A review protocol was developed and registered with the Open Scientific Framework registry (https://osf.io/a6s9j/), to ensure transparency.

A scoping literature review was conducted following the PRISMA extension for scoping reviews (PRISMA-ScR) guidelines (46–48), incorporating the methodology framework outlined by Arksey and O’Malley (49) and subsequently refined by Levac et al. (50). Searches were performed in five electronic databases that index peer-reviewed literature: EMBASE, MEDLINE, PubMed, Web of Science and Scopus, ensuring the reliability and credibility of our findings from sources that undergo rigorous evaluation by experts. However, we acknowledge potential biases, including publication bias and geographical gaps, which may limit the generalizability of our findings to the entire EAC. Consequently, in this review we focused on five EAC member states namely: Kenya, Tanzania, Uganda (joined EAC in 2000) and, Rwanda, Burundi (joined in 2007) (51), with robust data and more homogeneous ecological and climatic conditions to provide insights into disease transmission patterns and control strategies relevant to the majority of the EAC member states (52–56).

The literature searches used relevant terminologies related to MBDs transmitted by mosquito species of public health importance in urban EAC as outlined in the introduction section, the respective disease-transmitting mosquito genus, mosquito infection measures and the names of the EAC countries ( Table 1 ). The databases were searched for studies published from 1^st January 2000 to 13^th July 2024. The year 2000 was chosen as a starting point for our search to reflect the timing of increased interest in mosquito urban research on the potential public health impact of mosquito-borne diseases in urban settings in the EAC region (57, 58). A language restriction was applied to include articles only written in English and French. Full search strategies used for each database are provided in the review protocol (https://osf.io/a6s9j/).

Studies were eligible for inclusion in the review if they met the following inclusion criteria: (i) articles reporting data published between 2000 and 2024 in EAC (Kenya, Uganda, Mainland Tanzania, Rwanda, and Burundi); (ii) articles that included information on any of the following outcomes of interest: the distribution, abundance, density and urban ecology adaptations of mosquito population, mosquito species composition, feeding and breeding preferences, and mosquito infection rates in urban and/or peri-urban settings; (iii) studies reporting information on mosquito species responsible for a subset of MBDs (Malaria, Dengue, Chikungunya, Yellow fever, Rift valley fever, Zika and Lymphatic filariasis) prevalent in urban EAC settings and (iv) articles published in English or French. We excluded studies that (i) reported entomological outcomes in rural settings; (ii) provided modelled entomological outcomes such as the suitability indices of mosquito habitats or other vector outcomes such as insecticide resistance and molecular or genetic data of vector species; (iii) reported infection rates (seroprevalences) on humans and animals and (iv) evaluated arbovirus vectors other than mosquitoes such as flies and ticks.

All articles obtained from the searches were downloaded by one review author (NKJ) to EndNote 20 (Clarivate Analytics, PA, USA), and duplicates removed. After de-duplication, title- and-abstract screening and full-text screening were performed using the Rayyan systematic review open-source software (https://www.rayyan.ai/), that facilitates collaborative screening of articles while ensuring double-blinded article selection, reducing article selection bias. In addition, the software enables logs of reasons for exclusion and lists disagreements between reviewers. This ensures transparency and helps solve review discrepancies efficiently (59).

Three authors (NKJ, EM, English articles and CM, French articles) independently screened the titles and abstracts of all articles to filter studies that met the basic eligibility criteria. Eligible studies were selected through a questionnaire that specified the inclusion criteria as outlined in the review protocol (https://osf.io/a6s9j/). Two reviewers, NKJ and EM conducted full-text screening of the retained articles to ensure compliance with all inclusion criteria. Notably, at the full-text screening stage we reviewed the methods section describing the study sites to ascertain the urban/peri-urban focus of all the retrieved articles that may not be explicitly defined in the title and abstract. For example, when screening studies specifying a broader area, such as an administrative location or a major city as the study area in the title or abstract, we examined the methods section to identify if the sampled sites included were located within the vicinity of the city centre (urban strata), or peri-urban or rural settings. Citations of the included articles after full-text screening were manually screened to identify additional studies. Discrepancies concerning eligibility throughout the whole screening process were resolved through discussion among the reviewers.

All articles selected for inclusion were synthesised using a standardized Microsoft Excel spreadsheet data extraction form developed by NKJ and endorsed by other authors: PMM, CL and RWS. The Microsoft Excel form included the following data categories: study details (authorship, year of publication, study country, study location, geographical coordinates of sampled sites, study period), urbanicity (urban/peri-urban, key urban/peri urban characteristics linked to mosquito population), entomological surveillance metadata (mosquito collection techniques, species identification, indoor and/or outdoor sampling, mosquito life stage collected), mosquito-borne disease of study focus, transmission indices (disease-specific infection rates among mosquito populations sampled and human biting/blood meal rates), vector species involved in the transmission, vector abundance/density and vector bionomics (biting, feeding, and breeding preferences). Data extraction was limited to the information provided in the published work; authors were not contacted for further clarification or provision of missing information. NKJ extracted and recorded data manually to the Microsoft excel form including each listed variable for all selected articles and a second review author (EM), validated 20% of the extracted data. Finally, a geo-positioning entry matching the sampled sites of the selected studies was done by EM using electronic sources such as Google Earth to obtain the geographical coordinates of sampled sites when not provided.

Data extracted from the selected articles were thematically categorized to facilitate analysis while accounting for heterogeneity in various studies in terms of study scope and outcomes of interest. The thematic categories used included: i) ecological studies describing the different mosquito genera distributions and species compositions in urban/peri-urban study sites), ii) descriptive (studies providing the bionomic assessments of mosquito population such as mosquito genera co-occurrence, adaptations and preferred breeding sites), iii) transmission measures (studies reporting disease specific mosquito infectivity rates in urban/peri-urban contexts in EAC and iv) multiple scope category (consisted at least two categories previously mentioned).

Empirical data on disease-specific infection rates were pre-processed to obtain summaries following entomological adjustments from previous research (16) that account for variations in sampling methods (e.g., indoor/outdoor surveillance) and frequency of surveillance used in the studies reviewed. The following adjustments were applied: i) when multiple disease-specific infection rates were reported for the same site (infection rates corresponding to sub-locations within an urban/peri-urban region) at a particular point in time, the estimates were averaged; ii) when both indoor and outdoor disease-specific infection rates were reported, the rates were averaged iii) when data was available for two different seasons the infection rates corresponding to peak transmission seasons were considered and, iv) when data are available for different points in time but same season, the most recent rate was reported.

Overall, we summarized and presented data related to ‘urban’ definitions used in each study drawing converging and divergent definitions, a tally of the mosquito genera and species composition reported in each study site, the mosquito surveillance methods used, and the average disease infection rates in mosquito population using tables or figures to provide an overview of the urban typology in MBD research and mosquito population in EAC’s urban contexts. Summary tables and figures were produced using R version (4.3.2), and maps were produced using ArcGIS Pro version (3.1).

The search strategy yielded a total of 12,241 articles, with 5,577 articles remaining after removal of duplicate studies. The articles’ titles and abstracts were screened, and irrelevant studies excluded, resulting in 212 studies that were eligible for full-text screening. Two full texts were not accessible and hence excluded. A full-text screening of 210 articles was conducted and 108 articles with irrelevant information excluded, while 102 articles met the inclusion criteria. An additional three relevant articles were identified and included from the reference list of selected articles. Ultimately, a total of 105 articles were synthesised in the scoping review ( Supplementary File 1 ). A PRISMA flowchart summarizing the stages of the screening process is presented Figure 1 .

Most of the studies were conducted in Kenya (n=61; 58%) followed by Tanzania (n=31; 30%), Uganda (n=10, 10%) and Rwanda (n=3; 3%) ( Supplementary File 2: Figure 1A ). No studies were identified from urban Burundi. The thematic categories of articles included were distributed as follows: descriptive studies on mosquito genera bionomics, co-occurrence, and adaptation (n=51; 49%), transmission measures of disease-specific mosquito infection rates (n=23; 22%) and ecological studies highlighting mosquito genera distribution and species composition across countries (n=16; 15%), while 15 (14%) articles tackled multiple scopes of indicators of interest of this review ( Supplementary File 2: Figure 1B ).

Data presented were derived from 88 unique study sites conducted in urban (n=45), peri-urban (n=25), mixed (i.e., urban, and peri-urban) (n=14) and urban informal settlement (n=4) based on the authors’ descriptions across EAC. Among all the 88 unique sites, Kisumu city in Kenya had the most studies (n=23), followed by Dar es salaam in Tanzania (n=20) and Malindi town (n=14) in Kenya ( Figure 2 ).

Varied definitions of urban/peri-urban settings emerged within the context of mosquito population research. The majority of studies, 89.5% (n=94) reviewed, relied on conventional definitions to define an ‘urban’-rural dichotomy based on various metrics, including population counts or density thresholds, administrative definitions (e.g., capital city of a country), functional characteristics (e.g., type of economic activity such as the extent of trade and agriculture in a specific geographical area) and economic development indicators (e.g., type of infrastructure such as road networks). In contrast, 11 studies conducted in Tanzania (Dar es Salaam and Ifakara: n=4) and Kenya (Malindi, Ukunda and Kisumu; n=7) applied an urban-gradient definition indicating spatial variations of context-specific factors associated with mosquito population to distinguish urban centres and peri-urban areas within a city, shifting from the ‘urban’-rural dichotomous definition to an urban-peri-urban continuum. For example, urban areas were typically described based on development dynamics exhibiting higher population densities, intra-urban connectivity based on transport routes, and improved housing conditions, while peri-urban areas often demonstrated intermediate characteristics between urban and rural environments with varying levels of housing infrastructure development often sheltered by vegetation or agricultural land. Conversely, suburbs/informal settlements were characterized as rapidly expanding unplanned neighbourhoods with poor housing and socioeconomic factors such as unreliable water supply (water storage), unreliable sewer and waste management systems. In addition, topographical factors influencing the types of mosquito habitat proximity (natural habitats such as river valleys, lakes and swamps and artificial habitats such as flood plains) was highlighted as important site characteristic across all urban typologies in MBD research ( Supplementary File 2: Table 1 ).

Mosquito surveillance methods varied widely based on the different study designs tailored to account for the heterogeneity of each study location ( Table 2 ). Most of the studies, 45% (n=49) focused on outdoor mosquito collections followed by a substantial portion targeting both indoor and outdoor collections 41% (n=40), with a smaller proportion concentrating solely on indoor collections 14% (n=12). Regarding mosquito life stage, adult mosquitoes were the predominant target, with 47% (n=44) of studies focusing exclusively on this stage, 37% (n=34) targeting immature stages (reared into adults), and 13% (n=15) addressing both life stages. Various mosquito capture methods were used, with the CDC-light traps used in 23%(n=24) studies, followed by human landing catches in 20%(n=21) for adult mosquito catches while larval dipping 76% (n=35) was the most common method for mosquito immature collections. Morphological methods were the most preferred methods for genus identification utilized in 61%(n=41) studies, while molecular (e.g., Polymerase Chain Reaction) or a combination of molecular and morphological identification methods were used in the remaining studies 39%(n=26).

Among the studies reviewed, 11%(n=10) compared mosquito collection methods in urban EAC ( Supplementary File 2: Table 1 ). Nine of the ten studies assessed Anopheles species collection methods focusing mainly on An. gambiae s.l while one study evaluated the performance of three gravid traps [Sticky ovitraps (SO), MosquiTraps (MQT) and the CDC Gravid trap (CDC-GT)] to capture culex and aedes mosquitoes. These studies reported varied efficacy of various mosquito collection methods based on factors such as mosquito species diversity, habitat and biting preferences, and geographical context. For example, mosquito electrocuting grid traps, odour-baited CDC light traps and the Ifakara Tent Trap (ITT) were reported as sensitive tools to quantify epidemiologically relevant metrics such as mosquito biting densities, behaviours and human exposure distribution for An. gambiae s.l (An. Arabiensis, An. gambiae s.s. and An. Merus) that were statistically indistinguishable compared to Human landing catch (HLC) and BG-Sentinel traps. In addition, gravid traps were reported to be significantly efficient for Ae. aegypti and Cx. Quinquefasciatus collection ( Supplementary File 2: Table 2 ).

Collectively, 91 mosquito species were reported across urban and peri-urban EAC settings in studies published between the years 2000-2024. Species in the Culex, Aedes and Anopheles genera constituted 33% (n=30), 30% (n=27), 25%(n=23), respectively while others reported alongside the study focus genera were Coquillettidia (4%; n=4), Mansonia (2%; n=2) and other genera such as Lutzia, Eretmapodites, Toxorhynchites, Ficalbia (5%; n=5) ( Figure 3A ). The diversity of the mosquito species in the Aedes and Culex genera was greater in urban settings compared to peri-urban settings, while the diversity of mosquito species of the Anopheles genus was greater in peri-urban areas compared to urban settings ( Figure 3B ).

Within the Anopheles gambiae complex, An. gambiae sensu stricto and An. Arabiensis were prevalent in both urban and peri-urban settings. However, An. merus was predominantly found in urban areas, indicating a potential adaptation to urban environments. In addition, within the Aedes and Culex genera, Ae. aegypti and Cx.pipiens s.l especially Cx. quinquefasciatus were common in both urban and peri-urban settings ( Supplementary File 2: Figure 2 ). Seven studies highlighted varied adaptations of existing species to urban settings including changes in blood-seeking activities (biting), preference to outdoor breeding and species composition ( Supplementary File 2: Table 3 ). Of the 105 studies analysed, 44% (n=41) investigated factors associated to the co-occurrence of multiple mosquito genera in urban environments. Preference of breeding habitats and climatic variations (temperature and precipitation) were highlighted as contributing factors to the co-existence of Aedes, Anopheles and Culex mosquitoes. Aedes and Culex mosquitoes were commonly found to coexist in urban environments rich in artificial containers, small water bodies and discarded receptacles while Anopheles and Culex mosquitoes often overlap, predominantly in natural settings characterized by stagnant ponds and vegetated areas within urban landscapes ( Supplementary File 2: Table 4 ).

Thirty-two studies isolated pathogens from collected mosquitoes to assess the infection rates of varied MBDs prevalent in humans. Twenty-seven studies reported infection rates in field-caught mosquitoes while five studies (excluded from the infection rates analysis) were semi-field experimental assessments of vector competency for transmission. Studies to incriminate malaria vectors by detection of Plasmodium falciparum sporozoites were spread across the study period while those of other MBDs of interest were published post 2015 in the urban EAC. Consequently, many of the studies (n=18) evaluated P. falciparum sporozoites linked to malaria infections while both Dengue and Chikungunya virus isolates were reported in six and seven studies respectively. Other arboviruses namely Yellow Fever (n=5), Rift Valley Fever (n=1) and Zika viruses (n=1) were also reported in the EAC region for years post-2015. Three studies conducted in Kenya reported positive flavivirus isolates representing potential for co-infection of arboviruses in field-caught mosquitoes ( Supplementary File 2: Table 5 ).

The average infection rates in field-caught mosquito populations varied, ranging from 0.8% for Yellow Fever virus to 5.3% for Chikungunya virus ( Figure 4 ). Only studies on P. falciparum sporozoites infections evaluated infection rates in both urban and peri-urban contexts with no significant differences. Urban strata reported P. falciparum infection rates (n=4) ranging from 0.46% in 2009 to 1.14% in 2016 in Dar es salaam, Tanzania, while peri-urban strata reported infection rates (n=11) ranging from 0.02% in Jinja, Uganda to 3.92% in Kakamega, Kenya.

Extreme values were reported for Zika virus (67.1%) in Entebbe, Uganda, flavivirus (11.7%) and Rift valley fever virus (22%) in Sogan-Godud town in Kenya in studies that considered both domestic and zoonotic forest forms (Aedes) of mosquito vectors found in forests/national parks within the periphery of urban settings ( Supplementary File 2: Table 5 ). However, these extreme values were likely a result of testing small mosquito samples for pathogens, which may not accurately represent the broader mosquito population and its infection rates.