A team of 29 Subject Matter Experts (SMEs) convened in March 2024 in Fort Portal, Uganda, to conduct a horizon scanning exercise. They were drawn from academia (including the Universities of Busitema, Kabale, Kyambogo, Makerere, and the Mountains of the Moon); the National Research System (which comprises institutions under the National Agricultural Research Organisation, NARO); a department within the Ministry of Agriculture, Animal Industry and Fisheries (Department of Crop Protection); a regulatory agency (National Plant Protection Organisation (NPPO) of Uganda, the Department of Crop Inspection and Certification, DCIC); and international research organisations (the Alliance of Bioversity International and CIAT and CABI). The SMEs represented various disciplines, including bacteriology, entomology, mycology, nematology, and virology and demonstrated substantial experience in policy and phytosanitary matters.

Utilising the premium version of the Horizon Scanning Tool, a preliminary selection of plant pests not yet reported in Uganda was conducted. The parameters set in the tool included identifying the area at risk (Uganda) and selecting regions from which non-native pests are likely to be introduced (source areas). The source areas included all geographical regions in Africa, Asia, Europe, North America, Oceania, and South America. All parameters except for the type of organism were left open. The pest organisms considered included arthropods, bacteria (including phytoplasma), chromista, fungi, molluscs, protists, plant parasitic nematodes, and viruses (including viroids). Following the scan, a list was downloaded in Excel (.xlsx) format for further analysis.

The initial list was reviewed to eliminate pests represented only by their genera. Three criteria were then employed to prioritise pests for rapid risk assessment. First, the pest had to infect crops and trees cultivated in the area at risk (Uganda). Second, it had to be a vector and also on the horizon scanning list. Third, while invasiveness was not considered for bacteria, chromista, fungi, molluscs, nematodes, or protists, it was a criterion for selecting the arthropods due to their sheer numbers. Thus, invasive arthropods that affect the host (value chains) were thus prioritised. Following the assessment of bacteria, fungi, nematodes, phytoplasma, viroids, and viruses, arthropod vectors that are part of the horizon scanning output were incorporated into the list of already prioritised arthropods. Throughout the prioritisation, the SMEs also excluded pests known to occur in Uganda. The final list was subjected to a rapid risk assessment.

The risk-scoring guidelines employed were based on the descriptions provided by Roy et al. (2019) but have been modified in the works of Kenis et al., 2022 and Mulema et al., 2022. Roy et al. (2019) evaluated the likelihood of introduction (entry), establishment, spread, and the potential negative impact on biodiversity and ecosystem services. However, this study assessed the likelihood of introduction (entry), establishment (including aspects of spread), and potential socio-economic and environmental (biodiversity) impacts. A five-point scoring system detailed in Supplementary File S1 was utilised for the four parameters (entry, establishment, socio-economic, and biodiversity impact).

A score of one indicated that the organism was absent from Africa and unlikely to be found in an imported commodity; two indicated absence from Africa but likely to be infrequently imported on a commodity; three was ascribed to three scenarios, namely present in Africa (not in countries neighbouring Uganda) and spread slowly; or absent from Africa but shown to spread rapidly across several continents, or often associated to a commodity commonly imported, or frequently intercepted in Uganda; four indicated presence in Africa (not in neighbouring countries) and rapid spread or presence in a neighbouring country with slow spread; and five indicated presence in a neighbouring country (Democratic Republic of the Congo (DR Congo), Kenya, Rwanda, South Sudan, and Tanzania) with rapid spread.

An alien species may enter a new geographical or political region through three primary mechanisms that comprise six pathways. A pathway refers to any means that facilitates the entry and spread of a pest (IPPC Secretariat, 2021). The three mechanisms include the importation of a commodity (three pathways: contaminant, escape, and release), the arrival of a transport vector (one pathway: stowaway), and the natural spread from a neighbouring region (two pathways: corridor and unaided) (Hulme et al., 2008). However, for this study, only three pathways were considered: contaminant (CO), stowaway (ST), and unaided (UN).

A score of one indicated that Uganda was climatically unsuitable, or that host plants were not present; two meant that only a few areas in Uganda were climatically suitable, or that host plants were rare; three indicated that large regions of Uganda were climatically suitable, but host plants were rare; or that only a few areas in Uganda were climatically suitable, yet the host plants were at least moderately abundant; four signified that large regions of Uganda were climatically suitable, but the host plants were moderately abundant; and five denoted that large areas in Uganda were climatically suitable, but the host plants were very abundant.

A score of one indicated that the alien species do not attack plants that are cultivated or utilised; two, that the alien species damage plants that are only occasionally cultivated or utilised; three, that the alien species damage plants that are regularly cultivated or utilised but without threatening the cultivation, utilisation, or trade of this crop; four, that the alien species has the potential to threaten, at least locally, the cultivation of a plant that is regularly cultivated or utilised, or to periodically attack a crop that is key to the economy of Uganda without threatening the latter; and five, that the alien species has the potential to threaten, at least locally, a crop that is key to the economy of Uganda.

A score of one indicated that the alien species would not affect any native species; two, that the alien species would affect individuals of a native species without affecting its population level; three, that the alien species has the potential to lower the population levels of a native species; four, that the alien species has the potential to eradicate a native species locally or to affect populations of a protected or keystone species; and five, that the alien species has the potential to eliminate a native species or to eradicate a keystone species locally. Native species refers to species within their natural range, including shifts in range occurring without human intervention and includes animals, plants or any other organisms, including pathogens.

The SMEs were grouped according to their specialities, forming five groups, each with a minimum of three members. They included Group One (arthropods), Group Two (bacteriology, covering bacteria, protists, and phytoplasma), Group Three (mycology, encompassing chromista and fungi), Group Four (nematology, which also assessed molluscs), and Group Five (virology, addressing viruses and viroids). Due to the large number of arthropods requiring assessment, two subgroups were created. The scores for each species attribute were discussed comprehensively, and any discrepancies were resolved until a consensus was reached prior to confirming the final score. As detailed in Blackburn et al. (2014), a low, medium, and high confidence rating was indicated for each of the four scored attributes, the likely pathway of arrival, and the overall risk score. Appropriate groups assessed vectors and vectored organisms.

Risk is a function of the probability (likelihood) of an event occurring and the impact tied to that probability. Consequently, the overall risk score was derived from the following formula:

The highest expected overall risk score was 250, while the lowest stood at two.

An overall score of 54 was considered the cut-off for recommending an appropriate management action. This score was chosen as it is only achievable for species with a score of three in all assessable attributes or more than three in at least three parameters. A score of three or higher indicated a situation with an increased likelihood of entry, establishment, and greater impact (socio-economic or biodiversity). Scores below three were regarded as low risk since they signified a reduced likelihood of entry, establishment, and impact; a score of three was viewed as moderate, whereas scores above three (four and five) suggested a heightened likelihood of entry, establishment, and impact (as opposed to the lower scores of one and two). A no-action recommendation was made for species that recorded an overall risk score below 54. In contrast, a management action was advised for all pests that attained an overall risk score above 54. These actions included detection surveillance for pests reported in a neighbouring country to establish pest status in Uganda, regulation supported by Pest Risk Analysis (PRA ⁴ ), contingency planning for preparedness, raising awareness, industry initiatives to prevent pest introduction and management after introduction, and research.

Detection surveillance was also considered if the assessment team confirmed a previous interception or for a pest affecting a host commodity frequently imported from a country where the pest is endemic. Pest Risk Analysis is key in providing guidelines to manage pathways and limit the introduction of quarantine pests. However, in certain special cases, action was considered for some species that recorded an overall risk score below 54. These included species currently regarded by trading partners as high-risk A1 or A2 ⁵ quarantine pests, such as the subspecies of Xylella fastidiosa. A no-action recommendation was also suggested for some species that recorded an overall risk score above 54. This applied to species for which the main pathway of introduction was deemed implausible. This category comprised pests transmitted by vectors rather than through seed (seed-borne ⁶ or seed-transmitted ⁷ ), yet the vectors were unlikely to be introduced with a viable pathogenic organism. Others in this category included soil-borne pests that were not likely to be associated with the commodity. A good example would be soil-borne fungi that are not seed-transmitted. Furthermore, a no-action recommendation was also suggested when insufficient information was available for the assessment of a particular species or for vectors of assessed species and pests vectored by assessed species already reported in Uganda.

The global horizon scan identified 9,071 species not yet reported as present in Uganda. These species comprised 5,866 arthropods, 321 bacteria, 167 chromista, 1,684 fungi, 33 molluscs, 270 nematodes, 12 protists, and 718 viruses and viroids. The initial output from the Horizon Scanning Tool was subsequently filtered to include only species with complete names, resulting in 8,398 species that comprised 5,551 arthropods, 284 bacteria, 160 chromista, 1,569 fungi, 26 molluscs, 183 nematodes, 10 protists, and 645 viruses and viroids. The species reported as invasive and affecting crops and trees grown in Uganda were selected for a further detailed rapid risk assessment, resulting in a total of 1,517 species, of which 360 (24%) had been documented as invasive. These 1,517 species comprised 357 arthropods ( Supplementary File S2 ), 130 bacteria ( Supplementary File S3 ), 74 chromista ( Supplementary File S4 ), 417 fungi ( Supplementary File S5 ), 19 molluscs ( Supplementary File S6 ), 124 nematodes ( Supplementary File S7 ), nine protists ( Supplementary File S8 ), and 387 viruses and viroids ( Supplementary File S9 ). The 357 arthropods comprised 219 invasive species and 138 vectors that were part of the horizon scanning output. All vectors (arthropods, fungi, nematodes, plants and protists) and vectored species (bacteria, fungi, nematodes, protists, viruses and viroids) were subjected to a rapid risk assessment ( Supplementary File S10 ). All data has been consolidated in Supplementary File S11 .

The 357 arthropods prioritised for rapid risk assessment included 219 species (62%) documented as invasive. Of the 357 species, 148 (42%) had been reported in Africa, a proportion of which (38%; n=58 of 147) was present in a neighbouring country ( Table 1 ). Most arthropods were likely to be introduced exclusively as contaminants (74%, n=264 of 357), while the least (5%, n=19 of 357) could be introduced solely as stowaways. The remaining arthropods (21%; n=73 of 357) could be introduced through more than one pathway, of which 38% (n=28 of 73) could be introduced as contaminants or stowaways and 62% (n=45) as contaminants, stowaways or unaided ( Table 2 ). The highest overall risk score was 175 recorded for 11 species, which included Aphis spiraecola, Metopolophium dirhodum, Metopolophium festucae, Prays citri, Pseudaulacaspis pentagona, Rhopalosiphum padi, Rhyzopertha dominica, Thrips palmi, Trialeurodes vaporariorum, Xylosandrus crassiusculus, and Xylosandrus morigerus while the lowest was two recorded for Myzus ornatus, Nearctaphis bakeri. The 351 assessed species also comprised 156 (44%) that vectored other assessed species. All data from this assessment is presented in Supplementary File S2 .

The 130 species of bacteria prioritised for rapid risk assessment included 25 species (19%) documented as invasive. A proportion of 54% (n=70 of 130) had been reported in Africa, of which 24 species (34%) were reported as present in a neighbouring country ( Table 2 ). Most assessed bacteria were likely to be introduced exclusively as contaminants (67%, n=87 of 130), while the least (9%, n=11 of 130) could be introduced solely as stowaways. The remaining 25% (n=32 of 130) could be introduced through multiple pathways, specifically contaminants or stowaways ( Table 2 ). The highest overall risk score was 175 recorded for Xanthomonas vasicola pv. vasculorum, while the lowest was eight recorded for four species, including Strawberry lethal decline phytoplasma; Strawberry witches’ broom phytoplasma, Xanthomonas translucens pv. arrhenatheri, and Xanthomonas translucens pv. graminis. Twenty-seven (21%) of the assessed species were vectored, all of which were phytoplasmas, except for Dickeya zeae, Pantoea ananatis, Pantoea stewartii subsp. stewartii, Spiroplasma citri, Spiroplasma kunkelii, Xylella fastidiosa subsp. fastidiosa (xff), Xylella fastidiosa subsp. multiplex (xfm), and Xylella fastidiosa subsp. pauca (xfp). Xylella fastidioda has the most known and potential vectors. All data from this assessment is presented in Supplementary File S3 .

The 74 assessed Chromista (oomycetes) comprised six species documented as invasive. Most (61%, n=45 of 74) of the species had been reported in Africa, 14 of which (31%, n=14 of 45) had been reported in a neighbouring country ( Table 1 ). Half (50%, n=37 of 74) of the species were likely to be introduced exclusively as stowaways, while 16% (n=12 of 74) as contaminants. Others (34%; n=25 of 74) could be introduced through multiple pathways; for instance, 20 as contaminants or stowaways; one (Pythium aphanidermatum) as a contaminant or unaided; and four (Peronospora farinosa f.sp. betae, Phytophthora hibernalis, Phytophthora phaseoli and Trachysphaera fructigena) through all three pathways (contaminant, stowaway, and unaided) ( Table 2 ). The highest overall risk score was 125, recorded for Phytophthora nicotianae and Pythium aphanidermatum, while the lowest was six, recorded for seven species, including Aphanomyces raphani, Peronospora dianthicola, Phytophthora gloverana, Phytophthora pisi, Pythium mamillatum, Pythium sulcatum, and Pythium uncinulatum. All data from this assessment is presented in Supplementary File S4 .

The 417 fungi prioritised for assessment included 49 (12%) documented as invasive. More than half (53%, n=220) had been reported in Africa, with 41% (n=91 of 220) reported in a neighbouring country ( Table 1 ). Eight in every ten (81%, n=336 of 417) of the assessed species could be introduced solely as contaminants, whereas approximately one in every ten (1%, n=3 of 417) could be introduced as stowaways. The remaining assessed species could be introduced through multiple pathways. For instance, 6% (n=24 of 417) could be introduced as either contaminants or stowaways, 11% (n=46 of 417) as contaminants or unaided, and 2% (n=8 of 417) through all three pathways (contaminants, stowaways, and unaided) ( Table 2 ). The highest overall risk score was 125, noted for 17% (n=69 of 417) of the species, while the lowest score was 25, recorded for 28% (n=118 of 417) of the species. All data from this assessment is presented in Supplementary File S5 .

The 19 molluscs prioritised for assessment included eight species documented as invasive, representing 42%. Nine (47%) of the assessed molluscs had been reported in Africa, but only one (P. canaliculata) had been reported in a neighbouring country (Kenya) ( Table 1 ). Species documented in Africa included Arion hortensis, Bradybaena similaris, Cornu aspersum, Deroceras laeve, Deroceras reticulatum, Lehmannia valentiana, Limax maximus, Pomacea canaliculata, and Rumina decollata. Fourteen (74%) of the assessed molluscs could be introduced exclusively as stowaways, while the remaining five (26%) could be introduced as contaminants or stowaways ( Table 2 ). The highest overall risk score was 96, recorded for P. canaliculata, whereas the lowest was eight, recorded for Arion ater. All data from this assessment is presented in Supplementary File S6 .

The 124 prioritised parasitic plant nematodes included 31 (25%) species documented as invasive. Sixty-eight species, representing 58%, had been reported in Africa ( Table 1 ). One-quarter (25%; n=17 of 68) of the species had been reported in a neighbouring country ( Table 1 ). Four (3%) of the species, including Achlysiella williamsi, Anguina tritici, Aphasmatylenchus straturatus, and Ditylenchus gigas, could be introduced exclusively as contaminants, 32 (26%) exclusively as stowaways, while the majority (71%; n=88 of 124) either as contaminants or stowaways) ( Table 2 ). The highest overall risk score was 150, recorded for Meloidogyne enterolobii, while the lowest was six, recorded for Rotylenchus paravitis. Four of the nematodes in this category could be vectored and included Bursaphelenchus fungivorus, Bursaphelenchus mucronatus, Bursaphelenchus xylophilus, and Rhadinaphelenchus cocophilus. Thirteen of the assessed nematodes, representing 10%, are known vectors for bacteria and viruses. These include Anguina agrostis, A. tritici, Longidorus elongatus, Paratrichodorus minor, Paratrichodorus pachydermus, Paratrichodorus porosus, Trichodorus primitivus, Trichodorus similis, Trichodorus viruliferus, Xiphinema americanum, Xiphinema diversicaudatum, Xiphinema rivesi, and Zygotylenchus guevarai. All data from this assessment is presented in Supplementary File S7 .

The nine protists prioritised for assessment included four species reported in Africa, with only one (Spongospora subterranea) documented in a neighbouring country ( Table 1 ). The other three species reported in Africa were Plasmodiophora brassicae, Polymyxa betae, and Polymyxa graminis. Seven (78%) protists could be introduced exclusively as stowaways, while the remaining two (22%), Ligniera vasculorum and Spongospora subterranea could enter through two pathways (contaminants or stowaways) ( Table 2 ). The highest overall risk score was 90, attributed to Polymyxa graminis, while the lowest was 15, assigned to three species, Physarum cinereum, Phytomonas leptovasorum, and Phytomonas staheli. All data from this assessment is presented in Supplementary File S8 .

The 387 virus and viroid species prioritised for assessment included 15 (4%) viroids and 372 (96%) viruses ( Table 1 ). Among these, 22 had been reported as invasive, all being viruses ( Table 1 ). A proportion of 73% (n=11 of 15) of the viroids and 38% (n=140 of 372) of the viruses had been reported in Africa. Of the 11 viroids documented in Africa, one (avocado sunblotch viroid) was reported in a neighbouring country (Kenya) (Kibwage et al., 2023), while the 140 viruses included 31 reported in a neighbouring country ( Table 1 ). The majority (80%; n=12 of 15) of viroids were likely to be introduced as contaminants, whereas the least (20%; n=3 of 15) were likely to be introduced as contaminants or stowaways ( Table 2 ). For viruses, the majority (55%; n=204 of 372) of viruses were likely to be exclusively introduced as stowaways, while the least was likely to be exclusively introduced as contaminants ( Table 2 ). A proportion of 32% (n=119 of 372) were likely to be introduced either as contaminants or stowaways ( Table 2 ). For two of the viruses, Desmodium yellow mottle virus and pepper chlorotic spot virus, the main mechanism of spread could not be determined from the available information. The highest overall risk score for viroids was 120, recorded for tomato apical stunt viroid, while the lowest was 30, recorded for tomato chlorotic dwarf viroid. The highest overall risk score for viruses was 175, recorded for barley yellow dwarf virus, while the lowest was six, scored for 24 viruses. All data from this assessment is presented in Supplementary File S9 .

The total number of vectored species was 174, which included 26 bacteria, four fungi, three nematodes, one protist, 139 viruses, and one viroid. Eleven species were not assessed as they had already been reported as present in Uganda. These included Candidatus Phytoplasma aurantifolia, Ceratocystis fimbriata, citrus tristeza virus, cowpea aphid-borne mosaic virus, cucumber mosaic virus, Impatiens necrotic spot virus, maize chlorotic mottle virus, potato spindle tuber viroid, potato virus X, Ralstonia solanacearum, and tomato spotted wilt virus. The 163 species that were assessed comprised 24 bacteria, three fungi, three nematodes, one protist, and 132 viruses. Of the 163 species, 33% (n=54) were reported in Africa, with 32% (n=17 of 54) reported in a neighbouring country.

The arthropods vectored the majority of the pathogenic organisms. However, additional vectors included nematodes from the genera Longidorus, Paratrichodorus, Trichodorus, and Xiphinema; fungi from the Euwallacea genus; and protists in the genera Polymyxa and Spongospora. The highest overall risk score was 150, recorded for nine species, which included alfalfa mosaic virus, barley yellow dwarf viruses, Candidatus Liberibacter solanacearum, Candidatus Phytoplasma asteris, maize dwarf mosaic virus, Pectobacterium carotovorum, potato virus Y, Streptomyces scabiei, and tomato chlorosis virus. The lowest score was six recorded for nine species, which included broad bean true mosaic virus, lucerne transient streak virus, parsnip mosaic virus, rubus yellow net virus, ryegrass mosaic virus, strawberry latent C virus, strawberry mottle virus, tulip breaking virus, and wheat yellow leaf virus. All data from this assessment is presented in the relevant sheet in Supplementary File S10 .

The identified vector species totalled 323; however, 35 species were eliminated as they are reportedly present in Uganda, leaving only 288 for assessment. Of the 288 species, 28% (n=80) had been reported in Africa, with 29% (n=23 of 80) reported in a neighbouring country. The 288 species comprised 265 (92%) arthropods, three fungi, four plants, and three protists. The fungi belonged to the genus Olpidium (O. bornovanus, O. brassicae, and O. radicale); nematodes were from the genera Longidorus, Paratrichodorus, Trichodorus, and Xiphinema; the protists from Polymyxa (P. betae and P. graminis) and Spongospora (S. subterranea); and the plants were from Cuscuta (C. ceanothi, C. europaea, C. reflexa, and C. subinclusa). The highest overall risk score was 175 recorded for six species, which included Aphis spiraecola, M. dirhodum, Metopolophium festucae, R. padi, T. palmi, and Trialeurodes vaporariorum. The lowest overall risk score was two recorded for 21 species. Most of the arthropods were Hemiptera, specifically from the family Cicadellidae, followed by the Aphididae. All data from this assessment is presented in the relevant sheet in Supplementary File S10 .

Considering the crops prioritised by the ASSP, examples of pests for urgent prevention of introduction have been highlighted ( Table 4 ). For banana, they include, for instance, Banana mild mosaic virus; Ceroplastes stellifer, FoC TR4; cassava, cassava witches’ broom, Nipaecoccus nipae, Schistocerca nitens; citrus, Brevipalpus lewisi, Citrus cachexia viroid, and Xfp; cocoa, Phenacoccus hargreavesi, Phytophthora heveae, and Spodoptera litura; coffee, S. litura, Xff, and Xfp; common bean, bean pod mottle virus, Curtobacterium flaccumfaciens pv. flaccumfaciens, and Southern bean mosaic virus; cotton, Meloidogyne acronea, S. litura, and Tobacco streak virus; maize, Heterodera zeae, Maize bushy stunt phytoplasma, and Peronosclerospora sacchari; potatoes, Clavibacter sepedonicus, Dickeya dadantii, and Dickeya solani; rice, Alphanucleorhabdovirus oryzae, Ditylenchus angustus, and Hoplolaimus indicus; tea, P. porosus, Pseudococcus viburni, and S. litura.

Other key crops include sorghum, for which Oryzaephilus surinamensis, Peronosclerospora philippinensis, Solenopsis invicta have been prioritised; sugarcane, Exomala orientalis, Indian sugarcane yellow leaf phytoplasma, Sugarcane grassy shoot phytoplasma; and sweetpotato, Monilochaetes infuscans, S. invicta, and S. litura. For the oil crops, they include Indian peanut clump virus, Peanut clump virus, Peanut green mosaic virus, prioritised for groundnuts; oil palm, Hysteroneura setariae, Oryctes rhinoceros, and Rhynchophorus ferrugineus; sesame, Candidatus Phytoplasma trifolii, Neoaliturus haematoceps, and Orosius orientalis; soybean, Heterodera glycines, Pseudomonas savastanoi pv. glycinea, and Tylenchorhynchus claytoni; sunflower, Brachycaudus helichrysi, Phytophthora cryptogea, and S. invicta. Some of these pests have been highlighted for regulation in other countries. They include C. sepedonicus, C. flaccumfaciens pv. flaccumfaciens, D. solani, and FoC TR4 (EFSA PLH Panel et al., 2018, 2019, 2022).