Molecular epidemiology of human rhinoviruses

The first part of this work investigates the molecular epidemiology of a human enterovirus (HEV), echovirus 30 (E-30). This project is part of a series of studies performed in our research team analyzing the molecular epidemiology of HEV-B viruses. A total of 129 virus strains had been isolated in different parts of Europe. The sequence analysis was performed in three different genomic regions: 420 nucleotides (nt) in the VP4/VP2 capsid protein coding region, the entire VP1 capsid protein coding gene of 876 nt, and 150 nt in the VP1/2A junction region. The analysis revealed a succession of dominant sublineages within a major genotype. The temporally earlier genotypes had been replaced by a genetically homogenous lineage that has been circulating in Europe since the late 1970s. The same genotype was found by other research groups in North America and Australia. Globally, other cocirculating genetic lineages also exist. The prevalence of a dominant genotype makes E-30 different from other previously studied HEVs, such as polioviruses and coxsackieviruses B4 and B5, for which several coexisting genetic lineages have been reported. The second part of this work deals with molecular epidemiology of human rhinoviruses (HRVs). A total of 61 field isolates were studied in the 420-nt stretch in the capsid coding region of VP4/VP2. The isolates were collected from children under two years of age in Tampere, Finland. Sequences from the clinical isolates clustered in the two previously known phylogenetic clades. Seasonal clustering was found. Also, several distinct serotype-like clusters were found to co-circulate during the same epidemic season. Reappearance of a cluster after disappearing for a season was observed. The molecular epidemiology of the analyzed strains turned out to be complex, and we decided to continue our studies of HRV. Only five previously published complete genome sequences of HRV prototype strains were available for analysis. Therefore, all designated HRV prototype strains (n=102) were sequenced in the VP4/VP2 region, and the possibility of genetic typing of HRV was evaluated. Seventy-six of the 102 prototype strains clustered in HRV genetic group A (HRV-A) and 25 in group B (HRV-B). Serotype 87 clustered separately from other HRVs with HEV species D. The field strains of HRV represented as many as 19 different genotypes, as judged with an approximate demarcation of a 20% nt difference in the VP4/VP2 region. The interserotypic differences of HRV were generally similar to those reported between different HEV serotypes (i.e. about 20%), but smaller differences, less than 10%, were also observed. Because some HRV serotypes are genetically so closely related, we suggest that the genetic typing be performed using the criterion "the closest prototype strain". This study is the first systematic genetic characterization of all known HRV prototype strains, providing a further taxonomic proposal for classification of HRV. We proposed to divide the genus Human rhinoviruses into HRV-A and HRV-B. The final part of the work comprises a phylogenetic analysis of a subset (48) of HRV prototype strains and field isolates (12) in the nonstructural part of the genome coding for the RNA-dependent RNA polymerase (3D). The proposed division of the HRV strains in the species HRV-A and HRV-B was also supported by 3D region. HRV-B clustered closer to HEV species B, C, and also to polioviruses than to HRV-A. Intraspecies variation within both HRV-A and HRV-B was greater in the 3D coding region than in the VP4/VP2 coding region, in contrast to HEV. Moreover, the diversity of HRV in 3D exceeded that of HEV. One group of HRV-A, designated HRV-A', formed a separate cluster outside other HRV-A in the 3D region. It formed a cluster also in the capsid region, but located within HRV-A. This may reflect a different evolutionary history of distinct genomic regions among HRV-A. Furthermore, the tree topology within HRV-A in the 3D region differed from that in the VP4/VP2, suggesting possible recombination events in the evolution of the strains. No conflicting phylogenies were observed in any of the 12 field isolates. Possible recombination was further studied using the Similarity and Bootscanning analyses of the complete genome sequences of HRV available in public databases. Evidence for recombination among HRV-A was found, as HRV2 and HRV39 showed higher similarity in the nonstructural part of the genome. Whether HRV2 and HRV39 strains - and perhaps also some other HRV-A strains not yet completely sequenced - are recombinants remains to be determined.Työn ensimmäinen osa koostuu molekyyliepidemiologisesta tutkimuksesta, jossa tutkittiin erään ihmisen enteroviruksen (HEV), echovirus 30:n kliinisiä isolaatteja. Tämä tutkimus on osa HEV-B virusten molekyyliepidemiologiaa tutkivaa sarjaa. Tutkimuksessa mukana olleet kaikkiaan 130 viruskantaa oli eristetty eri puolella Eurooppaa. Sekvenssianalyysi käsitti kolme erillistä genomialuetta; 420 nukleotidin pituisen VP4/VP2-kapsidiproteiineja koodaavan osan, koko 876 nukleotidin pituisen VP1-kapsidiproteiinia koodaavan geenin sekä 150 nukleotidin pituisen VP1/2A- risteysalueen. Analyysi paljasti vallitsevien geneettisten alaryhmien jatkumon yhden päägenotyypin sisällä. Aiemmat genotyypit olivat korvautuneet geneettisesti yhteinäisellä alatyypillä, joka oli kiertänyt Euroopassa 1970-luvun lopulta lähtien. Muut tutkimusryhmät olivat havainneet saman genotyypin myös Pohjois-Americassa ja Australiassa. Kuitenkin maailmanlaajuisesti muitakin yhtä aikaa kiertäviä genotyyppejä on havaittu. Echovirus 30:lla havaittu yhden päägenotyypin vallitsevuus eroaa muista enterovirusserotyypeistä, joita on tutkittu molekyyliepidemiologian keinoin. Tällaisia ovat esimerkiksi poliovirukset sekä coxsackievirukset B4 ja B5, joilla on havaittu useita samanaikaisia geneettisesti eroavia alatyyppejä. Työn toisessa osassa ihmisen rinovirusten molekyyliepidemiologiaa tutkittiin 61 kliinisen isolaatin geneettisellä analyysillä 420 nukleotidin pituisella VP4/VP2- kapsidiproteiinialueella. Virusisolaatit oli kerätty alle kaksivuotiaista lapsista Tampereen alueella. Kliinisistä isolaateista saadut sekvenssit jakautuivat kahteen ennalta tunnettuun fylogeneettiseen pääryhmään. Alaryhmiä muodostui vuodenaikaisvaihtelun mukaan. Myös saman epidemiakauden aikana havaittiin kiertäneen useita erillisiä serotyypin kaltaisia klustereita. Lisäksi, klusterin havaittiin ilmestyneen uudelleen yhden epidemiakauden poissaolon jälkeen. Analysoitujen rinoviruskantojen molekyyliepidemiologia näytti monimutkaiselta, joten päätimme jatkaa rinovirustutkimuksia. Rinovirusten sekvenssianalyysiin oli saatavilla vain viisi aiemmin sekvensoitua prototyyppikantaa. Sen vuoksi kaikki nimetyt 102 rinovirusten prototyyppikantaa sekvensoitiin VP4/VP2-alueelta ja mahdollisuutta rinovirusten geneettiseen tyypitykseen tutkittiin. 76 prototyyppikantaa klusteroitui rinovirusten geneettiseen ryhmään A ja 25 ryhmään B. Serotyyppi 87 erosi muista rinoviruksista ja klusteroitui enterovirus D- ryhmään. Rinovirusten kliiniset isolaatit edustivat 19 erillistä serotyyppiä, kun kriteerinä käytettiin 20% eroavuutta sekvenssissä. Serotyyppien väliset erot rinoviruksilla olivat yleensä samaa luokkaa kuin enteroviruksilla on havaittu (noin 20%), mutta myös pienempiä, alle 10%, eroja havaittiin. Koska osa rinovirusserotyypeistä on geneettisesti hyvin lähellä toisiaan, ehdotamme, että geneettisen tyypityksen kriteerinä käytetään "lähintä prototyyppiä". Tämä tutkimus oli ensimmäinen kaikkien tunnettujen rinovirusprototyyppikantojen systemaattinen geneettinen kartoitus ja se tarjoaa pohjan ihmisen rinovirusten taksonomiselle luokittelulle kahteen ryhmään Human rhinovirus A (HRV-A) ja Human rhinovirus B (HRV-B). Työn viimeinen osa käsittelee fylogeneettistä analyysia, jossa oli mukana 48 rinovirusten prototyyppikantaa sekä 12 kliinistä isolaattia. Tutkittavana genomialueena oli ei-strukturaalinen viruksen RNA polymeraasia koodaava 3D-alue. Rinoviruskannat jakautuivat aiemmin määriteltyihin ryhmiin HRV-A ja HRV-B myös 3D-alueella. HRV-B klusteroitui geneettisesti lähemmäs enterovirus-B, -C ja poliovirusryhmiä kuin HRV-A:ta. Ryhmien sisäinen variaatio sekä HRV-A:ssa että HRV-B:ssä oli suurempaa 3D- kuin VP4/VP2-kapsidialueella, toisin kuin enteroviruksilla. Lisäksi rinovirusten variaatio 3D:ssa oli suurempaa kuin enteroviruksilla. 3D-alueella havaittiin erillinen klusteri, joka kapsidialueella kuului HRV-A:han. Se nimettiin HRV-A':ksi. Tämä havainto saattaa olla seurausta HRV-A rinovirusten eri genomialueiden erilaisesta evoluutiohistoriasta. Myös HRV-A:n fylogeneettisten puiden topologiassa havaittiin eroja kapsidialueen ja ei-strukturaalialueen välillä, mikä saattaa viitata eri kantojen rekombinaatioon. Kuitenkin kaikki 12 tutkittua kliinistä isolaattia klusteroitui samoin kuin kapsidialueella. Mahdollista rekombinaatiota selvitettiin julkisissa tietokannoissa saatavissa olevien rinovirusten kokogenomisekvenssien Similarity ja Bootscanning -analyyseillä. Todisteita rekombinaatiosta HRV-A:ssa saatiin, kun HRV2 ja HRV39 osoittivat keskimääräistä suurempaa samankaltaisuutta genomin ei-strukturaaliosassa. Ovatko juuri HRV2 ja HRV39 rekombinoituneita kantoja vai kenties jotkut muut toistaiseksi sekvensoimattomat HRV-A serotyypit, jää vielä selvitettäväksi

Long-lasting heterologous antibody responses after sequential vaccination with A/Indonesia/5/2005 and A/Vietnam/1203/2004 pre-pandemic influenza A(H5N1) virus vaccines

Background: Avian influenza A(H5N1) viruses have caused sporadic infections in humans and thus they pose a significant global health threat. Among symptomatic patients the case fatality rate has been ca. 50%. H5N1 viruses exist in multiple clades and subclades and several candidate vaccines have been developed to prevent A(H5N1) infection as a principal measure for preventing the disease.Methods: Serum antibodies against various influenza A(H5N1) Glade viruses were measured in adults by ELISA-based microneutralization and haemagglutination inhibition tests before and after vaccination with two different A(H5N1) vaccines in 2009 and 2011.Results: Two doses of AS03-adjuvanted A/Indonesia/5/2005 vaccine induced good homologous but poor heterologous neutralizing antibody responses against different Glade viruses. However, non-adjuvanted A/Vietnam/1203/2004 booster vaccination in 2011 induced very strong and long-lasting homologous and heterologous antibody responses while homologous response remained weak in naive subjects.Conclusions: Sequential vaccination with two different A(H5N1) pre-pandemic vaccines induced long-lasting high level cross-Glade immunity against influenza A(H5N1) strains, thus supporting a prime-boost vaccination strategy in pandemic preparedness plans. </div

Kansallinen varautumissuunnitelma polion paluun torjumiseksi 2018-2020 : Päivitetty v. 2017-2019 versiosta

Tämän vanhan painoksen korvaa uusi, muutettu painos osoitteessa https://urn.fi/URN:ISBN:978-952-343-870-5</A

Exposure to persons with symptoms of respiratory or gastrointestinal infection and relative risk of disease : self-reported observations by controls in a randomized intervention trial

Abstract Background Little is known about the quantitative relationships between a self-recognized exposure to people with symptoms of respiratory (RTI) or gastrointestinal tract infection (GTI) and subsequent occurrence of homologous symptoms in the exposed person. Methods Adult office employees, controls in an intervention trial, reported weekly own symptoms of RTI or GTI and exposures to other persons with similar symptoms. To ascertain the reliability of the self-reported data, the participants received both in-advance training and repeated instructions in the weekly Email requests for reports. The relationship of self-reported exposures to self-reported homologous symptoms during the same or the following week was analyzed including, in the statistical models, cluster effects and longitudinal aspects in the data, seasonality, and cluster-specific baseline values. Results Altogether 11,644 weekly reports were received from 230 participants during the 16-month duration of the study. The mean age of the reporters was 42.9 years (standard deviation 11.1 years), and the female/male ratio 157/68 (for 5 participants this information was not available). A reported exposure to RTI was associated with an almost 5-fold higher relative risk for a reported homologous infection during the same week (4.9; 95% confidence interval (CI) 4.0 to 5.9), and with a 3-fold risk during the following week (3.3; CI 2.8 to 3.8). For GTI the corresponding figures were 15.1 (CI 10.4 to 21.8) and 4.3 (CI 3.1 to 5.8), respectively. On the other hand, for 24% of the designated RTI episodes, a homologous exposure had been reported during neither the same nor the preceding week. For GTI this figure was even greater (40%). For both RTI and GTI, weeks with a reported exposure were more frequent outside the workplace than only at the workplace (434 versus 262, and 109 versus 41, respectively). Conclusion A reported exposure to persons with obvious symptoms of RTI or GTI significantly increased the relative risk of reported homologous infection in the exposed adult persons. Yet, a substantial part of reported designated RTI and, especially, GTI episodes occurred without a reported exposure during the same or the previous week. Trial registration ClinicalTrials.gov with an identifier of NCT00821509 (12 March 2009)