Adapting Longstanding Public Health Collaborations between Government of Kenya and CDC Kenya in Response to the COVID-19 Pandemic, 2020-2021.

Kenya's Ministry of Health (MOH) and the US Centers for Disease Control and Prevention in Kenya (CDC Kenya) have maintained a 40-year partnership during which measures were implemented to prevent, detect, and respond to disease threats. During the COVID-19 pandemic, the MOH and CDC Kenya rapidly responded to mitigate disease impact on Kenya's 52 million residents. We describe activities undertaken jointly by the MOH and CDC Kenya that lessened the effects of COVID-19 during 5 epidemic waves from March through December 2021. Activities included establishing national and county-level emergency operations centers and implementing workforce development and deployment, infection prevention and control training, laboratory diagnostic advancement, enhanced surveillance, and information management. The COVID-19 pandemic provided fresh impetus for the government of Kenya to establish a national public health institute, launched in January 2022, to consolidate its public health activities and counter COVID-19 and future infectious, vaccine-preventable, and emerging zoonotic diseases.

Methods for conducting trends analysis: roadmap for comparing outcomes from three national HIV Population-based household surveys in Kenya (2007, 2012, and 2018).

BACKGROUND: For assessing the HIV epidemic in Kenya, a series of independent HIV indicator household-based surveys of similar design can be used to investigate the trends in key indicators relevant to HIV prevention and control and to describe geographic and sociodemographic disparities, assess the impact of interventions, and develop strategies. We developed methods and tools to facilitate a robust analysis of trends across three national household-based surveys conducted in Kenya in 2007, 2012, and 2018. METHODS: We used data from the 2007 and 2012 Kenya AIDS Indicator surveys (KAIS 2007 and KAIS 2012) and the 2018 Kenya Population-based HIV Impact Assessment (KENPHIA 2018). To assess the design and other variables of interest from each study, variables were recoded to ensure that they had equivalent meanings across the three surveys. After assessing weighting procedures for comparability, we used the KAIS 2012 nonresponse weighting procedure to revise normalized KENPHIA weights. Analyses were restricted to geographic areas covered by all three surveys. The revised analysis files were then merged into a single file for pooled analysis. We assessed distributions of age, sex, household wealth, and urban/rural status to identify unexpected changes between surveys. To demonstrate how a trend analysis can be carried out, we used continuous, binary, and time-to-event variables as examples. Specifically, temporal trends in age at first sex and having received an HIV test in the last 12 months were used to demonstrate the proposed analytical approach. These were assessed with respondent-specific variables (age, sex, level of education, and marital status) and household variables (place of residence and wealth index). All analyses were conducted in SAS 9.4, but analysis files were created in Stata and R format to support additional analyses. RESULTS: This study demonstrates trends in selected indicators to illustrate the approach that can be used in similar settings. The incidence of early sexual debut decreased from 11.63 (95% CI: 10.95-12.34) per 1,000 person-years at risk in 2007 to 10.45 (95% CI: 9.75-11.2) per 1,000 person-years at risk in 2012 and to 9.58 (95% CI: 9.08-10.1) per 1,000 person-years at risk in 2018. HIV-testing rates increased from 12.6% (95% CI: 11.6%-13.6%) in 2007 to 56.1% (95% CI: 54.6%-57.6%) in 2012 but decreased slightly to 55.6% [95% CI: 54.6%-56.6%) in 2018. The decrease in incidence of early sexual debut could be convincingly demonstrated between 2007 and 2012 but not between 2012 and 2018. Similarly, there was virtually no difference between HIV Testing rates in 2012 and 2018. CONCLUSIONS: Our approach can be used to support trend comparisons for variables in HIV surveys in low-income settings. Independent national household surveys can be assessed for comparability, adjusted as appropriate, and used to estimate trends in key indicators. Analyzing trends over time can not only provide insights into Kenya's progress toward HIV epidemic control but also identify gaps.

Reflections on 40 Years of AIDS.

June 2021 marks the 40th anniversary of the first description of AIDS. On the 30th anniversary, we defined priorities as improving use of existing interventions, clarifying optimal use of HIV testing and antiretroviral therapy for prevention and treatment, continuing research, and ensuring sustainability of the response. Despite scientific and programmatic progress, the end of AIDS is not in sight. Other major epidemics over the past decade have included Ebola, arbovirus infections, and coronavirus disease (COVID-19). A benchmark against which to compare other global interventions is the HIV/AIDS response in terms of funding, coordination, and solidarity. Lessons from Ebola and HIV/AIDS are pertinent to the COVID-19 response. The fifth decade of AIDS will have to position HIV/AIDS in the context of enhanced preparedness and capacity to respond to other potential pandemics and transnational health threats.

Long-term immunological responses to treatment among HIV-2 patients in Côte d'Ivoire.

BACKGROUND: Studies indicate that responses to HIV-2 treatment regimens are worse than responses to HIV-1 regimens during the first 12 months of treatment, but longer-term treatment responses are poorly described. We utilized data from Côte d'Ivoire's RETRO-CI laboratory to examine long-term responses to HIV-2 treatment. METHODS: Adult (≥15 years) patients with baseline CD4 counts < 500 cells/µl that initiated treatment at one of two HIV treatment centers in Abidjan, Côte d'Ivoire between 1998 and 2004 were included in this retrospective cohort study. Patients were stratified by baseline CD4 counts and survival analyses were employed to examine the relationship between HIV type and time to achieving CD4 ≥ 500 cells/µl during follow up. RESULTS: Among 3487 patients, median follow-up time was 4 years and 57% had documented ART regimens for > 75% of their recorded visits. Kaplan-Meier estimates for achievement of CD4 ≥ 500 cells/µl after 6 years of follow-up for patients in the lower CD4 strata (< 200 cells/µl) were 40% (HIV-1), 31% (HIV-dual), and 17% (HIV-2) (log-rank p < 0.001). Cox Regression indicated that HIV-1 was significantly associated with achievement of CD4 ≥ 500 cells/µl during follow-up, compared to HIV-2. CONCLUSIONS: Sub-optimal responses to long-term HIV-2 treatment underscore the need for more research into improved and/or new treatment options for patients with HIV-2. In many West African countries, effective treatment of both HIV-1 and HIV-2 will be essential in the effort to reach epidemic control.

Ebola: Anatomy of an Epidemic.

As of the end of March 2016, the West Africa epidemic of Ebola virus disease (Ebola) had resulted in a total of 28,646 cases, 11,323 of them fatal, reported to the World Health Organization. Guinea, Liberia, and Sierra Leone were most heavily affected, but Ebola cases were exported to several other African and European countries as well as the United States, with limited further transmission, including to healthcare workers. We review the descriptive epidemiology of the outbreak, novel aspects and insights concerning the unprecedented response, scientific observations, and public health implications. The large number of Ebola survivors has highlighted the frequency of persistent symptoms and the possibility of virus persistence in sanctuary sites, sometimes leading to delayed transmission. Although transmission appears to have ceased in 2016, the West Africa Ebola epidemic has profoundly influenced discussions and practice concerning global health security.

Noncommunicable disease burden among HIV patients in care: a national retrospective longitudinal analysis of HIV-treatment outcomes in Kenya, 2003-2013.

BACKGROUND: Over the last decade, the Kenyan HIV treatment program has grown exponentially, with improved survival among people living with HIV (PLHIV). In the same period, noncommunicable diseases (NCDs) have become a leading contributor to disease burden. We sought to characterize the burden of four major NCDs (cardiovascular diseases, cancer, chronic respiratory diseases and diabetes mellitus) among adult PLHIV in Kenya. METHODS: We conducted a nationally representative retrospective medical chart review of HIV-infected adults aged ≥15 years enrolled in HIV care in Kenya from October 1, 2003 through September 30, 2013. We estimated proportions of four NCD categories among PLHIV at enrollment into HIV care, and during subsequent HIV care visits. We compared proportions and assessed distributions of co-morbidities using the Chi-Square test. We calculated NCD incidence rates and their confidence intervals in assessing cofactors for developing NCDs. RESULTS: We analyzed 3170 records of HIV-infected patients; 2115 (66.3%) were from women. Slightly over half (51.1%) of patient records were from PLHIVs aged above 35 years. Close to two-thirds (63.9%) of PLHIVs were on ART. Proportion of any documented NCD among PLHIV was 11.5% (95% confidence interval [CI] 9.3, 14.1), with elevated blood pressure as the most common NCD 343 (87.5%) among PLHIV with a diagnosed NCD. Despite this observation, only 17 (4.9%) patients had a corresponding documented diagnosis of hypertension in their medical record. Overall NCD incidence rates for men and women were (42.3 per 1000 person years [95% CI 35.8, 50.1] and 31.6 [95% CI 27.7, 36.1], respectively. Compared to women, the incidence rate ratio for men developing an NCD was 1.3 [95% CI 1.1, 1.7], p = 0.0082). No differences in NCD incidence rates were seen by marital or employment status. At one year of follow up 43.8% of PLHIV not on ART had been diagnosed with an NCD compared to 3.7% of patients on ART; at five years the proportions with a diagnosed NCD were 88.8 and 39.2% (p < 0.001), respectively. CONCLUSIONS: PLHIV in Kenya have a high prevalence of NCD diagnoses. In the absence of systematic, effective screening, NCD burden is likely underestimated in this population. Systematic screening and treatment for NCDs using standard guidelines should be integrated into HIV care and treatment programs in sub-Saharan Africa.

Building laboratory capacity to detect and characterize pathogens of public and global health security concern in Kenya.

Since 1979, multiple CDC Kenya programs have supported the development of diagnostic expertise and laboratory capacity in Kenya. In 2004, CDC's Global Disease Detection (GDD) program within the Division of Global Health Protection in Kenya (DGHP-Kenya) initiated close collaboration with Kenya Medical Research Institute (KEMRI) and developed a laboratory partnership called the Diagnostic and Laboratory Systems Program (DLSP). DLSP built onto previous efforts by malaria, human immunodeficiency virus (HIV) and tuberculosis (TB) programs and supported the expansion of the diagnostic expertise and capacity in KEMRI and the Ministry of Health. First, DLSP developed laboratory capacity for surveillance of diarrheal, respiratory, zoonotic and febrile illnesses to understand the etiology burden of these common illnesses and support evidenced-based decisions on vaccine introductions and recommendations in Kenya. Second, we have evaluated and implemented new diagnostic technologies such as TaqMan Array Cards (TAC) to detect emerging or reemerging pathogens and have recently added a next generation sequencer (NGS). Third, DLSP provided rapid laboratory diagnostic support for outbreak investigation to Kenya and regional countries. Fourth, DLSP has been assisting the Kenya National Public Health laboratory-National Influenza Center and microbiology reference laboratory to obtain World Health Organization (WHO) certification and ISO15189 accreditation respectively. Fifth, we have supported biosafety and biosecurity curriculum development to help Kenyan laboratories safely and appropriately manage infectious pathogens. These achievements, highlight how in collaboration with existing CDC programs working on HIV, tuberculosis and malaria, the Global Health Security Agenda can have significantly improve public health in Kenya and the region. Moreover, Kenya provides an example as to how laboratory science can help countries detect and control of infectious disease outbreaks and other public health threats more rapidly, thus enhancing global health security.

Molecular Evidence of Sexual Transmission of Ebola Virus.

A suspected case of sexual transmission from a male survivor of Ebola virus disease (EVD) to his female partner (the patient in this report) occurred in Liberia in March 2015. Ebola virus (EBOV) genomes assembled from blood samples from the patient and a semen sample from the survivor were consistent with direct transmission. The genomes shared three substitutions that were absent from all other Western African EBOV sequences and that were distinct from the last documented transmission chain in Liberia before this case. Combined with epidemiologic data, the genomic analysis provides evidence of sexual transmission of EBOV and evidence of the persistence of infective EBOV in semen for 179 days or more after the onset of EVD. (Funded by the Defense Threat Reduction Agency and others.).

Systems, supplies, and staff: a mixed-methods study of health care workers' experiences and health facility preparedness during a large national cholera outbreak, Kenya 2015.

BACKGROUND: From December 2014 to September 2016, a cholera outbreak in Kenya, the largest since 2010, caused 16,840 reported cases and 256 deaths. The outbreak affected 30 of Kenya's 47 counties and occurred shortly after the decentralization of many healthcare services to the county level. This mixed-methods study, conducted June-July 2015, assessed cholera preparedness in Homa Bay, Nairobi, and Mombasa counties and explored clinic- and community-based health care workers' (HCW) experiences during outbreak response. METHODS: Counties were selected based on cumulative cholera burden and geographic characteristics. We conducted 44 health facility cholera preparedness checklists (according to national guidelines) and 8 focus group discussions (FGDs). Frequencies from preparedness checklists were generated. To determine key themes from FGDs, inductive and deductive codes were applied; MAX software for qualitative data analysis (MAXQDA) was used to identify patterns. RESULTS: Some facilities lacked key materials for treating cholera patients, diagnosing cases, and maintaining infection control. Overall, 82% (36/44) of health facilities had oral rehydration salts, 65% (28/43) had IV fluids, 27% (12/44) had rectal swabs, 11% (5/44) had Cary-Blair transport media, and 86% (38/44) had gloves. A considerable number of facilities lacked disease reporting forms (34%, 14/41) and cholera treatment guidelines (37%, 16/43). In FDGs, HCWs described confusion regarding roles and reporting during the outbreak, which highlighted issues in coordination and management structures within the health system. Similar to checklist findings, FGD participants described supply challenges affecting laboratory preparedness and infection prevention and control. Perceived successes included community engagement, health education, strong collaboration between clinic and community HCWs, and HCWs' personal passion to help others. CONCLUSIONS: The confusion over roles, reporting, and management found in this evaluation highlights a need to adapt, implement, and communicate health strategies at the county level, in order to inform and train HCWs during health system transformations. International, national, and county stakeholders could strengthen preparedness and response for cholera and other public health emergencies in Kenya, and thereby strengthen global health security, through further investment in the existing Integrated Disease Surveillance and Response structure and national cholera prevention and control plan, and the adoption of county-specific cholera control plans.

Ebola and Its Control in Liberia, 2014-2015.

The severe epidemic of Ebola virus disease in Liberia started in March 2014. On May 9, 2015, the World Health Organization declared Liberia free of Ebola, 42 days after safe burial of the last known case-patient. However, another 6 cases occurred during June-July; on September 3, 2015, the country was again declared free of Ebola. Liberia had by then reported 10,672 cases of Ebola and 4,808 deaths, 37.0% and 42.6%, respectively, of the 28,103 cases and 11,290 deaths reported from the 3 countries that were heavily affected at that time. Essential components of the response included government leadership and sense of urgency, coordinated international assistance, sound technical work, flexibility guided by epidemiologic data, transparency and effective communication, and efforts by communities themselves. Priorities after the epidemic include surveillance in case of resurgence, restoration of health services, infection control in healthcare settings, and strengthening of basic public health systems.

Notes from the Field: Ongoing Cholera Outbreak - Kenya, 2014-2016.

On January 6, 2015, a man aged 40 years was admitted to Kenyatta National Hospital in Nairobi, Kenya, with acute watery diarrhea. The patient was found to be infected with toxigenic Vibrio cholerae serogroup O1, serotype Inaba. A subsequent review of surveillance reports identified four patients in Nairobi County during the preceding month who met either of the Kenya Ministry of Health suspected cholera case definitions: 1) severe dehydration or death from acute watery diarrhea (more than four episodes in 12 hours) in a patient aged ≥5 years, or 2) acute watery diarrhea in a patient aged ≥2 years in an area where there was an outbreak of cholera. An outbreak investigation was immediately initiated. A confirmed cholera case was defined as isolation of V. cholerae O1 or O139 from the stool of a patient with suspected cholera or a suspected cholera case that was epidemiologically linked to a confirmed case. By January 15, 2016, a total of 11,033 suspected or confirmed cases had been reported from 22 of Kenya's 47 counties (Table). The outbreak is ongoing.

Evolution of ebola virus disease from exotic infection to global health priority, Liberia, mid-2014.

Over the span of a few weeks during July and August 2014, events in West Africa changed perceptions of Ebola virus disease (EVD) from an exotic tropical disease to a priority for global health security. We describe observations during that time of a field team from the Centers for Disease Control and Prevention and personnel of the Liberian Ministry of Health and Social Welfare. We outline the early epidemiology of EVD within Liberia, including the practical limitations on surveillance and the effect on the country's health care system, such as infections among health care workers. During this time, priorities included strengthening EVD surveillance; establishing safe settings for EVD patient care (and considering alternative isolation and care models when Ebola Treatment Units were overwhelmed); improving infection control practices; establishing an incident management system; and working with Liberian airport authorities to implement EVD screening of departing passengers.

The movement of multidrug-resistant tuberculosis across borders in East Africa needs a regional and global solution.

Kevin Cain and colleagues reflect on the cross border movement of people from Somalia with MDR-TB and the implications for MDR-TB programs in East Africa.

Scale-up of HIV Viral Load Monitoring--Seven Sub-Saharan African Countries.

To achieve global targets for universal treatment set forth by the Joint United Nations Programme on human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) (UNAIDS), viral load monitoring for HIV-infected persons receiving antiretroviral therapy (ART) must become the standard of care in low- and middle-income countries (LMIC) (1). CDC and other U.S. government agencies, as part of the President's Emergency Plan for AIDS Relief, are supporting multiple countries in sub-Saharan Africa to change from the use of CD4 cell counts for monitoring of clinical response to ART to the use of viral load monitoring, which is the standard of care in developed countries. Viral load monitoring is the preferred method for immunologic monitoring because it enables earlier and more accurate detection of treatment failure before immunologic decline. This report highlights the initial successes and challenges of viral load monitoring in seven countries that have chosen to scale up viral load testing as a national monitoring strategy for patients on ART in response to World Health Organization (WHO) recommendations. Countries initiating viral load scale-up in 2014 observed increases in coverage after scale-up, and countries initiating in 2015 are anticipating similar trends. However, in six of the seven countries, viral load testing coverage in 2015 remained below target levels. Inefficient specimen transport, need for training, delays in procurement and distribution, and limited financial resources to support scale-up hindered progress. Country commitment and effective partnerships are essential to address the financial, operational, technical, and policy challenges of the rising demand for viral load monitoring.

Possible sexual transmission of Ebola virus - Liberia, 2015.

On March 20, 2015, 30 days after the most recent confirmed Ebola Virus Disease (Ebola) patient in Liberia was isolated, Ebola was laboratory confirmed in a woman in Monrovia. The investigation identified only one epidemiologic link to Ebola: unprotected vaginal intercourse with a survivor. Published reports from previous outbreaks have demonstrated Ebola survivors can continue to harbor virus in immunologically privileged sites for a period of time after convalescence. Ebola virus has been isolated from semen as long as 82 days after symptom onset and viral RNA has been detected in semen up to 101 days after symptom onset. One instance of possible sexual transmission of Ebola has been reported, although the accompanying evidence was inconclusive. In addition, possible sexual transmission of Marburg virus, a filovirus related to Ebola, was documented in 1968. This report describes the investigation by the Government of Liberia and international response partners of the source of Liberia's latest Ebola case and discusses the public health implications of possible sexual transmission of Ebola virus. Based on information gathered in this investigation, CDC now recommends that contact with semen from male Ebola survivors be avoided until more information regarding the duration and infectiousness of viral shedding in body fluids is known. If male survivors have sex (oral, vaginal, or anal), a condom should be used correctly and consistently every time.

A rapid assessment of drinking water quality in informal settlements after a cholera outbreak in Nairobi, Kenya.

Populations living in informal settlements with inadequate water and sanitation infrastructure are at risk of epidemic disease. In 2010, we conducted 398 household surveys in two informal settlements in Nairobi, Kenya with isolated cholera cases. We tested source and household water for free chlorine residual (FCR) and Escherichia coli in approximately 200 households. International guidelines are ≥0.5 mg/L FCR at source, ≥0.2 mg/L at household, and <1 E. coli/100 mL. In these two settlements, 82% and 38% of water sources met FCR guidelines; and 7% and 8% were contaminated with E. coli, respectively. In household stored water, 82% and 35% met FCR guidelines and 11% and 32% were contaminated with E. coli, respectively. Source water FCR≥0.5 mg/L (p=0.003) and reported purchase of a household water treatment product (p=0.002) were associated with increases in likelihood that household stored water had ≥0.2 mg/L FCR, which was associated with a lower likelihood of E. coli contamination (p<0.001). These results challenge the assumption that water quality in informal settlements is universally poor and the route of disease transmission, and highlight that providing centralized water with ≥0.5 mg/L FCR or (if not feasible) household water treatment technologies reduces the risk of waterborne cholera transmission in informal settlements.

Assessment of ebola virus disease, health care infrastructure, and preparedness - four counties,Southeastern Liberia, august 2014.

Ebola virus disease (Ebola) is a multisystem disease caused by a virus of the genus Ebolavirus. In late March 2014, Ebola cases were described in Liberia, with epicenters in Lofa County and later in Montserrado County. While information about case burden and health care infrastructure was available for the two epicenters, little information was available about remote counties in southeastern Liberia. Over 9 days, August 6-14, 2014, Ebola case burden, health care infrastructure, and emergency preparedness were assessed in collaboration with the Liberian Ministry of Health and Social Welfare in four counties in southeastern Liberia: Grand Gedeh, Grand Kru, River Gee, and Maryland. Data were collected by health care facility visits to three of the four county referral hospitals and by unstructured interviews with county and district health officials, hospital administrators, physicians, nurses, physician assistants, and health educators in all four counties. Local burial practices were discussed with county officials, but no direct observation of burial practices was conducted. Basic information about Ebola surveillance and epidemiology, case investigation, contact tracing, case management, and infection control was provided to local officials.

Cluster of Ebola cases among Liberian and U.S. health care workers in an Ebola treatment unit and adjacent hospital -- Liberia, 2014.

The ongoing Ebola virus disease (Ebola) epidemic in West Africa, like previous Ebola outbreaks, has been characterized by amplification in health care settings and increased risk for health care workers (HCWs), who often do not have access to appropriate personal protective equipment. In many locations, Ebola treatment units (ETUs) have been established to optimize care of patients with Ebola while maintaining infection control procedures to prevent transmission of Ebola virus. These ETUs are considered essential to containment of the epidemic. In July 2014, CDC assisted the Ministry of Health and Social Welfare of Liberia in investigating a cluster of five Ebola cases among HCWs who became ill while working in an ETU, an adjacent general hospital, or both. No common source of exposure or chain of transmission was identified. However, multiple opportunities existed for transmission of Ebola virus to HCWs, including exposure to patients with undetected Ebola in the hospital, inadequate use of personal protective equipment during cleaning and disinfection of environmental surfaces in the hospital, and potential transmission from an ill HCW to another HCW. No evidence was found of a previously unrecognized mode of transmission. Prevention recommendations included reinforcement of existing infection control guidance for both ETUs and general medical care settings, including measures to prevent cross-transmission in co-located facilities.

Developing an incident management system to support Ebola response -- Liberia, July-August 2014.

The ongoing Ebola virus disease (Ebola) outbreak in West Africa is the largest and most sustained Ebola epidemic recorded, with 6,574 cases. Among the five affected countries of West Africa (Liberia, Sierra Leone, Guinea, Nigeria, and Senegal), Liberia has had the highest number cases (3,458). This epidemic has severely strained the public health and health care infrastructure of Liberia, has resulted in restrictions in civil liberties, and has disrupted international travel. As part of the initial response, the Liberian Ministry of Health and Social Welfare (MOHSW) developed a national task force and technical expert committee to oversee the management of the Ebola-related activities. During the third week of July 2014, CDC deployed a team of epidemiologists, data management specialists, emergency management specialists, and health communicators to assist MOHSW in its response to the growing Ebola epidemic. One aspect of CDC's response was to work with MOHSW in instituting incident management system (IMS) principles to enhance the organization of the response. This report describes MOHSW's Ebola response structure as of mid-July, the plans made during the initial assessment of the response structure, the implementation of interventions aimed at improving the system, and plans for further development of the response structure for the Ebola epidemic in Liberia.