SARS-CoV-2 Variants, South Sudan, January-March 2021.

As the coronavirus pandemic continues, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence data are required to inform vaccine efforts. We provide SARS-CoV-2 sequence data from South Sudan and document the dominance of SARS-CoV-2 lineage B.1.525 (Eta variant) during the country's second wave of infection.

Implementation of tuberculosis preventive treatment among people living with HIV, South Sudan.

OBJECTIVE: To describe an intervention to scale up tuberculosis preventive treatment for people living with human immunodeficiency virus (HIV) in South Sudan, 2017-2020. METHODS: Staff of the health ministry and United States President's Emergency Plan for AIDS Relief designed an intervention targeting the estimated 30 400 people living with HIV on antiretroviral therapy across South Sudan. The intervention comprised: (i) developing sensitization and operational guidance for clinicians to put tuberculosis preventive treatment delivery into clinical practice; (ii) disseminating monitoring and evaluation tools to document scale-up; (iii) implementing a programmatic pilot of tuberculosis preventive treatment; and (iv) identifying a mechanism for procurement and delivery of isoniazid to facilities dispensing tuberculosis preventive treatment. Staff aggregated routine programme data from facility registers on the numbers of people living with HIV who started on tuberculosis preventive treatment across all clinical sites providing this treatment during July 2019-March 2020. FINDINGS: Tuberculosis preventive treatment was implemented in 13 HIV treatment sites during July-October 2019, then in 26 sites during November 2019-March 2020. During July 2019-March 2020, 6503 people living with HIV started tuberculosis preventive treatment. CONCLUSION: Lessons for other low-resource settings may include supplementing national guidelines with health ministry directives, clinician guidance and training, and an implementation pilot. A cadre of field supervisors can rapidly disseminate a standardized approach to implementation and monitoring of tuberculosis preventive treatment, and this approach can be used to strengthen other tuberculosis-HIV services. Procuring a reliable and steady supply of tuberculosis preventive treatment medication is crucial.

Epidemiological description of a protracted cholera outbreak in Tonj East and Tonj North counties, former Warrap State, South Sudan, May-Oct 2017.

BACKGROUND: On 18th May 2017, State Ministry of Health of former Warrap State received a report from Tonj East County of an outbreak of acute watery diarrhoea and vomiting in Makuac payam. We conducted this investigation to confirm the causative organism and describe the epidemiology of the outbreak in order to support evidence-based control measures. METHODS: We defined a suspected case as a resident of Tonj East or Tonj North County with sudden onset of acute watery diarrhoea and vomiting between May 1 and October 15, 2017. A probable case was defined as a suspected case with a positive rapid test for Vibrio cholerae; a confirmed case was a probable case with a positive stool culture for V. cholerae. We conducted systematic case finding by visiting health facilities and villages in the affected payams. We reviewed patient records from 1 May 2017 to 15 October 2017, to identify suspected cholera case-patients. We conducted a descriptive epidemiologic study, examining the distribution of the cases. We computed the attack rates by age, sex, and payam of residence. Case fatality rate was calculated as the ratio of the total number of suspected cholera death to the total number of cholera case-patients. We conducted an oral cholera vaccination campaign after the peak of the outbreak to control and prevent the spread to other payams. RESULTS: We identified 1451 suspected cholera cases between May and October 2017. Of these, 81% (21/26) had a positive rapid diagnostic test for V. cholerae; out of the 16 rectal swabs transported to the National Public Laboratory, 88% (14/16) were confirmed to be V. cholerae O1 serotype Inaba. The epidemic curve shows continuous common source outbreak with several peaks. The mean age of the case-patients was 24 years (Range: 0.2-75y). The clinical presentations of the case-patients were consistent with cholera. Males had an attack rate of 9.9/10000. The highest attack rate was in ≥30y (14 per 10,000). Among the six payams affected, Makuac had the highest attack rate of 3/100. The case fatality rate (CFR) was 3.0% (44/1451). Paliang and Wunlit had an oral cholera vaccination coverage of ≥100%, while 4 payams had a vaccination coverage of < 90%. CONCLUSION: This was a continuous common source cholera outbreak caused by V. cholerae 01 sero type Inaba. We recommended strengthening of the surveillance system to improve early detection and effective response.

SARS-CoV-2 seroprevalence in people living with HIV in South Sudan.

Objectives: The burden of SARS-CoV-2 infection in people living with HIV (PLHIV) in South Sudan is unknown. Methods: We conducted a cross-sectional seroprevalence survey of SARS-CoV-2 immunoglobulin (Ig) G antibodies and other diseases of public health importance (strongyloidiasis, toxoplasmosis) in PLHIV in South Sudan during April 1, 2020-April 30, 2022. We used a multiplex SARS-CoV-2 immunoassay to detect IgG antibodies targeting the SARS-CoV-2 spike, receptor binding domain, and nucelocapsid (N) proteins, and antigens for other pathogens (Strongyloides stercoralis and Toxoplasma gondii). Results: Among 3518 samples tested, seroprevalence of IgG antibodies to SARS-CoV-2 spike protein and receptor binding domain 591 and nucleocapsid ranged from 1.4% (95% confidence interval [CI]: 0.9-2.1%) in April-June 2020 to 53.3% (95% CI: 49.5-57.1%) in January-March 2022. The prevalence of S. stercoralis IgG ranged between 27.3% (95% CI: 23.4-31.5%) in October-December 2021 and 47.2% (95% CI: 37.8-56.8%) in July-September 2021, and, for T. gondii IgG, prevalence ranged from 15.5% (95% CI: 13.3-17.9%) in April-June 2020 to 36.2% (95% CI: 27.4-46.2%) July-September 2021. Conclusions: By early 2022, PLHIV in South Sudan had high rates of SARS-CoV-2 seropositivity. Surveillance of diseases of global health concern in PLHIV is crucial to estimate population-level exposure and inform public health responses.

Viral load scale-up in south Sudan: Strategic implementation of tools to monitor HIV treatment success among people living with HIV.

INTRODUCTION: As access to antiretroviral therapy (ART) for people with HIV (PWH) in the Republic of South Sudan (RSS) increases, viral load (VL) suppression is critical to protect global HIV response investments. We describe VL scale-up between 2017-2020 in the RSS President's Emergency Plan for AIDS Relief (PEPFAR)-supported program. METHODS: President's Emergency Plan for AIDS Relief (PEPFAR) South Sudan developed a VL scale-up plan and tools spanning the VL cascade: pre-test, test and post-test and included assessment of clinical facility and laboratory readiness; clinical and laboratory forms and standard operating procedures for test ordering, specimen collection, processing, results return and utilization; procedures to map clients, monitor turn-around-times (TAT), and an electronic system to monitor VL performance. RESULTS: Between 2017 to 2020, VL monitoring was established in 58 facilities, with 59,600 VL samples processed, and improvements in TAT (150-28 days) and rejection rates (1.9%-0.8%). VL documentation improved for dates of ART initiation, VL test request and dispatch, and HIV regimen. Total average time from high VL to repeat VL decreased from 15.9 months to 6.4 months in 2017 and 2019, respectively. CONCLUSIONS: A concerted approach to VL scale-up has been fundamental as South Sudan strives towards UNAIDS 95-95-95 targets for PWH on ART.

Prevalence of plasmid-mediated AmpC beta-lactamases in Enterobacteria isolated from urban and rural folks in Uganda.

Background: AmpC beta-lactamase-producing bacteria are associated with increased resistance to third-generation cephalosporins. Here, we describe plasmid-mediated AmpC beta-lactamase-producing enterobacteria isolated from urban and rural dwellers in Uganda. Methods: Stool and urine from 1,448 individuals attending outpatient clinics in Kampala and two rural districts in central Uganda were processed for isolation of Escherichia coli and Klebsiella. Following antibiotic susceptibility testing, cefoxitin resistant isolates, and amoxicillin/clavulanate resistant but cefoxitin susceptible isolates, were tested for AmpC beta-lactamase production using the cefoxitin-cloxacillin double-disc synergy test. Carriage of plasmid-mediated AmpC beta-lactamase-encoding genes (pAmpC) and extended spectrum beta-lactamase (ESBL) encoding genes was determined by PCR. Results: Nine hundred and thirty E. coli and 55 Klebsiella were recovered from the cultured samples, yielding 985 isolates investigated (one per participant). One hundred and twenty-nine isolates (13.1%, 129/985) were AmpC beta-lactamase producers, of which 111 were molecularly characterized for pAmpC and ESBL gene carriage. pAmpC genes were detected in 60% (67/111) of the AmpC beta-lactamase producers; pAmpC genes were also detected in 18 AmpC beta-lactamase non-producers and in 13 isolates with reduced susceptibility to third-generation cephalosporins, yielding a total of 98 isolates that carried pAmpC genes. Overall, the prevalence of pAmpC genes in cefoxitin resistant and/or amoxicillin/clavulanate resistant E. coli and Klebsiella was 59% (93/157) and 26.1% (5/23), respectively. The overall prevalence of pAmpC-positive enterobacteria was 10% (98/985); 16.4% (45/274) in Kampala, 6.2% (25/406) Kayunga, and 9.2% (28/305) Mpigi. Ciprofloxacin use was associated with carriage of pAmpC-positive bacteria while residing in a rural district was associated with protection from carriage of pAmpC-positive bacteria. Conclusion: pAmpC beta-lactamase producing enterobacteria are prevalent in urban and rural dwellers in Uganda; therefore, cefoxitn should be considered during routine susceptibility testing in this setting.

Field evaluation of SD BIOLINE HIV/Syphilis Duo assay among pregnant women attending routine antenatal care in Juba, South Sudan.

The SD BIOLINE HIV/Syphilis Duo assay is the first World Health Organization prequalified dual rapid diagnostic test for simultaneous detection of HIV and Treponema pallidum antibodies in human blood. Prior to introducing the test into antenatal clinics across South Sudan, a field evaluation of its clinical performance in diagnosing both HIV and syphilis in pregnant women was conducted. SD Bioline test performance on venous blood samples was compared with (i) Vironostika HIV1/2 Uniform II Ag/Ab reference standard and Alere Determine HIV 1/2 non-reference standard for HIV diagnosis, and (ii) Treponema pallidum hemagglutination reference standard and Rapid plasma reagin non-reference standard for syphilis. Sensitivity, specificity, positive predictive value (PPN), negative predictive value (NPV) and kappa (κ) value were calculated for each component against the reference standards within 95% confidence intervals (CIs); agreements between Determine HIV 1/2 and SD Bioline HIV tests were also calculated. Of 442 pregnant women recruited, eight (1.8%) were HIV positive, 22 (5.0%) had evidence of syphilis exposure; 14 (3.2%) had active infection. For HIV diagnosis, the sensitivity, specificity, PPV and NPV were 100% (95% CI: 63.1-100), 100% (95% CI: 99.2-100), 100% (95% CI: 63.1-100) and 100% (95% CI: 99.2-100) respectively with κ value of 1 (95% CI: 0.992-1.000). Overall agreement of the Duo HIV component and Determine test was 99.1% (95% CI: 0.977-0.998) with 66.7% (95% CI: 34.9-90.1) positive and 100% (95% CI: 0.992-1.000) negative percent agreements. For syphilis, the Duo assay sensitivity was 86.4% (95% CI: 65.1-97.1) and specificity 100% (95% CI: 99.1-100) with PPV 100% (95% CI: 82.4-100), NPV 99.2% (95% CI: 97.9-99.9) and κ value 0.92 (95% CI: 0.980-0.999). Our findings suggest the SD Bioline HIV/Syphilis Duo Assay could be suitable for HIV and syphilis testing in women attending antenatal services across South Sudan. Women with positive syphilis results should receive treatment immediately, whereas HIV positive women should undergo confirmatory testing following national HIV testing guidelines.