Whole-genome analyses of rotavirus strains circulating pre- and post- Rotateq™ vaccine introduction in Rwanda
| dc.contributor.advisor | Nyaga, Martin | en_ZA |
| dc.contributor.advisor | Sabiu, Saheed | en_ZA |
| dc.contributor.author | Rasebotsa, Sebotsana Paula | en_ZA |
| dc.date.accessioned | 2021-07-16T09:27:12Z | |
| dc.date.available | 2021-07-16T09:27:12Z | |
| dc.date.issued | 2020 | en_ZA |
| dc.description | Dissertation (M.Sc.(Medical Microbiology and Virology))--University of the Free State, 2020 | en_ZA |
| dc.description.abstract | 𝑬𝒏𝒈𝒍𝒊𝒔𝒉 Children living in developing countries are constantly faced with the burden of diarrheal infections that account for over 1.6 million death cases globally. Rotavirus group A (RVA) has been identified as one of the viruses implicated in most viral-induced diarrhoeal infections in children less than five years worldwide. In Rwanda, over 3500 RVA related mortality cases were reported yearly prior to the implementation of the RotaTeq® vaccine in 2012 to overcome this burden, which led to a significant decrease in rotavirus infections. Africa has a huge diversity of rotavirus strains compared to other developed continents especially Europe and North America, thus requiring a deeper understanding of this phenomenon. This study aimed at characterizing all the 11-segments of RVA strains circulating in Rwanda pre- and post-vaccine introduction as part of the World Health Organization (WHO) supported African rotavirus pilot surveillance program. The study was based on 158 rotavirus positive samples that were collected from children presenting symptoms associated with rotavirus infection between 2011 and 2016. The rotavirus double-stranded ribonucleic acid (dsRNA) was extracted from the viral particles and converted into complementary deoxyribonucleic acid (cDNA) prior to library preparation for whole-genome sequencing with an Illumina MiSeq platform. Several bioinformatics tools were utilized to construct phylogenetic trees and the proteins structures. From the sequenced samples, 36 samples were identified as G1P[8] strains, and five samples were reassortant strains. Ten G1P[8] strains were identified pre-vaccine introduction while 26 were identified post-vaccine introduction. Thirty-five of the G1P[8] strains expressed pure Wa-like genome constellations, while one of the strains that was identified in 2012 exhibited a genome constellation typical of a RotaTeq® vaccine strain. On the other hand, the five reassortant strains were identified post-vaccine introduction between 2013-2015. Whole-genome analysis revealed that the G4P[4], G9P[4] and one G12P[8] reassortant strains exhibited both the Wa-like and the DS-1-like genome constellations while two G12P[8] strains had all the three genogroup constellations. Furthermore, the phylogenetic analysis of most of the G1P[8] strains revealed that they segregated according to their vaccination status; strains identified pre-vaccine introduction clustered together while post-vaccine strains also formed a separate cluster. The five reassortant strains were closely related to human RVA strains in all the gene segments and RotaTeq® vaccine strains in the VP1, VP2, NSP2, NSP4, and NSP5 gene segments. Analysis of the neutralization epitopes and cytotoxic T-lymphocytes (CTL) of the G1P[8] strains revealed multiple amino acid substitutions, with some changes influencing the change in polarity thus deemed to be radical in nature. A similar trend was also observed in the reassortant strains, with 27 amino acid substitutions in the VP7 epitope region and only three substitutions in the VP4 epitope region. Changes observed in these epitope regions have the potential of generating vaccine-escape mutants that may undermine the effectiveness of the rotavirus vaccine with time. Whole-genome sequencing has proven to provide information that could have been missed when looking only at the outer capsid proteins. It is thus important to continue conducting rotavirus whole-genome studies to unpack the hidden information behind the huge diversity of rotavirus strains in African countries such as Rwanda. ___________________________________________________________________ | en_ZA |
| dc.description.abstract | 𝑨𝒇𝒓𝒊𝒌𝒂𝒂𝒏𝒔 Kinders wat in ontwikkelende lande woon, word voortdurend gekonfronteer met die las van diarree-infeksies wat verantwoordelik is vir meer as 1,6 miljoen sterfgevalle wêreldwyd. Rotavirus groep A (RVA) is geïdentifiseer as een van die virusse wat betrokke is by die meeste virale-geïnduseerde diarree-infeksies by kinders jonger as vyf jaar wêreldwyd. In Rwanda is meer as 3500 RVA-verwante sterfgevalle jaarliks aangemeld voor die implementering van die RotaTeq®-entstof in 2012 om hierdie las te oorkom, wat gelei het tot 'n beduidende afname in rotavirusinfeksies. Afrika het 'n groot verskeidenheid rotavirus-stamme in vergelyking met ander ontwikkelde vastelande, veral Europa en Noord-Amerika, wat dus 'n dieper begrip van hierdie verskynsel vereis. Hierdie studie het ten doel gehad om al 11 segmente van die RVA-stamme wat in Rwanda gesirkuleer het voor en ná die entstof se bekendstelling, te karakteriseer as deel van die Wêreldgesondheidsorganisasie (WGO) se nuwe ondersteunde Afrika-rotavirustoesigprogram. Die studie is gebaseer op 158 rotavirus-positiewe monsters wat ingesamel is van kinders wat simptome getoon het wat met rotavirusinfeksie geassosieer word tussen 2011 en 2016. Die rotavirus dubbelstring ribonukleïensuur (dsRNS) is uit die virale deeltjies onttrek en in komplementêre deoksiribonukleïensuur (kDNS) omgeskakel voor biblioteekvoorbereiding vir heelgenoomvolgordebepaling met 'n Illumina MiSeq-platform. Verskeie bioinformatika-instrumente is gebruik om filogenetiese bome en die proteïenstrukture te konstrueer. Uit die opeenvolgende monsters is 36 monsters geïdentifiseer as G1P[8]-stamme, en vyf monsters was reassortante stamme. Tien G1P[8]-stamme is voor die entstofbekendstelling geïdentifiseer terwyl 26 ná die entstofbekendstelling geïdentifiseer is. Vyf-en-dertig van die G1P[8]-stamme het suiwer Wa-agtige genoomkonstellasies uitgedruk, terwyl een van die stamme wat in 2012 geïdentifiseer is, 'n genoomkonstellasie vertoon het wat tipies is van 'n RotaTeq®-entstofstam. Aan die ander kant, is die vyf reassortante stamme geïdentifiseer ná die entstof bekendstelling tussen 2013-2015. Heel-genoom-analise het aan die lig gebring dat die G4P[4], G9P[4] en een G12P[8] reassortante stamme beide die Wa-agtige en die DS-1-agtige genoomkonstellasies vertoon het terwyl twee G12P[8]-stamme al drie genogroep-konstellasies gehad het. Verder, die filogenetiese ontleding van die meeste van die G1P[8]-stamme het aan die lig gebring dat hulle volgens hul inentingstatus geskei het; stamme wat voor-entstof bekendstelling geïdentifiseer is, het saam gegroepeer terwyl post-entstof stamme ook 'n aparte groep gevorm het. Die vyf reassortant-stamme was nou verwant aan menslike RVA-stamme in al die geensegmente en RotaTeq®-entstofstamme in die VP1-, VP2-, NSP2-, NSP4- en NSP5-geensegmente. Ontleding van die neutralisasie-epitope en sitotoksiese T-limfosiete (CTL) van die G1P[8]-stamme het veelvuldige aminosuursubstitusies aan die lig gebring, met sommige veranderinge wat die verandering in polariteit beïnvloed wat dus as radikaal van aard beskou word. 'n Soortgelyke neiging is ook waargeneem in die reassortante stamme, met 27 aminosuursubstitusies in die VP7 epitoop streek en slegs drie substitusies in die VP4 epitoop-streek. Veranderinge wat in hierdie epitoopstreke waargeneem word, het die potensiaal mutante te genereer wat ’n entstof kan omseil en die doeltreffendheid van die rotavirus-entstof mettertyd kan ondermyn. Heelgenoom xv-volgordebepaling het bewys dat dit inligting verskaf wat gemis kon word wanneer slegs na die buitenste kapsiedproteïene gekyk word. Dit is dus belangrik om voort te gaan met rotavirus-heelgenoomstudies om die verborge inligting agter die groot diversiteit van rotavirusstamme in Afrikalande soos Rwanda, blot te stel. ___________________________________________________________________ | af_ZA |
| dc.description.abstract | 𝑺𝒆𝑺𝒐𝒕𝒉𝒐 Bana ba phelang dinaheng tse ntseng di tswela pele ho hola, hangata ba tobana le bothata ba tshwaetso ya letshollo e bakang palo e fetang dimiliyone tse 1.6 tsa mafu ka lefatshe lohle. Rotavirus group A (RVA) e hlwailwe e le e nngwe ya dikokwanahloko tse bakang ditshwaetso tsa letshollo ho bana ba dilemo tse ka tlase ho tse hlano ka lefatshe hohle. Mane Rwanda, palo e fetang 3500 ya mafu a amanang le RVA a tsebahaditswe ka selemo le selemo pele ho tshebediso ya ente ya RotaTeq® ka selemo sa ente ka 2012 ho fedisa bothata bona, e leng ho bakileng phokotseho e kgolo ya tshwaetso tsa kokwanahloko ya rotavirus. Afrika e na le mefuta e mengata e fapaneng ya rotavirus ha e bapiswa le dinaha tse ding tse tswetseng pele, haholoholo Yuropo le Amerika Leboya, mme ka hona ho batleha kutlwisiso e tebileng ya bothata bona. Diphuputso tsena di reretswe ho hlakisa dikarolo tsohle tse 11 tsa tshwaetso ya RVA e fumanwang hohle mane Rwanda pele le kamora tlhahiso ya ente e le karolo ya World Health Organization (WHO) e tsheheditse lenaneo lena la pulamadiboho la patlisiso la African rotavirus. Diphuputso tsena di ne di theilwe hodima disampole tse amohelehang tse 158 tsa rotavirus tse bokeletsweng ho bana ba hlahisang matshwao a amanywang le tshwaetso ya rotavirus pakeng tsa 2011 le 2016. Rotavirus double-stranded ribonucleic acid (dsRNA) e ile ya ntshwa ho dikarolwana tsa kokwanahloko mme ya fetolwa ho sebetsa hammoho le complementary deoxyribonucleic acid (cDNA) pele e ka sebetswa laeboraring bakeng sa ho ba whole-genome sequencing ka Illumina MiSeq platform. Disebediswa tse fapaneng tsa bioinformatics di sebedisitswe ho etsa difate tsa phylogenetic le dipopeho tsa diproteine. Ho tswa ho disampole tse hlophisitsweng ka tatelano, disampole tse 36 di ile tsa hlwauwa e le G1P[8] strains, athe tse hlano tsona ya ba reassortant strains. Tse leshome tsa G1P[8] di hlailwe pele ho hlahiswa ente athe tse 26 tsona di hlwailwe kamora tlhahiso ya ente. Tse mashome a mararo a metso e mehlano tsa G1P[8] strains di totobaditse Wa-like genome constellations, ha ente e nngwe ya mahloko e neng e hlwailwe ka 2012 e totobaditse genome constellation e tsejwang haholo ka ente ya RotaTeq® vaccine. Ka lehlakoreng le leng, reassortant strains tse hlano di ile tsa hlwauwa kamora ente pakeng tsa 2013-2015. Tshekatsheko ya whole-genome e sibolotse hore G4P[4], G9P[4] esita le e nngwe ya G12P[8] reassortant strains di bontshitse ka bobedi Wa-like le DS-1-like genome constellations athe G12P[8] strains tse pedi tsona di bontshitse genogroup constellations tsohle tse tharo. Ho feta mona, tshekatsheko ya phylogenetic ya bongata ba G1P[8] strains e senotse hore di kgetholotse ho ya ka maemo a ente; mahloko a hlwailweng pele ho tlhahiso ya ente a bokeletswe hammoho athe a kamora tshebediso ya ente ona a theile sehlotshwana sa ona se ikgethileng. Reassortant strains tse hlano di amantswe le RVA strains tsa botho ho dikarolo tsohle tsa dijini le RotaTeq® vaccine strains ho VP1, VP2, NSP2, NSP4, le dikarolo tsa dijini tsa NSP5. Tshekatsheko ya neutralization epitopes and cytotoxic T-lymphocytes (CTL) ya G1P[8] strains e bontshitse hore diphetolo tse ngata tsa amino acid, le tse ding tsa diphetoho tse bakang phetoho ho ya ka mahlakore, di bonahala jwale di sa hlalosehe hantle haholo. Ketso ya mofuta o jwalo e bonahetse hape le ho reassortant strains, tse nang le diphetolo tse 27 tsa amino acid ho VP7 epitope region le diphetolo tse tharo feela ho lebatowa la VP4 epitope. Diphetoho tsena tse bonahetseng mabatoweng ana a epitope di na le bokgoni ba ho hlahisa vaccine-escape mutants tse ka nnang tsa fokotsa bohlwahlwa ba ente ya rotavirus ho ya ka nako le ho kgema le yona. Whole-genome xv sequencing e itshupile hore e ka fana ka dintlha tse sa hlahiswang ha ho tadingwa feela bokantle ba capsid proteins. Ho molemo ke hona ho tswela pele ho etsa diphuputso tsa rotavirus whole-genome e le ho hlakisa dintlha tse patilweng mabapi le diphetoho tse ngata tsa rotavirus strains dinaheng tsa Afrika tse kang Rwanda. ___________________________________________________________________ | st_ZA |
| dc.description.abstract | 𝑰𝒔𝒊𝒁𝒖𝒍𝒖 Izingane ezihlala emazweni asathuthuka zihlala zibhekene nomthwalo wezifo zohudo ezibangela ukufa kwabantu abangaphezu kwesigidi nezingxenye eziyisithupha (-1.6) emhlabeni jikelele. Iqembu leRotavirus A (RVA) likhonjwe njengelinye lamagciwane athinteka kakhulu ezifweni zohudo ezibangelwa yigciwane ezinganeni ezingaphansi kweminyaka emihlanu emhlabeni jikelele. E-Rwanda, zingaphezu kwezi-3500 izigameko zokufa okuhlobene ne-RVA ezibikwe minyaka yonke ngaphambi kokuqaliswa komgomo we- RotaTeq ® ngonyaka wezi-2012 ukuze kunqotshwe lo mthwalo, okwaholela ekwehleni okukhulu kwezifo ze-rotavirus. I-Afrika inokuhlukahluka okukhulu kwezinhlobo ze-rotavirus uma kuqhathaniswa namanye amazwekazi athuthukile ikakhulukazi i-Europe neNorth America, ngaleyo ndlela idinga ukuqonda okujulile kwalesi simo. Lolu cwaningo luhlose ukuveza zonke izingxenye eziyi-11 zezinhlobo ze-RVA ezizungeza eRwanda ngaphambi nangemuva kokuthulwa komgomo njengengxenye yeNhlangano Yezempilo Yomhlaba esekela uhlelo lokuhlola irotavirus lwase-Afrika. Ucwaningo belusekelwe kumasampuli ayi-158 erotavirus aqoqwe kusukela ezinganeni ezinezimpawu ezihlobene zokutheleleka ngerotavirus phakathi konyaka wezi-2011 nowezi-2016. Irotavirus enedouble-stranded ribonucleic acid (dsRNA) yakhishwa ezinhlayiyeni zegciwane futhi yaguqulwa yaba icomplementary deoxyribonucleic acid (cDNA) ngaphambi kokulungiswa okumqoka kokulandelana kwegenome ephelele ngeplatifomu yeIllumina MiSeq. Amathuluzi amaningana ebioinformatics asetshenziselwa ukwakha izihlahla zephylogenetic kanye nezakhiwo zamaprotheni. Kusuka kumasampuli alandelanayo, amasampula angama-36 akhonjwe njengezinhlobo zeG1 P[8], futhi amasampula amahlanu bekuyizinhlobo ezivuselelayo. Izinhlobo eziyishumi ze-G1 P[8] zihlonzwe njengezethulo zangaphambi kokugoma ezingama-26 zihlonzwe isingeniso ngemva kokugoma. Amashumi amathathu nanhlanu ezinhlobo ze-G1 P[8] ziveze amaqoqo ezinkanyezi afana ne-Wa-like genome, kuyilapho enye yezinhlobo ezahlonzwa ngonyaka wezi-2012 ibonise umlaza wegenome ovamile wohlobo lokugoma lweRotaTeq ® . Ngakolunye uhlangothi, izinhlobo ezinhlanu ze-reassortant zihlonzwe ukwethulwa komuthi wokugoma phakathi kuka-2013 – 2015. Ukuhlaziywa kwe-Whole-genome kwembula ukuthi i-G4 P[4], G9P[4] kanye ne-G12P[8] eyodwa ye- reassortant strains ibonise kokubili i-Wa-like kanye ne-DS-1-like genome constellations kuyilapho izinhlobo ezimbili ze-G12P[8] zinakho konke. Imilaza emithathu ye-genogroup. Ngaphezu kwalokho, ukuhlaziywa kwe-phylogenetic kwezinhlobo eziningi ze-G1 P[ 8] kwembula ukuthi bahlukanisa ngokuvumelana nesimo sabo sokugoma; izinhlobo ezihlonze isingeniso somuthi wangaphambi kokugoma zihlanganiswe ndawonye kuyilapho izinhlobo zangemuva kokugoma nazo zakha iqoqo elihlukile. Izinhlobo ezinhlanu zereassortant zazihlobene eduze nezinhlobo ze-RVA yabantu kuzo zonke izingxenye zofuzo kanye nezinhlobo zomuthi wokugomela iRotaTeq ® ezingxenyeni zofuzo ze-VP1, VP2, NSP2, NSP4, kanye ne-NSP5. Ukuhlaziywa kwama-epitopes eneutralization kanye ne-cytotoxic T-lymphocytes (CTL) yezinhlobo ze-G1 P[8] kwembule ukushintshwa kwama-amino acid amaningi, nolunye ushintsho olunomthelela ekushintsheni kwepholarithi okuthathwa njengokushintsha okukhulu ngokwemvelo. Ukuthambekela okufanayo kuphinde kwabonwa ezinhlotsheni zereassortant, nokushintshwa kwe-amino acid okungama-27 endaweni ye-VP7 epitope kanye nokushintshwa okuthathu kuphela endaweni ye-VP4 epitope. Izinguquko ezibonwe kulezi zifunda ze-epitope zinamandla okukhiqiza izinto eziguquguqukayo zomgomo ezingase zibukele phansi ukusebenza komgomo werotavirus ngokuhamba kwesikhathi. Ukulandelana kwegenome ephelele xv kufakazele ukunikeza ulwazi obelungaphuthelwa uma kubhekwa kuphela amaprotheni ecapsid angaphandle. Ngakho-ke kubalulekile ukuqhubeka nokwenza izifundo zerotavirus ze-genome ephelele ukuze uvule ulwazi olufihliwe ngemuva kwezinhlobonhlobo ezinkulu zerotavirus emazweni ase-Afrika njengeRwanda. ___________________________________________________________________ | isiZ_ZA |
| dc.identifier.uri | http://hdl.handle.net/11660/11204 | |
| dc.language.iso | en | en_ZA |
| dc.publisher | University of the Free State | en_ZA |
| dc.publisher | Abstract in other languages 𝘚𝘤𝘳𝘰𝘭𝘭 𝘥𝘰𝘸𝘯 𝘧𝘰𝘳 𝘈𝘧𝘳𝘪𝘬𝘢𝘢𝘯𝘴, 𝘚𝘦𝘚𝘰𝘵𝘩𝘰 𝘢𝘯𝘥 𝘐𝘴𝘪𝘡𝘶𝘭𝘶 | |
| dc.rights.holder | University of the Free State | en_ZA |
| dc.subject | Rotavirus | en_ZA |
| dc.subject | Rwanda | en_ZA |
| dc.subject | Whole-genome characterization | en_ZA |
| dc.subject | Reassortment | en_ZA |
| dc.subject | Epitope region | en_ZA |
| dc.subject | RotaTeq® | en_ZA |
| dc.subject | Rotarix® | en_ZA |
| dc.subject | Diarrhoea | en_ZA |
| dc.subject | Vaccine-derived strain | en_ZA |
| dc.subject | Genome constellation | en_ZA |
| dc.title | Whole-genome analyses of rotavirus strains circulating pre- and post- Rotateq™ vaccine introduction in Rwanda | en_ZA |