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  • 1.
    Baroni de Moraes, Marcia Terezinha
    et al.
    Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Olivares Olivares, Alberto Ignacio
    Univ Fed Roraima, Brazil; Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Fialho, Alexandre Madi
    Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Malta, Fabio Correia
    Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    da Silva e Mouta Junior, Sergio
    Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Bispo, Romanul de Souza
    Univ Fed Roraima, Brazil.
    Velloso, Alvaro Jorge
    Oswaldo Cruz Fdn FIOCRUZ, Brazil; Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Alves Leitao, Gabriel Azevedo
    Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Cantelli, Carina Pacheco
    Oswaldo Cruz Fdn FIOCRUZ, Brazil; Oswaldo Cruz Fdn FIOCRUZ, Brazil; Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Nordgren, Johan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Miagostovich, Marize Pereira
    Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Gagliardi Leite, Jose Paulo
    Oswaldo Cruz Fdn FIOCRUZ, Brazil.
    Phenotyping of Lewis and secretor HBGA from saliva and detection of new FUT2 gene SNPs from young children from the Amazon presenting acute gastroenteritis and respiratory infection2019In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 70, p. 61-66Article in journal (Refereed)
    Abstract [en]

    The Histo-blood group antigens (HBGA) are host genetic factors associated with susceptibility to rotavirus (RV) and human norovirus (HuNoV), the major etiological agents of viral acute gastroenteritis (AGE) worldwide. The FUT2 gene expressing the alpha-1, 2-L- fucosyltransferase enzyme is important for gut HBGA expression, and also provides a composition of the phenotypic profile achieved through mutations occurring in populations with different evolutionary histories; as such, it can be considered a genetic population marker. In this study, Lewis and secretor HBGA phenotyping was performed using 352 saliva samples collected from children between three months and five years old born in the Amazon (Brazil, Venezuela and English Guyana) presenting AGE or acute respiratory infection (ARI), the latter considered as control samples. The total of children phenotyped as secretors was 323, corresponding to 91.80%. From these, 207 (58.80%) had a Le (a + b +) profile. The HBGA profiles were equally found in children with AGE as well as with ARI. The rs1047781 of the FUT2 gene was not detected in DNA from saliva cells with a Le (a + b +) profile. However, mutations not yet described in the FUT2 gene were observed: missense 325A amp;gt; T, 501C amp;gt; T, 585C amp;gt; T, 855A amp;gt; T and missense substitutions 327C amp;gt; T [S (Ser) amp;gt; C (Cys)], 446 T amp;gt; C [L(Leu) amp;gt; P(Pro)], 723C amp;gt; A [N(Asn) amp;gt; K(Lys)], 724A amp;gt; T [I(Ile) amp;gt; F(Phe)], 736C amp;gt; A [H(His) amp;gt; N(Asn)]. The SNP distribution in the FUT2 gene of the analyzed samples was very similar to that described in Asian populations, including indigenous tribes.

  • 2.
    Bucardo, Filemon
    et al.
    National Autonomous University of Leon, Nicaragua.
    Nordgren, Johan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Impact of vaccination on the molecular epidemiology and evolution of group A rotaviruses in Latin America and factors affecting vaccine efficacy2015In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 34, p. 106-113Article, review/survey (Refereed)
    Abstract [en]

    Despite high rotavirus (RV) vaccine coverage (similar to 83%) and good effectiveness (similar to 77%) against RV-diarrhea hospitalization, RV is still contributing to the burden of diarrhea that persists in hospital settings in several Latin American countries, where RV vaccination is being implemented. Due to the extensive genomic and antigenic diversity, among co-circulating human RV, a major concern has been that the introduction of RV vaccination could exert selection pressure leading to higher prevalence of strains not included in the vaccines and/or emergence of new strains, thus, reducing the efficacy of vaccination. Here we review the molecular epidemiology of RV in Latin America and explore issues of RV evolution and selection in light of vaccination. We further explore etiologies behind the large burden of diarrhea remaining after vaccination in some countries and discuss plausible reasons for vaccine failures. (C) 2015 Elsevier B.V. All rights reserved.

  • 3.
    Bucardo, Filemon
    et al.
    National Autonomous University of Nicaragua, Nicaragua.
    Reyes, Yaoska
    National Autonomous University of Nicaragua, Nicaragua.
    Becker-Dreps, Sylvia
    University of N Carolina, NC USA.
    Bowman, Natalie
    University of N Carolina, NC USA.
    Gruber, Joann F.
    University of N Carolina, NC USA.
    Vinje, Jan
    National Centre Immunizat and Resp Disease, GA USA.
    Espinoza, Felix
    National Autonomous University of Nicaragua, Nicaragua.
    Paniagua, Margarita
    National Autonomous University of Nicaragua, Nicaragua.
    Balmaseda, Angel
    Minist Heatlh, Nicaragua.
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Nordgren, Johan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Pediatric norovirus GII.4 infections in Nicaragua, 1999-20152017In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 55, p. 305-312Article in journal (Refereed)
    Abstract [en]

    Objectives: Investigate clinical and epidemiological factors of pediatric GII.4 norovirus infections in children with acute gastroenteritis (AGE) in Nicaragua between 1999 and 2015. Methods: We retrospectively analyzed laboratory and epidemiologic data from 1,790 children amp;lt;= 7 years with AGE from 6 hospitals in Nicaragua (n = 538), and 3 community clinics (n = 919) and households (n = 333) in Leon, between 1999 and 2015. Moreover, asymptomatic children from community clinics (n = 162) and households (n = 105) were enrolled. Norovirus was detected by real-time PCR and genotyped by sequencing the N-terminal and shell region of the capsid gene. Results: Norovirus was found in 19% (n = 338) and 12% (n = 32) of children with and without AGE, respectively. In total, 20 genotypes including a tentatively new genotype were detected. Among children with AGE, the most common genotypes were GII.4 (53%), GII.14 (7%), GII.3 (6%) and GI.3 (6%). In contrast, only one (1.4%) GII.4 was found in asymptomatic children. The prevalence of GII.4 infections was significantly higher in children between 7 and 12 months of age. The prevalence of GII.4 was lowest in households (38%), followed by community clinics (50%) and hospitals (75%). Several different GII.4 variants were detected and their emergence followed the global temporal trend. Conclusions: Overall our study found the predominance of pediatric GII.4 norovirus infections in Nicaragua mostly occurring in children between 7 and 12 months of age, implicating GII.4 as the main norovirus vaccine target.

  • 4.
    Bucardo, Filemon
    et al.
    University of Leon, Nicaragua .
    Rippinger, Christine M.
    NIAID, USA .
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology. Linköping University, Faculty of Health Sciences.
    Patton, John T.
    NIAID, USA .
    Vaccine-derived NSP2 segment in rotaviruses from vaccinated children with gastroenteritis in Nicaragua2012In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 12, no 6, p. 1282-1294Article in journal (Refereed)
    Abstract [en]

    Rotavirus (RV) vaccination programs have been established in several countries using the human-attenuated G1P[8] monovalent vaccine Rotarix (TM) (GlaxoSmithKline) and/or the human-bovine reassortant G1, G2, G3, G4, P[8] pentavalent vaccine Rotaleq (TM) (Merck). The efficacy of both vaccines is high (similar to 90%) in developed countries, but can be remarkably lower in developing countries. For example, a vaccine efficacy against severe diarrhea of only 58% was observed in a 2007-2009 Nicaraguan study using RotaTeq. To gain insight into the significant level of vaccine failure in this country, we sequenced the genomes of RVs recovered from vaccinated Nicaraguan children with gastroenteritis. The results revealed that all had genotype specificities typical for human RVs (11G1P[8], 1G3P[8]) and that the sequences and antigenic epitopes of the outer capsid proteins (VP4 and VP7) of these viruses were similar to those reported for RVs isolated elsewhere in the world. As expected, nine of the G1 P[8] viruses and the single G3P[8] virus had genome constellations typical of human G1 P[8] and G3P[8] RVs: G1/3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. However, two of the G1P[8] viruses had atypical constellations, G1-P[8]-I1-R1-C1-M1-A1-N2-T1-E1-H1, due to the presence of a genotype-2 NSP2 (N2) gene. The sequence of the N2 NSP2 gene was identical to the bovine N2 NSP2 gene of RotaTeq, indicating that the two atypical viruses originated via reassortment of human G1P[8] RVs with RotaTeq viruses. Together, our data suggest that the high level of vaccine failure in Nicaraguan is probably not due to antigenic drift of commonly circulating virus strains nor the emergence of new antigenetically distinct virus strains. Furthermore, our data suggest that the widespread use of the RotaTeq vaccine has led to the introduction of vaccine genes into circulating human RVs.

  • 5.
    Karlsson, Anneli
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Ryberg, Anna
    Linköping University, Department of Clinical and Experimental Medicine, Clinical Microbiology. Linköping University, Faculty of Health Sciences.
    Nosouhi Dehnoei, Marjan
    Linköping University, Department of Clinical and Experimental Medicine, Clinical Microbiology. Linköping University, Faculty of Health Sciences.
    Borch, Kurt
    Linköping University, Department of Clinical and Experimental Medicine, Surgery. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Centre for Surgery, Orthopaedics and Cancer Treatment, Department of Surgery in Östergötland.
    Monstein, Hans-Jürg
    Linköping University, Department of Clinical and Experimental Medicine, Clinical Microbiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Centre for Diagnostics, Department of Clinical Microbiology.
    Variation in number of cagA EPIYA-C phosphorylation motifs between cultured Helicobacter pylori and biopsy strain DNA2012In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 12, no 1, p. 175-179Article in journal (Refereed)
    Abstract [en]

    The Helicobacter pylori cagA gene encodes a cytotoxin which is activated by phosphorylation after entering the host epithelial cell. Phosphorylation occurs on specific tyrosine residues within EPIYA motifs in the variable 3'-region. Four different cagA EPIYA motifs have been defined according to the surrounding amino acid sequence; EPIYA-A, -B, -C and -D. Commonly, EPIYA-A and -B are followed by one or more EPIYA-C or -D motif. Due to observed discrepancies in cagA genotypes in cultured H. pylori and the corresponding DNA extracts it has been suggested that genotyping assays preferentially should be performed directly on DNA isolated from biopsy specimens. Gastric biopsies randomly selected from a Swedish cohort were homogenised and used for both direct DNA isolation and for H. pylori specific culturing and subsequent DNA isolation. In 123 of 153 biopsy specimens, the cagA EPIYA genotypes were in agreement with the corresponding cultured H. pylori strains. A higher proportion of mixed cagA EPIYA genotypes were found in the remaining 30 biopsy specimens. Cloning and sequencing of selected cagA EPIYA amplicons revealed variations in number of cagA EPIYA-C motifs in the mixed amplicons. The study demonstrates that culturing of H. pylori introduces a bias in the number of EPIYA-C motif. Consistent with other H. pylori virulence genotyping studies, we suggest that cagA EPIYA analysis should be performed using total DNA isolated from biopsy specimens.

  • 6.
    Matussek, Andreas
    et al.
    County Hospital Ryhov, Sweden.
    Dienus, Olaf
    County Hospital Ryhov, Sweden.
    Djeneba, Ouermi
    University of Ouagadougou, Burkina Faso.
    Simpore, Jacques
    University of Ouagadougou, Burkina Faso.
    Nitiema, Leon
    University of Ouagadougou, Burkina Faso.
    Nordgren, Johan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Molecular characterization and genetic susceptibility of sapovirus in children with diarrhea in Burkina Faso2015In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 32, p. 396-400Article in journal (Refereed)
    Abstract [en]

    Sapoviruses (Says) are a common cause of gastroenteritis in children. In sub-Saharan Africa, there is a scarcity of information regarding SaV as an etiological agent of diarrhea. Here, we investigated the prevalence, molecular characterization and clinico-epidemiological features of SaV infections in children less than 5 years of age with diarrhea in Burkina Faso. We further investigated the role of type 1 histo blood group antigens as susceptibility factors. In total, 309 fecal and 208 saliva samples from diarrheal children in Ouagadougou, Burkina Faso, were collected between May 2009 and March 2010. Say was detected using real-time PCR, and genogrouped/genotyped by PCR or sequencing. Saliva samples were ABO, Lewis and secretor phenotyped using in house ELISA assays. We found a high prevalence (18%) and large genetic diversity with all 4 human genogroups, and 9 genotypes/genoclusters circulating during the study period. The SaV infections were generally associated with milder symptoms, and neither ABH, Lewis or secretor phenotypes affected susceptibility to Say infections. (C) 2015 Published by Elsevier B.V.

  • 7.
    Nordgren, Johan
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology. Linköping University, Faculty of Health Sciences.
    Juste O Bonkoungou, Isidore
    Laboratoire National de Santé Publique du Burkina Faso, Ouagadougou, Burkina Faso, Laboratoire de Biologie Moléculaire, d’Epidémiologie et Surveillance des Bactéries et Virus Transmissibles par les Aliments, CRSBAN/UFR-SVT, Université de Ouagadougou, Ouagadougou, Burkina Faso.
    Nitiema, Leon W.
    Centre de Recherche Biomoléculaire Pietro Annigoni, Saint Camille CERBA/LABIOGENE, Université de Ouagadougou, Ouagadougou, Burkina Faso, Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université de Ouagadougou, Ouagadougou, Burkina Faso.
    Sharma, Sumit
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology. Linköping University, Faculty of Health Sciences.
    Ouermi, Djeneba
    Centre de Recherche Biomoléculaire Pietro Annigoni, Saint Camille CERBA/LABIOGENE, Université de Ouagadougou, Ouagadougou, Burkina Faso.
    Simpore, Jacques
    Centre de Recherche Biomoléculaire Pietro Annigoni, Saint Camille CERBA/LABIOGENE, Université de Ouagadougou, Ouagadougou, Burkina Faso.
    Barro, Nicolas
    Laboratoire de Biologie Moléculaire, d’Epidémiologie et Surveillance des Bactéries et Virus Transmissibles par les Aliments, CRSBAN/UFR-SVT, Université de Ouagadougou, Ouagadougou, Burkina Faso.
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Molecular Virology. Linköping University, Faculty of Health Sciences.
    Rotavirus in diarrheal children in rural Burkina Faso: High prevalence of genotype G6P[6]2012In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 12, no 8, p. 1892-1898Article in journal (Refereed)
    Abstract [en]

    Group A rotavirus (RVA) is the most common cause of severe gastroenteritis in young children globally, and responsible for a significant number of deaths in African countries. While vaccines are available, trials have shown a lesser efficacy in Africa. One of the reasons could be the prevalence and/or emergence of unusual or novel RVA strains, as many strains detected in African countries remain uncharacterized. less thanbrgreater than less thanbrgreater thanIn this study, we characterized RVA positive specimens from two remote rural areas in Burkina Faso, West Africa. In total 56 RVA positive specimens were subgrouped by their VP6 gene, and G-and P typed by PCR and/or sequencing of the VP7 and VP4 genes, respectively. less thanbrgreater than less thanbrgreater thanNotably, we found a high prevalence of the unusual G6P[6]SGI strains (23%). It was the second most common constellation after G9P[8]SGII (32%); and followed by G1P[8]SGII (20%) and G2P[4]SGI (9%). We also detected a G8P[6]SGI strain, for the first time in Burkina Faso. The intra-genetic diversity was high for the VP4 gene with two subclusters within the P[8] genotype and three subclusters within the P[6] genotype which were each associated with a specific G-type, thereby suggesting a genetic linkage. The G6P[6]SGI and other SGI RVA strains infected younger children as compared to SGII strains (p andlt; 0.05). less thanbrgreater than less thanbrgreater thanTo conclude, in this study we observed the emergence of unusual RVA strains and high genetic diversity of RVA in remote rural areas of Burkina Faso. The results highlight the complexity of RVA epidemiology which may have implication for the introduction of rotavirus vaccines currently being evaluated in many African countries.

  • 8.
    Skar, H.
    et al.
    Department of Virology, Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden, Department of Microbiology Tumor and Cell Biology, Karolinska Institute, SE-17177 Stockholm, Sweden, Theoretical Biology and Biophysics, Group T-10, Los Alamos National Laboratory, MS K710, Los Alamos, NM 87545, United States.
    Sylvan, S.
    Regional Center for Infectious Disease Control and Prevention, Dag Hammarskjölds väg 17, SE-751 85 Uppsala, Sweden.
    Hansson, H.-B.
    Regional Center for Infectious Disease Control and Prevention, University Hospital MAS, SE-20502 Malmö, Sweden.
    Gustavsson, Olle
    Östergötlands Läns Landsting, Centre for Laboratory Medicine, Department of Clinical Microbiology.
    Boman, H.
    Department of Communicable Diseases Control, Sundsvall Hospital, SE-851 86 Sundsvall, Sweden.
    Albert, J.
    Department of Virology, Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden, Department of Microbiology Tumor and Cell Biology, Karolinska Institute, SE-17177 Stockholm, Sweden.
    Leitner, T.
    Theoretical Biology and Biophysics, Group T-10, Los Alamos National Laboratory, MS K710, Los Alamos, NM 87545, United States.
    Multiple HIV-1 introductions into the Swedish intravenous drug user population2008In: Infection, Genetics and Evolution, ISSN 1567-1348, E-ISSN 1567-7257, Vol. 8, no 5, p. 545-552Article in journal (Refereed)
    Abstract [en]

    In 2001, an increase of HIV-1 diagnoses among intravenous drug users (IVDU) was reported in Sweden. In nearby countries, Finland, Russia and the Baltic states, recent outbreaks had been described. Since there was a concern that these outbreaks would carry over to Sweden a study was initiated to determine the factors leading to the Swedish increase of HIV-1 diagnosed IVDUs. HIV-1 env V3 sequences were obtained from 97 patients enrolled in ongoing epidemiological studies encompassing the years 1987-2004 with a focus on 2001-2002. The sequences were used for maximum likelihood and Bayesian inference of the molecular epidemiology. Among the virus spreading in 2001-2002, we found that four different subtypes/CRFs were present in the Swedish IVDU population (A, B, CRF01_AE and CRF06_cpx). Subtype B constituted 85% of the infections, established by 12 independent introductions into the IVDU population. The worrisome increase in 2001 was mainly not a result of import of the outbreaks in nearby countries, but rather a higher detection rate of secondary cases due to efficient epidemiological tracing of the generally slow spread of established forms of subtype B in the IVDU community. However, a few of the non-subtype B cases were linked to the outbreaks in Finland, Estonia and Latvia. Because HIV-1 outbreaks can easily be exported from one country to another amongst IVDUs, this prompts continued surveillance in the Baltic Sea Region.

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