*2.2. Setting*

#### 2.2.1. General Setting: Kenya and Nairobi

Kenya is an East African country located along the Equator. The country is bordered by Somalia, Sudan, Ethiopia, Uganda and Tanzania. In 2019, the population was estimated at almost 53 million, with 32% living in urban areas, and life expectancy at birth was estimated at 66 years [16,17]. The major drivers of the country's economy have been agriculture, fishing, forestry, education, retail trade, construction and financial services [16]. In 2019, the gross national income per capita was approximately USD 1750 [17].

Nairobi is the capital city and one of the 47 semi-autonomous counties in the country. In 2019, it had an estimated population of 4.4 million. The current study took place in the City County of Nairobi because nearly 80% of COVID-19 cases in Kenya were reported from this area at the onset of the outbreak. The County of Nairobi is divided into 10 TB control zones with just over 1000 registered health facilities [18]. To achieve good county geographical representation, two well-established facilities from each of these 10 TB control zones were purposively selected in consultation with the head of the TB Programme and the County TB and Leprosy coordinator. Selected facilities had the following on-site characteristics: TB diagnostic capability (smear microscopy and/or the Xpert MTB/RIF® assay); TB treatment and monitoring services; HIV testing and ART referral or treatment services.

The initial sites included seven hospitals, nine health centers and four dispensaries. Two of these health facilities had to be excluded before starting. One health center on the Kenyatta University Campus closed at the start of lockdown and remained closed indefinitely thereafter. One of the hospitals required its own ethics approval for the study. However, this was going to take too long and the hospital had to be excluded. This left 18 health facilities in total available for the duration of the study. The established staff who were already working in these facilities delivering TB and HIV services helped with the monthly collection of data.

#### 2.2.2. TB and HIV Services

The diagnosis and treatment of TB and HIV/AIDS in Kenya are the responsibility of the Ministry of Health. People with symptoms suggestive of TB (cough, fever, weight loss and night sweats) are classified as having presumptive pulmonary TB (PTB). They are recorded as such when attending a health facility, along with their demographic details. Investigations are carried out according to national guidelines [19], using sputum smear microscopy and/or the Xpert MTB/RIF® assay to establish a bacteriologically confirmed diagnosis of PTB. In the other patients, clinical assessment, radiography and other circumstantial evidence are used to establish a diagnosis of clinically diagnosed PTB or extrapulmonary TB (EPTB). Patients with diagnosed TB (drug-susceptible and drug-resistant) are registered and started on anti-TB treatment in line with national and international guidelines [19,20]. Treatment outcomes are monitored, recorded and reported according to international guidelines [21].

HIV testing is institutionalized in the public health facilities and routinely offered to anyone attending for care and also to TB patients according to national and international guidelines [22,23]. HIV testing is carried out using rapid testing algorithms. Those diagnosed HIV-positive are referred to ART services for immediate start of ART regardless of WHO clinical stage or CD4 cell count.

There is generally good quality data capture and reporting for TB and HIV/AIDS at all levels due to regular supervision by county and national programme supervisors.

#### 2.2.3. Data Monitoring, Recording and Reporting

For this study, we selected only patients with drug-susceptible TB who were treated and monitored with the standard six month regimen [19,20]. Data were routinely collected on a daily basis by healthcare workers in each study site using the standard existing monitoring tools. These included: the TB presumptive and/or the TB laboratory register for presumptive TB depending on the facility; the TB patient register for those diagnosed and registered with TB and in which TB treatment outcomes were also recorded; and the HIV Testing Services (HTS) Register in which those diagnosed HIV-positive and referred for ART were recorded. These registers were mainly paper-based. One to two weeks after the end of each month, the project country coordinator (IM—who was appointed specifically for the study) visited each site along with her team of trained data collectors. They collated the individual data on TB and HIV variables for the previous month into monthly aggregate data, which they then entered into a data form developed using an EpiCollect5 mobile application (https://five.epicollect.net, accessed on 19 April 2021).

For TB treatment outcomes, we took the monthly cohorts of patients who had been enrolled onto treatment eight months previously – this allowed for six months of treatment to be completed and a further two months for outcomes to be validated and documented in the records. Thus, for example, the August 2020 TB treatment outcome data were obtained for the TB patients enrolled and started on treatment in January 2020. National data on COVID-19 cases and deaths reported to WHO on the last day of the month were obtained from WHO situation and epidemiological reports [1]. When collecting the monthly data during the COVID-19 period, the same procedures were used to collect data for the same month one year previously (termed the pre-COVID-19 period).

Once all the data for the month had been entered into EpiCollect5, they were checked and validated by the project country coordinator and the overall project monitoring and evaluation officer (PT) based at The Union. Data were then presented in a monthly report to the heads of the NTLD-P and NASCOP and all other relevant stakeholders involved in the project. Key policy or practice changes made at the local facility, county, or national level during that month to explain and/or counteract the effects of COVID-19 on TB and HIV parameters were documented in a narrative table within the report. These monthly reports always reached the national programme staff heads within four weeks of closure of that month to enable timely surveillance and possible action.

### *2.3. Study Population*

The study population included all patients presenting to TB services with presumptive TB, all TB patients registered for TB treatment and all persons tested for HIV in 18 health facilities in Nairobi, Kenya, between March 2019 and February 2021: the COVID-19 period was designated as March 2020 to February 2021, and the pre-COVID-19 period was designated as March 2019 to February 2020. For assessment of TB treatment outcomes, we included TB patients who started on treatment from (i) August 2018 to July 2019 (pre-COVID-19 cohort) and (ii) August 2019 to July 2020 (COVID-19 cohort).

#### *2.4. Data Variables, Sources of Data and Timing of Data Collection*

Data variables for TB included aggregate numbers of presumptive PTB patients, stratified by male and female and adults ( ≥15 years) and children (<15 years); presumptive PTB patients who were diagnosed bacteriologically positive by either smear microscopy and/or Xpert MTB/RIF®; registered TB patients, stratified by bacteriologically confirmed PTB, clinically diagnosed PTB and EPTB; registered TB patients who were newly tested for HIV in that month after being diagnosed with TB—this excluded patients who already knew they were HIV-positive; standardized TB treatment outcomes of those patients enrolled for treatment eight months previously–these outcomes included treatment success (a combination of those cured and those who completed treatment with no sputum smear examination), lost to follow-up (LTFU), died, failed treatment or not evaluated [21]. Not evaluated is an outcome given to those who transfer from one facility to another and for whom the final treatment outcome is not recorded. Data variables for HIV included an aggregate number of persons who were HIV tested, stratified by male and female and adults ( ≥15 years) and children (<15 years); persons diagnosed HIV-positive; HIV-positive persons referred to ART services.

Sources of primary individual data were the TB presumptive and/or TB laboratory register, the TB patient register, and the HTS register. The national COVID-19 cases and deaths reported to WHO on the last day of the month were obtained from WHO situation and epidemiological reports [1]. Aggregate data were collected from the primary data sources and uploaded to an EpiCollect5 application, where they were checked and validated, and this was carried out between June 2020 and March 2021.

#### *2.5. Analysis and Statistics*

Aggregate data were presented as frequencies and proportions, and comparisons were made between the COVID-19 period and the pre-COVID-19 period. The percentage difference (decline or increase) in numbers during each month of the COVID-19 period was calculated relative to the numbers during the same month of the pre-COVID-19 period. The relative percentage differences observed between the first six months of COVID-19 (March to August 2020) and the second six months of COVID-19 (September 2020 to February 2021) were also calculated.
