan 7 Cholera Fatality Density Map for cases per population and CFR Figure.: incidence (cases per,) and case Weeks -9 6 Map Date: 6 December, 6 fatality rate (%) as of October 6 Central African Republic Legend xx Case fatality rate (CFR) Counties with Cholera alert Cases per, population No case reported River Raga Aweil North Aweil West Wau Tambura Aweil East Nagero Ezo Nzara Abyei Twic Jur River Yambio Sudan Wulu Ibba Pariang Abiemnhom Rubkona Guit Mayom. Aweil South Gogrial East Koch Aweil Centre Gogrial West Tonj North Leer Mayendit.8 Tonj East Rumbek NorthPanyijiar Tonj SouthCueibet Rumbek Centre Mvolo Yei Democratic Republic of Congo Fangak.8 Ayod Yirol East Rumbek East Yirol West Duk 8.7 Twic East 6. Mundri WestMundri East Maridi Juba Lainya Morobo Panyikang Fashoda Malakal Nyirol Uror Bor South Awerial.. Pigi.98 Kajo-Keji Terekeka Manyo Melut Baliet Lafon Torit Magwi. Pageri Uganda Renk Akobo Ikotos Maban Longochuk Luakpiny/NasirMaiwut Ulang Pochalla Budi Pibor Kapoeta North Kapoeta South Ethiopia World Health Organization The boundaries and names shown and the designations used on this map do not imply official endorsement or acceptance by the United Nations. Kilometers Kapoeta East Kenya

12 Mortality Table Mortality from IDSR reports countrywide W 6 Mayendit Total deaths COUNTY Cholera yrs AWD yrs Malaria yrs <yrs Aweil North Longochuk Total deaths yrs Total deaths 6 Table 6 Proportional mortality by cause of death in IDPs W 6 Cause of Death by IDP site Akobo Bentiu Juba <yrs <yrs yrs <yrs yrs Total deaths Proportionate mortality [%] Chronic Disease 6 GSW Heart Failure 6 Hepatitis B 6 malaria 6 SAM 6 Sepsis 6 Unknown cholera 6 shigellosis 6 wasting syndrome 6 liver cirrolosis 6 LRTI 6 Grand Total 8 7 A total of six deaths were reported from the stable areas with two attributed to malaria and one to suspect cholera (Table ). Among the IDPs, Akobo, Juba, and Bentiu PoC submitted mortality data (Table 6). This week (); 7 deaths were reported including 9 (%) in Bentiu PoC and 6 (%) in children < years (Table 6). This week, complications related to Gun Shot wounds were the leading cause of mortality in IDPs. (Table 6). The UMR in all the IDP sites that submitted mortality data in week of 6 were below the emergency threshold of deaths per, per day (Fig. ). The Crude Mortality Rates [CMR] in all the IDP sites that submitted mortality data in week of 6 were below the emergency threshold of death per, per day (Fig. ). The other causes of mortality in the week are shown in Tables and 6. 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, per day Figure EWARN UMR by Site - W to W of Bentiu Juba Malakal Mingkaman deaths per, per day Figure EWARN Crude Mortality Rate for W to W of Bentiu Juba Malakal Mingkaman Melut Melut Akobo Wau Shiluk Threshold Akobo Wau Shiluk Threshold Wau PoC Overall mortality in 6 IDP site Table 7 Mortality by IDP site and cause of death W to W 6 Acute watery diarrhoea Cancer GSW Heart Failure Hepatitis E Hypertension Kala-Azar Malaria Maternal death Bentiu Juba Malakal Melut Mingkaman 7 Tomping Akobo Wau Shiluk 8 Wau PoC 6 Total deaths Proportionate mortality [%] Measles Meningitis Perinatal death Pneumonia Rabies SAM Septicemia Stroke TB/HIV/AIDS Cholera Others Total deaths Since the beginning of 6, a total 67 deaths have been reported from the IDP sites of which 6 (7%) were children under- years (Table 7). Most of deaths occurred in Bentiu, Malakal and Juba PoC (Table 7). Since the beginning of 6, TB/HIV/AIDS has registered the highest proportionate mortality of % (Table 7). During 6, commonest causes of death in Us were medical complications of malnutrition, perinatal complications, severe pneumonia, and severe malaria.

13 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. Alice L. Igale, Dr. Abraham Adut, Korsuk L. Scopus, Robert M. Lasu, Rose A. Dagama, Jane Pita, Dr. Patrick, R. Otim, Gabriel Waat, Dr. Allan M. Mpairwe, Dr. Joseph F. Wamala, Dr. John P. Rumunu Acknowledgements MoH and WHO gratefully acknowledge the support of all MoH staff in the states, WHO Field Officers, and implementing-health 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 toll-free line using vivacell: This bulletin is produced by the Ministry of Health with technical support from the WHO Supported by the Global EWARS project