Patient-reported outcome measures in the management of neovascular age related macular degeneration: a 1-year prospective study

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Quarantine status of selected fungal pathogens on Malus, Prunus and Vitis species

Thesis (MSc)--University of Stellenbosch, 2006.ENGLISH ABSTRACT: Invasions of alien species into non-native environments pose one of the largest, but least addressed international threats to biodiversity, both within natural ecosystems and agricultural settings. It is without exception ranked as the greatest environmental threat of the 21st century. Their introduction and spread have been identified as one of the six major categories of change that could potentially alter the world's biodiversity. The number and variety of species introduced make it clear that it is no exaggeration to state that biological invasions are breaking down biogeographic barriers that created and maintained the major floral and faunal regions of Earth. It is, however, difficult to conceive that a single indicator could measure the impact of an invader on a country due to the difficulty in measuring their environmental as well as their financial impacts. Another contributing factor to this problem is the scarcity of data available on the impact of the thousands of invaders in other countries. For the agricultural sectors, alien invasive species are likened to a two-edged sword: on the one hand they are used in the development of new plant varieties and products and on the other hand they have the potential to threaten agricultural production and as a consequence agricultural economic development. An important challenge for countries lies in the development of improved protocols for the prevention, identification and managing of potential invasive alien species. Plant health has always influenced international trade and the backbone for nondiscriminatory, fair, predictable and transparent international trade is the set of rules that national governments have agreed to follow with the foundation of the World Trade Organisation (WTO) in 1995. With the establishment of the WTO, the "WTO - Agreement on the Application of Sanitary and Phytosanitary measures (WTO-SPS)" also came into force. This agreement lays out the provisions, rights and obligations of countries in setting measures to protect human, animal and plant life and health. It also guides quarantine policy and decision-making, with the objective to prevent the use of quarantine measures by governments as disguised or unjustified trade barriers to protect their agricultural industries from import competition. As a signatory member of the WTO-SPS, South Africa has the right to implement appropriate measures to protect our plant health and environment. To set the appropriate levels for protection, South Africa must either apply to international standards or undertake a scientific based risk analysis process, to justify quarantine measures. These measures must also be the minimum necessary to protect plant health. A key element in negotiations for market access is the provision of a list of regulated pests, as well as a list of all pests associated with the crop within the exporting country, to the trading partners. In this study lists of fungal pathogens associated with Malus spp. and Vitis spp. worldwide, including South Africa, were compiled to enable the National Plant Protection Organisation in South Africa to comply with their responsibilities as a signatory member of the international regulatory bodies and to assist them to safeguard our country against harmful invasive species. It was concluded that to have access to accurate plant health status information, all researchers are summoned to validate new pest records and to submit voucher specimen to our National Collection. Geographical distribution records of pathogens and pests are the basis for phytosanitary decision-making and therefore it is imperative for countries to have access to accurate information regarding the geographical distribution of pathogens within their boundaries. For a pathogen to be classified as an A 1-pest, the pest should be of economic importance to the endangered area and not yet present there or present, but not widely distributed and being officially controlled. Many disputes have arisen during the past years concerning the classification for Monilinia fructicola and Neonectria galligena as A 1- regulated pests for South Africa, due to official records of the presence of these pathogens dating back as early as 1917. The situation was further complicated by recent reports from some European countries that M fructicola was detected on stone fruit imported from South Africa. These issues were resolved in this study by following a molecular approach and guidelines as stipulated by the international regulatory bodies. The absence of M fructicola as well as N galligena from South African stone and pome fruit orchards was confirmed. The regulated status of M fructicola and N galligena in South Africa is therefore scientifically justified.AFRIKAANSE OPSOMMING: Die inbring van vreemde, skadelike spesies bedreig biodiversiteit binne natuurlike ekosisteme en landbou-omgewings. Hierdie aspek, wat ongelukkig nie die steun of aandag geniet wat dit verdien nie, word sonder uitsondering gereken as die bedreiging vir die omgewing van die 21 ste eeu. Die inbring en verspreiding van hierdie spesies is ook reeds ge1dentifiseer as een van die ses belangrikste potensiele faktore wat tot verandering in die wereld se biodiversiteit kan lei. Statistieke van die aantal en verskeidenheid spesies wat reeds nuwe omgewings suksesvol binnegedring het, is 'n duidelike bewys dat dit geen oordrywing is <lat hierdie verskynsels afbreek maak aan bio-geografiese grense nie, wat tot die ontstaan en instandhouding van die wereld se vemaamste plantegroei- en dierelewestreke gelei het. Die moeilikheidsgraad verbonde aan die bepaling van die impak wat hierdie spesies op omgewings en ekonomiee het, maak dit onmoontlik om 'n enkele indikator te bepaal om hierdie impakte te meet. 'n Verdere bydraende faktor tot hierdie probleem, is die gebrek aan beskikbare data oor die impak wat die menigte van spesies op ander lande gehad het. Hierdie vreemde spesies is vir die landbousektor soos 'n tweesnydende swaard: enersyds word dit benodig vir die ontwikkeling en teling van nuwe kultivars en produkte, en andersyds beskik hul oor die potensiaal om bedreigings vir landbou, en gevolglik ook vir landbou-ekonomiese ontwikkeling, in te hou. Die uitdaging le dus daarin vir lande om riglyne daar te stel en te ontwikkel vir die voorkoming, identifikasie en bestuur van vreemde en potensieel skadelike spesies. Internasionale handel is nog altyd deur die fitosanitere status van plante bemvloed. Die grondbeginsels vir nie-diskriminerende, regverdige, voorspelbare en deursigtige internasionale handel word saamgevat in die stel reels wat nasionale regerings ooreengekom het om te volg met die stigting van die Wereldhandelsorganisasie (WHO) in 1995. Tesame met die stigting van die WHO het die "WTO - Agreement on the Application of Sanitary and Phytosanitary measures" (WTO-SPS) ook van krag geword. Die doel van hierdie ooreenkoms is om riglyne neer te le waarbinne lande moet optree met die daarstelling van maatreels om mens, <lier en plant te beskerm. Dit verskaf ook riglyne vir kwarantynmaatreels en -beleide om sodoende te voorkom <lat lande kwarantynmaatreels kan gebruik as onregverdige handelsbeperkinge om hul eie industriee teen kompetisie te beskerm. As 'n ondertekenaar van die WTO-SPS, beskik Suid-Afrika oor die reg om toepaslike maatreels te implementeer om ons plante en omgewing te beskerm. Om hierdie maatreels te bepaal, moet Suid-Afrika egter aan intemasionale standaarde voldoen of risiko-bepalings uitvoer wat op wetenskaplike beginsels gebaseer is. Hierdie maatreels moet ook die minimum wees wat nodig is om plantgesondheid in Suid-Afrika te beskerm. 'n Sleutelfaktor in die onderhandelingsprosesse vir marktoegang, is die voorsiening van 'n lys van beheerde peste aan die invoerland, asook 'n lys van alle peste en plae wat in die uitvoerland met die gewas geassosieer word, aan die invoerland. In hierdie studie is lyste saamgestel van swampatogene wat wereldwyd met Ma/us en Vitis spp. geassosieer word, insluitende SuidAfrika. Die doelstelling van die lyste is om die Nasionale Plantbeskermingsorganisasie van Suid-Afrika in staat te stel om hul verantwoordelikhede as ondertekenaar van intemasionale ooreenkomste na te kom en sodoende ook ons land teen vreemde en potensieel skadelike spesies te beskerm. Hierdie lyste bied akkurate inligting rakende plantgesondheidstatus in Suid-Afrika, maar <lien ook as werksdokumente vir navorsers wat rekords van nuwe peste moet valideer en ook kulture as bewysstukke in ons Nasionale Versamelings deponeer. Geografiese verspreidingsrekords van patogene en peste vorm die basis van fitosanitere besluitnerning en dit is dus noodsaaklik vir lande om toegang te he tot akkurate inligting met betrekking tot die geografiese verspreiding van patogene binne hul landsgrense. Vir 'n patogeen om as 'n Al-pes geklassifiseer te word, moet die pes van ekonomiese belang wees vir die bedreigde area en nog nie daar voorkom nie, 6f voorkom, maar wel nie wydverspreid nie en amptelik onder beheer is. Verskeie dispute het gedurende die afgelope jare ontstaan rakende die klassifikasie van Monilinia fructicola en Neonectria galligena as Alpeste vir Suid-Afrika as gevolg van amptelike rekords wat vanuit 1917 dateer dat hierdie patogene wel in Suid-Afrika teenwoordig is. Die situasie is verder vererger deur onlangse verslae van Europese lande dat M fructicola op steenvrugte wat vanuit Suid-Afrika ingevoer is, ontdek is. Hierdie probleemgevalle is in hierdie studie aangespreek deur 'n molekulere benadering en riglyne, gebaseer op intemasionale standaarde, te volg. Die afwesigheid van M fructicola en N galligena in Suid-Afrikaanse kern- en steenvrugteboorde is bevestig. Die klassifikasie van M fructicola en N galligena as Al- peste vir Suid-Afrika is dus wetenskaplik geregverdig

Population structure, sex and spatial distribution of phyllosticta citricarpa, the citrus black spot pathogen

Thesis (PhDAgric)—Stellenbosch University, 2018.ENGLISH ABSTRACT: Citrus Black Spot (CBS), caused by Phyllosticta citricarpa, is a fungal disease that influences citrus industries worldwide. All commercial Citrus spp. are susceptible to the disease. The pathogen was first described 117 years ago from Australia; subsequently, from summer rainfall citrus production regions in China, Africa, and South America; and, recently, the United States. Limited information is available on the pathogen’s population structure, mode of reproduction, and introduction pathways at a global scale and at a regional (provincial) scale in South Africa. This is also true for the effect of distance (spatial), season (temporal) and Citrus spp. on population structure at the orchard scale. The aforementioned aspects were investigated in the current study. Since limited co-dominant markers are available for P. citricarpa population genetic analyses, one of the first aims of the study was to develop new simple-sequence repeat (SSR) markers. The population structure of P. citricarpa was investigated at a global scale in 12 populations from South Africa, the United States, Australia, China, and Brazil. Seven published and eight newly developed polymorphic SSR markers were used for genotyping populations. The Chinese and Australian populations had the highest genetic diversities, whereas populations from Brazil, the United States, and South Africa exhibited characteristics of founder populations. Based on population differentiation and clustering analyses, the Chinese populations were distinct from the other populations. High connectivity was found, and possibly linked introduction pathways, between South Africa, Australia and Brazil. With the exception of the clonal United States populations that only contained one mating type, the other populations contained both mating types in a ratio that did not deviate significantly from 1:1. Although most populations exhibited sexual reproduction, linkage disequilibrium analyses indicated that asexual reproduction is also important. The effects of distance (spatial) and season (temporal) on the population structure of P. citricarpa were investigated over two seasons, in two lemon orchards in South Africa; one in the Mpumalanga province and the other in the North West province. Spatial analyses indicated that subpopulations separated by a short distance (within 200 m) were typically not significantly genetically differentiated, but that those separated by longer distances were sometimes significantly differentiated. Temporal analyses in the North West orchard showed that seasonal populations were not significantly genetically differentiated. In contrast, seasonal populations from the Mpumalanga orchard were significantly differentiated, most likely due to higher rainfall and disease pressure, and the spatial scale of sampling. Based on linkage disequilibrium analyses, sexual and asexual reproduction occurred in both orchards. In each orchard, two dominant multilocus genotypes (MLGs) were identified in most of the subpopulations, as well as in the seasonal populations. Pycnidiospores are therefore important in the development of CBS at the temporal and spatial scales in South African lemon orchards. Population genetic studies on a regional (provincial) scale in South Africa showed that ten P. citricarpa populations, representing five provinces (North West, Mpumalanga, Limpopo, KwaZulu-Natal and Eastern Cape), were not significantly genetically differentiated. Based on gene and genotypic diversities and private allele richness, the KwaZulu-Natal or the Limpopo provinces are likely the provinces where the pathogen was first introduced. There might have been at least two separate introductions of the pathogen into the country. The Eastern Cape province was confirmed as being the province where the latest introduction occurred in South Africa. Despite lemon trees having overlapping fruit crops, potentially providing increased opportunities for clonal reproduction, Citrus spp. (lemons vs. oranges) did not have an effect on population structure; not all lemon populations were significantly genetically differentiated from all orange populations. The current study has revealed novel information on the population structure of P. citricarpa at global and regional (South Africa) scales, which have implications for the epidemiology and management of the disease. The finding that pycnidiospores, in addition to ascospores, are also important in the epidemiology of the disease in South Africa, contradicts previous reports that pycnidiospores are of minor significance. Future studies should reinvestigate the role of these spore types in the epidemiology of CBS in South Africa using conventional orchard inoculation and leaf removal studies, combined with a population genetic data analyses. The role that distance and season have on the population structure should also be considered in orchard trial designs. Ascospore spore trap data should be generated that involve the differentiation of P. citricarpa from P. capitalensis.AFRIKAANSE OPSOMMING: Sitrus Swartvlek (SSV) is 'n swamsiekte wat deur Phyllosticta citricarpa veroorsaak word, en wat sitrusbedrywe wêreldwyd beïnvloed. Alle kommersiële Sitrus spp. is vatbaar vir die siekte. Die patogeen is 117 jaar gelede vir die eerste maal in Australië beskryf en daarna van sitrus produserende streke in somerreënval gebiede in Sjina, Afrika en Suid-Amerika en mees onlangs van die Verenigde State. Beperkte inligting oor die patogeen se populasie-struktuur, wyse van voortplanting en introduksie roetes is op ‘n globale vlak beskikbaar, sowel as op ‘n provinsiale vlak in Suid-Afrika. Op ʼn boordvlak, is inlgiting ook beperk oor die effek wat afstand (“spatial”), seisoen (temporaal) en Sitrus spp. op die populasie-struktuur het. Voorafgenoemde aspekte is in die studie ondersoek. Aangesien beperkte dominante merkers vir P. citricarpa populasie genetiese analises beskikbaar is, was een van die eerste doelstellings van die studie om nuwe mikrosatelliet merkers te ontwikkel. Die populasie-struktuur van P. citricarpa is op ‘n globale vlak in 12 populasies van SuidAfrika, die Verenigde State, Australië, Sjina en Brasilië ondersoek. Sewe gepubliseerde en agt nuut ontwikkelde polimorfiese mikrosatelliet merkers is gebruik om die populasies te genotipeer. Die Sjinese en Australiese populasies het die hoogste genetiese diversiteit getoon, terwyl populasies van Brasilië, die Verenigde State en Suid-Afrika eienskappe van stigterspopulasies toon. Gebaseer op populasie-differensiasie en groeperings-analises verskil die Sjinese populasies van die ander populasies. Hoë konnektiwiteit en moontlik gedeelde introduksie roetes is tussen Suid-Afrika, Australië en Brasilië gevind. Met die uitsondering van die klonale populasies van die Verenigde State, met net een paringstipe, het die ander populasies beide paringstipes gehad in 'n verhouding wat nie beduidend van 1:1 afwyk nie. Alhoewel die meeste populasies geslagtelike voortplanting getoon het, het “linkage disequilibrium” analises getoon dat ongeslagtelike voortplanting ook belangrik is. Die effek van afstand (ruimtelik) en seisoen (temporaal) op die populasie-struktuur van P. citricarpa is oor twee seisoene in twee suurlemoenboorde in Suid-Afrika ondersoek; een boord in die Mpumalanga-provinsie en die ander in die Noordwes-provinsie. Ruimtelike analises het getoon dat subpopulasies wat deur 'n kort afstand (binne 200 m) geskei word, tipies nie betekenisvol geneties gedifferensieerd was nie, maar dat die wat deur langer afstande geskei is, soms betekenisvol gedifferensieerd was. Temporale analises in die Noordwes boord het getoon dat seisoenale populasies nie betekenisvol geneties gedifferensieerd was nie. In teenstelling hiermee, was seisoenale populasies van die Mpumalanga-boord betekenisvol gedifferensieerd, waarskynlik weens hoër reënval en siektedruk en die ruimtelike skaal van monsterneming. Gebaseer op “linkage disequilibrium” analises, het geslagtelike en ongeslagtelike voortplanting in beide boorde plaasgevind. In elke boord het twee dominante multi-lokus genotipes (MLG's) in die meeste van die subpopulasies, sowel as in die seisoenale populasies, voorgekom. Piknidiospore is dus belangrik in die ontwikkeling van SSV op temporale en ruimtelike vlakke in Suid-Afrikaanse suurlemoenboorde. Populasie genetika studies op 'n streeks- (provinsiale) vlak in Suid-Afrika het getoon dat tien P. citricarpa-populasies wat vyf provinsies verteenwoordig (Noordwes, Mpumalanga, Limpopo, KwaZulu-Natal en Oos-Kaap), nie betekenisvol geneties gedifferensieerd was nie. Gebaseer op geen- en genotipiese diversiteit en die aantal privaat allele, is die KwaZulu-Natal provinsie of die Limpopo provinsie waarskynlik die provinsies waar die patogeen eerste gevestig het. Daar is moontlik ten minste twee afsonderlike introduksies van die patogeen. Daar is bewys dat die Oos-Kaap die provinsie is waar die laaste introduksie in Suid-Afrika plaasgevind het. Ten spyte daarvan dat suurlemoenbome wat oorvleuende oeste het, moontlik verhoogde geleenthede vir klonale voortplanting bied, het Citrus spp. (suurlemoene vs. lemoene) nie 'n effek op die populasie-struktuur gehad nie, omdat nie al die suurlemoenpopulasies betekenisvol geneties gedifferensieerd van al die lemoenpopulasies was nie. Die studie het nuwe inligting oor die populasie-struktuur van P. citricarpa op ‘n globale en streeks- (Suid-Afrika) vlak gebring, wat implikasies vir die epidemiologie en bestuur van die siekte inhou. Die bevinding dat piknidiospore, bykomend tot askospore, ook belangrik in die epidemiologie van die siekte in Suid-Afrika is, weerspreek vorige verslae dat piknidiospore van geringe belang is. Verdere studies moet die rol van hierdie spoortipes in die epidemiologie van SSV in Suid-Afrika deur middel van konvensionele boord-inokulasies en blaarverwyderingstudies ondersoek. Dit moet met 'n populasie genetika studie gekombineer word. Die rol wat afstand en seisoen op die populasie-struktuur het, moet ook vir die ontwerp van boordproewe oorweeg word. Askospoor lokval-data moet gegenereer word wat tussen P. citricarpa en P. capitalensis kan onderskei.Doctora

Scientific critique of the paper “Climatic distribution of citrus black spot caused by Phyllosticta citricarpa. A historical analysis of disease spread in South Africa” by Martínez-Minaya et al. (2015)

The global distribution of citrus black spot (CBS) disease, caused by Phyllosticta citricarpa, is climatically constrained, which is evident from its occurrence in citrus growing areas with warm, summer rainfall and its absence from areas with cooler, Mediterranean-type winter rainfall. Various epidemiological and modelling studies have supported this observation, predominantly estimating unsuitability for P. citricarpa in Mediterranean type climates, with no more than marginal suitability estimated at a few localities within some regions with Mediterranean type climates. The study by Martínez-Minaya et al. (European Journal of Plant Pathology, 143, 69–83, 2015), describes an historic sequence of recorded CBS occurrence in parts of South Africa, conducts an autocorrelation analysis and a correlative analysis with Köppen-Geiger climate zones and makes observations about the occurrence of certain Köppen-Geiger climate zones in the European Union. The study suggests that significant portions of the European Union and the broader Mediterranean basin are climatically similar to warm, summer rainfall areas in South Africa where P. citricarpa persists and causes CBS disease and concludes that the potential distribution of P. citricarpa is less constrained by climatic factors than spatial contagion. However, in this critique we expose methodological shortcomings in the Martínez-Minaya et al. (European Journal of Plant Pathology, 143, 69–83, 2015) study and conclude that the study grossly overestimated the extent of the geographical area that could support P. citricarpa, thereby rendering the findings scientifically unreliable

Citrus black spot is absent in the Western Cape, Northern Cape and Free State Provinces

The South African citrus industry is strongly focused on exports and South Africa is a signatory member of both the World Trade Organisation Agreement on the application of Sanitary and Phytosanitary Measures and the International Plant Protection Convention. Citrus black spot, caused by Guignardia citricarpa, does not occur in all the South African citrus production areas and, therefore, South Africa has a responsibility to provide those trading partners that have identified G. citricarpa as a regulated pest with reliable information about the distribution of citrus black spot within South Africa. Detection surveys were conducted in citrus production areas in the Western Cape, Northern Cape and Free State Provinces and appropriate diagnostic protocols were used to ensure reliable detection of G. citricarpa. Trees in commercial orchards and home gardens on farms and in towns of 17, 9 and 5 magisterial districts in the Western Cape, Northern Cape and Free State Provinces, respectively, were sampled between 1995 and 2010. Fruit samples were taken during June and July, and leaf samples from November to January. None of the 3060 fruit and leaf samples collected during these surveys tested positive for G. citricarpa. Phyllosticta capitalensis, a non-pathogenic, ubiquitous, endophytic species was, however, detected during these surveys. In compliance with relevant International Standards for Phytosanitary Measures and based on the outcome of these official surveys, these three provinces in South Africa can be recognised as citrus black spot pest free areas

Citrus black spot is absent in the Western Cape, Northern Cape and Free State Provinces

CITATION: Carstens, E. et al. 2012. Citrus black spot is absent in the Western Cape, Northern Cape and Free State Provinces. South African Journal of Science, 108(7/8), Art. #876, doi: 10.4102/sajs.v108i7/8.876.The original publication is available at http://sajs.co.zaThe South African citrus industry is strongly focused on exports and South Africa is a signatory member of both the World Trade Organisation Agreement on the application of Sanitary and Phytosanitary Measures and the International Plant Protection Convention. Citrus black spot, caused by Guignardia citricarpa, does not occur in all the South African citrus production areas and, therefore, South Africa has a responsibility to provide those trading partners that have identified G. citricarpa as a regulated pest with reliable information about the distribution of citrus black spot within South Africa. Detection surveys were conducted in citrus production areas in the Western Cape, Northern Cape and Free State Provinces and appropriate diagnostic protocols were used to ensure reliable detection of G. citricarpa. Trees in commercial orchards and home gardens on farms and in towns of 17, 9 and 5 magisterial districts in the Western Cape, Northern Cape and Free State Provinces, respectively, were sampled between 1995 and 2010. Fruit samples were taken during June and July, and leaf samples from November to January. None of the 3060 fruit and leaf samples collected during these surveys tested positive for G. citricarpa. Phyllosticta capitalensis, a non-pathogenic, ubiquitous, endophytic species was, however, detected during these surveys. In compliance with relevant International Standards for Phytosanitary Measures and based on the outcome of these official surveys, these three provinces in South Africa can be recognised as citrus black spot pest free areas.http://sajs.co.za/citrus-black-spot-absent-western-cape-northern-cape-and-free-state-provinces/carstens-elma-le-roux-hendrik-holtzhausen-michael-van-rooyen-liezl-coetzee-joey-wentzel-riaPublisher's versio

Citrus black spot is absent in the Western Cape, Northern Cape and Free State Provinces

The South African citrus industry is strongly focused on exports and South Africa is a signatory member of both the World Trade Organisation Agreement on the application of Sanitary and Phytosanitary Measures and the International Plant Protection Convention. Citrus black spot, caused by Guignardia citricarpa, does not occur in all the South African citrus production areas and, therefore, South Africa has a responsibility to provide those trading partners that have identified G. citricarpa as a regulated pest with reliable information about the distribution of citrus black spot within South Africa. Detection surveys were conducted in citrus production areas in the Western Cape, Northern Cape and Free State Provinces and appropriate diagnostic protocols were used to ensure reliable detection of G. citricarpa. Trees in commercial orchards and home gardens on farms and in towns of 17, 9 and 5 magisterial districts in the Western Cape, Northern Cape and Free State Provinces, respectively, were sampled between 1995 and 2010. Fruit samples were taken during June and July, and leaf samples from November to January. None of the 3060 fruit and leaf samples collected during these surveys tested positive for G. citricarpa. Phyllosticta capitalensis, a non-pathogenic, ubiquitous, endophytic species was, however, detected during these surveys. In compliance with relevant International Standards for Phytosanitary Measures and based on the outcome of these official surveys, these three provinces in South Africa can be recognised as citrus black spot pest free areas