scholarly journals Wading pool water contaminated with both noroviruses and astroviruses as the source of a gastroenteritis outbreak

2004 ◽  
Vol 132 (4) ◽  
pp. 737-743 ◽  
Author(s):  
L. MAUNULA ◽  
S. KALSO ◽  
C.-H. VON BONSDORFF ◽  
A. PÖNKÄ

In July 2001, an outbreak of gastroenteritis occurred in Helsinki among children and adults after bathing in an outdoor wading pool. The epidemiological survey revealed that at least 242 persons were affected. Microbiological testing of both patient stool samples and of the pool water revealed the presence of two different gastroenteritis viruses: a norovirus (NV) and an astrovirus. Amplicon sequencing of the NV samples showed nucleotide sequence identity between the virus from patients and the water. After changing the pool water and the sand at the bottom of the pool followed by shock chlorination, no virus could be detected in the water. However, NV was continuously detected in the water outlet well as much as 8 months after the incident. Here we show how molecular methods aided in tracing the source of the epidemic and in finding the causative pathogens both in patients and in the environment.

Genetics ◽  
1991 ◽  
Vol 128 (3) ◽  
pp. 595-606
Author(s):  
B L Hibner ◽  
W D Burke ◽  
T H Eickbush

Abstract The multigene families that encode the chorion (eggshell) of the silk moth, Bombyx mori, are closely linked on one chromosome. We report here the isolation and characterization of two segments, totaling 102 kb of genomic DNA, containing the genes expressed during the early period of choriogenesis. Most of these early genes can be divided into two multigene families, ErA and ErB, organized into five divergently transcribed ErA/ErB gene pairs. Nucleotide sequence identity in the major coding regions of the ErA genes was 96%, while nucleotide sequence identity for the ErB major coding regions was only 63%. Selection pressure on the encoded proteins cannot explain this difference in the level of sequence conservation between the ErA and ErB gene families, since when only fourfold redundant codon positions are considered, the divergence within the ErA genes is 8%, while the divergence within the ErB genes (corrected for multiple substitutions at the same site) is 110%. The high sequence identity of the ErA major exons can be explained by sequence exchange events similar to gene conversion localized to the major exon of the ErA genes. These gene conversions are correlated with the presence of clustered copies of the nucleotide sequence GGXGGX, encoding paired glycine residues. This sequence has previously been correlated with gradients of gene conversion that extend throughout the coding and noncoding regions of the High-cysteine (Hc) chorion genes of B. mori. We suggest that the difference in the extent of the conversion tracts in these gene families reflects a tendency for these recombination events to become localized over time to the protein encoding regions of the major exons.


Plant Disease ◽  
2004 ◽  
Vol 88 (8) ◽  
pp. 907-907 ◽  
Author(s):  
M. Juarez ◽  
V. Truniger ◽  
M. A. Aranda

In late spring 2003, field-grown melon plants (Cucumis melo L.) showing bright yellowing of older leaves were observed near Valladolises in Campo de Cartagena, Murcia, Spain. Symptoms resembled those caused by viruses of the genus Crinivirus (family Closteroviridae), but absence or very low populations of whiteflies were observed. However, diseased foci showed clear indications of heavy aphid infestations. Later, during the fall of 2003, squash plants (Cucurbita pepo L.) grown in open fields in the same area showed similar symptoms. Tissue print hybridizations to detect Cucurbit yellow stunting disorder virus (CYSDV) and Beet pseudo yellows virus (BPYV) in symptomatic samples were negative. CYSDV and BPYV are two yellowing-inducing criniviruses previously described in Spain. In contrast, standard double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) with antiserum against Cucurbit aphid-borne yellows virus (CABYV; genus Polerovirus, family Luteoviridae) that was kindly provided by H. Lecoq (INRA-Montfavet Cedex, France) were consistently positive. Definitive confirmation of CABYV associated with symptomatic samples was obtained by performing reverse-transcription polymerase chain reaction (RT-PCR) analyses for the CABYV coat protein gene. Total RNA extracts (TRI reagent; Sigma Chemical, St. Louis, MO) were obtained from symptomatic and asymptomatic leaf samples and RT-PCR reactions were carried out using the primers 5′-GAATACGGTCGCGGCTAGAAATC-3′ (CE9) and 5′-CTATTTCGGGTTCTGGACCTGGC-3′ (CE10) based on the CABYV sequence published by Guilley et al. (2). A single DNA product of approximately 600 bp was obtained only from symptomatic samples. Amplified DNA fragments from two independent samples (samples 36-2 and 37-5) were cloned in E. coli and sequenced (GenBank Accession Nos. AY529653 and AY529654). Sequence comparisons showed a 95% nucleotide sequence identity between the two sequences. A 97% and 94% nucleotide sequence identity was found among 36-2 and 37-5, respectively and the CABYV sequence published by Guilley et al. (2). CABYV seems to be widespread throughout the Mediterranean Basin (1,3) but to our knowledge, it has not previously been described in Spain. Additionally, our data suggest that significant genetic variability might be present in the Spanish CABYV populations. References: (1) Y. Abou-Jawdah et al. Crop Prot. 19:217, 2000. (2) H. Guilley et al. Virology 202:1012, 1994. (3) H. Lecoq et al. Plant Pathol. 41:749, 1992.


Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 148-148 ◽  
Author(s):  
J. Zhang ◽  
Z. J. Wu

Kudzu (Pueraria montana), a weed widely distributed in southern China, is common in the Fuzhou region of Fujian Province, where many plants show yellow vein mosaic disease. In September 2008, four leaf samples from different plants exhibiting yellow vein mosaic symptom were collected in suburban district of Fuzhou (25°15′ N, 118°08′ E). Whitefly (Bemisia tabaci) infestation was also observed in this region. Total DNA was extracted from all samples using a CTAB method (4). Universal primers (PA/PB) were used to amplify part of the intergenic region and coat protein gene of DNA-A of begomoviruses (1). An amplicon of approximately 500 bp was obtained from all four samples and then sequenced. Comparison of 500-bp fragments (GenBank Accession Nos. FJ539016-18 and FJ539014) revealed the presence of the same virus (98.8 to 99.4%). A pair of back-to-back primers (Yg3FL-F: 5′-GGATCCTTTGTTGAACGCCTTTCC-3′/Yg3FL-R: 5′-GGATCCCACATGTTTAAAGTAAAGC-3′) were designed to amplify the full-length DNA-A from the Chinese isolate identified as Yg3. Sequence analysis showed that full-length DNA-A of Yg3 isolate comprised 2,729 nucleotides (GenBank Accession No. FJ539014) and shared the highest nucleotide sequence identity (91.9%) with Kudzu mosaic virus (KuMV, GenBank Accession No. DQ641690) from Vietnam. To further test the association of DNA-B fragments with the four samples from southern China, rolling circle amplification (RCA) was performed (3). When RCA products were digested with Sph I, approximately 2.7 kb was obtained from all samples. Yg3 isolate was chosen to be sequenced. Sequence analysis showed that full-length DNA-B of Yg3 isolate comprised 2,677 nucleotides (GenBank Accession No. FJ539015) and shared the highest nucleotide sequence identity (76.8%) with KuMV DNA-B (GenBank Accession No. DQ641691) from Vietnam. Based on the current convention of begomovirus species demarcation of <89% sequence identity cut-off criterion (2), Yg3 was identified as an isolate of KuMV. To our knowledge, this is the first report of association of KuMV with yellow vein mosaic symptom of kudzu in China. References: (1). D. Deng et al. Annals Appl. Biol. 125:327, 1994. (2). C. M. Fauquet et al. Arch. Virol. 148:405, 2003. (3). D. Haible et al. J. Virol. Methods 135:9, 2006. (4). Y. Xie et al. Chinese Sci. Bull. 47:197, 2002.


1999 ◽  
Vol 73 (10) ◽  
pp. 8040-8052 ◽  
Author(s):  
Geraldina Dominguez ◽  
Timothy R. Dambaugh ◽  
Felicia R. Stamey ◽  
Stephen Dewhurst ◽  
Naoki Inoue ◽  
...  

ABSTRACT Human herpesvirus 6 variants A and B (HHV-6A and HHV-6B) are closely related viruses that can be readily distinguished by comparison of restriction endonuclease profiles and nucleotide sequences. The viruses are similar with respect to genomic and genetic organization, and their genomes cross-hybridize extensively, but they differ in biological and epidemiologic features. Differences include infectivity of T-cell lines, patterns of reactivity with monoclonal antibodies, and disease associations. Here we report the complete genome sequence of HHV-6B strain Z29 [HHV-6B(Z29)], describe its genetic content, and present an analysis of the relationships between HHV-6A and HHV-6B. As sequenced, the HHV-6B(Z29) genome is 162,114 bp long and is composed of a 144,528-bp unique segment (U) bracketed by 8,793-bp direct repeats (DR). The genomic sequence allows prediction of a total of 119 unique open reading frames (ORFs), 9 of which are present only in HHV-6B. Splicing is predicted in 11 genes, resulting in the 119 ORFs composing 97 unique genes. The overall nucleotide sequence identity between HHV-6A and HHV-6B is 90%. The most divergent regions are DR and the right end of U, spanning ORFs U86 to U100. These regions have 85 and 72% nucleotide sequence identity, respectively. The amino acid sequences of 13 of the 17 ORFs at the right end of U differ by more than 10%, with the notable exception of U94, the adeno-associated virus type 2 rep homolog, which differs by only 2.4%. This region also includes putative cis-acting sequences that are likely to be involved in transcriptional regulation of the major immediate-early locus. The catalog of variant-specific genetic differences resulting from our comparison of the genome sequences adds support to previous data indicating that HHV-6A and HHV-6B are distinct herpesvirus species.


Plant Disease ◽  
2014 ◽  
Vol 98 (10) ◽  
pp. 1445-1445 ◽  
Author(s):  
N. A. N. Fernandes-Acioli ◽  
L. S. Boiteux ◽  
M. E. N. Fonseca ◽  
L. R. G. Segnana ◽  
E. W. Kitajima

Leonurus sibiricus L. (Lamiaceae) is a subtropical weed frequently found with golden mosaic symptoms. Leonurus mosaic virus (LeMV) was the first begomovirus reported on L. sibiricus in Brazil (3). Later, a new bipartite species (Tomato yellow spot virus, ToYSV) was reported affecting tomatoes, beans, and also L. sibiricus (1,2). A survey of begomovirus isolates was conducted within tomato fields also displaying high incidence of plants with begomovirus-induced symptoms. Thirty L. sibiricus and 33 tomato samples were collected (2007 to 2012) in nine districts in Paraná State, Brazil. Two L. sibiricus isolates were also obtained within citrus orchards in Major Otaño, Itapúa, Paraguay. Total DNA was extracted from all 65 isolates and PCR assays were conducted with primers for conserved DNA-A (PAL1v1978/PAR1c496) and DNA-B (PBL1v2040/PCRc1) regions (3). Nucleotide sequence identity of the 1,193-bp DNA-A amplicons of our L. sibiricus isolates ranged from 93.4 to 98.2% with LeMV (GenBank Accession No. U925321) and from 92.4 to 94.8% with ToYSV isolates from tomato (DQ336350.1) and bean (FJ538207). None of the 33 tomato samples was found to be infected by ToYSV, with all having high nucleotide sequence identity (92 to 99%) only with Tomato severe rugose virus (GU358449). Complete DNA-A genome sequence was obtained via a rolling circle amplification-based strategy for one Brazilian L. sibiricus isolate (PR-088) and one isolate from Paraguay (PAR-07). The entire DNA-A genome of PR-088 (JQ429791) had 96.8% nucleotide sequence identity with PAR-07 (KC683374) and ranged from 95.6 to 96.3% with ToYSV isolates from bean, tomato, and L. sibiricus (JX513952). The nucleotide sequence identity of the 487-bp DNA-B amplicon ranged from 87 to 92% among PR-088 (KC 683374); PAR-07 (KC740619) and ToYSV isolates from tomato (DQ336351.1) and L. sibiricus (JX513953.1). Leonurus cuttings infected with the ToYSV (PR-088) were caged together with healthy L. sibiricus and tomato ‘Alambra’ seedlings. Hybridization assays with ToYSV-specific probes (2) and sequencing of PCR amplicons indicated that Bemisia tabaci biotype B adults were able to transmit ToYSV to both hosts as reported (1). Our results suggest that L. sibiricus is the main ToYSV reservoir under natural conditions and tomato seems to be an occasional alternative host. In fact, ToYSV has not often detected in tomatoes as observed in a number of extensive surveys (4). So far, the complete LeMV genome is not available for comparison (3). However, our analyses with a DNA-A segment indicated that LeMV and ToYSV isolates might represent strains of single virus at the current threshold of 89% nucleotide sequence identity for Begomovirus species discrimination (4). Thus, a reappraisal of the taxonomic status of ToYSV is necessary to clarify its genetic relationship with LeMV. This is the first report of ToYSV on L. sibiricus in Paraguay. References: (1) J. C. Barbosa et al. Plant Dis. 97:289, 2013. (2) R. F. Calegario et al. Pesq. Agrop. Bras. 42:1335, 2007. (3) J. C. Faria and D. P. Maxwell, Phytopathology 89:262, 1999. (4) F. R. Fernandes et al. Virus Genes 36:251, 2008.


Plant Disease ◽  
2012 ◽  
Vol 96 (7) ◽  
pp. 1074-1074 ◽  
Author(s):  
I. S. Cho ◽  
B. N. Chung ◽  
J. D. Cho ◽  
G. S. Choi ◽  
H. S. Lim

Blueberry red ringspot virus (BRRSV) of the Soymovirus genus in the family Caulimovididae causes red ringspot diseases in highbush blueberry (Vaccinium corymbosum L.) on leaves, stems, and fruits. The virus has been identified in the United States, Japan, Czech Republic, Slovenia, and Poland (1). In July 2010, highbush blueberry with red ringspots on leaves and circular blotches on ripening fruits was found in one plant of cv. Duke in Pyeongtaek, Korea. The symptoms were similar to red ringspot disease caused by BRRSV (3), although stems did not show any characteristic symptoms. Red ringspots on the upper surface of leaves were the most visible symptom and became more prominent as leaves matured in August through October. Leaves of the symptomatic plant were collected and tested for BRRSV infection by PCR, and were also embedded for electron microscopy. DNA was extracted from leaves using DNeasy Plant Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. Primer pairs BR1512F/BR2377R (5′-ACAGGACGATTAGAAGATGG-3′/5′-CCTTTAGGGCAATATTTCTG-3′, amplifying a fragment of the coat protein region with an expected size of 865 bp) and BR2961F/BR3726R (5′-ACCGATACATCACAGTTCAC-3′/5′-TGGTTGTGATAAGATGATTCC-3′, amplifying a fragment of the reverse transcriptase region with an expected size of 766 bp) were used to amplify the indicated region of BRRV in PCR. Primers were designed on the basis of the BRRSV isolate from New Jersey (GenBank Accession No. AF404509). DNA fragments of the expected sizes were obtained from the symptomatic plant, while no amplification products were obtained from highbush blueberry without symptoms. The PCR products were cloned into pGEM-T easy vector (Promega, Madison, WI) and sequenced. BLAST analyses of obtained fragments revealed 91 to 98% nucleotide sequence identity with the coat protein gene (GenBank Accession No. JQ706341) and 96 to 98% nucleotide sequence identity with the reverse transcriptase gene (GenBank Accession No. JQ706340) of known BRRV isolates. Electron microscopy of thin sections revealed particles approximately 50 nm diameter within electron-dense inclusion bodies, characteristic of BRRSV (2) To our knowledge, this is the first report of BRRSV infection of highbush blueberry in Korea. Highbush blueberries are usually propagated by cutting, so BRRSV suspicious plants should be tested with PCR before they are propagated. References: (1) E. Kalinowska et al. Virus Genes. DOI 10.1007/s11262-011-0679-4, 2011. (2) K. S. Kim et al. Phytopathology 71:673, 1981. (3) M. Isogai et al. J. Gen. Plant Pathol. 75:140, 2009.


Plant Disease ◽  
2015 ◽  
Vol 99 (2) ◽  
pp. 290-290
Author(s):  
C. S. Xue ◽  
Y. Y. Lu ◽  
S. Q. Xiao ◽  
Y. X. Duan

During July 2012, leaf spots affecting 60% of the leaves were observed on soybean cultivar He Feng 60 in fields near Shenyang City, Liaoning Province, leading to 5 to 10% yield loss. The leaf spots were associated with the leaf margins and were irregularly shaped, with brown to black margins and surrounded by a thin, yellow halo. Often, several spots merged to form large necrotic areas, which contained numerous pycnidia on the underside of the leaf. Small pieces (5 mm2) were excised from the margin of diseased and healthy tissue, surface-sterilized in 70% ethanol solution for 30 s and 0.1% mercuric chloride solution for 1 min, washed in three changes of sterile distilled water, and transferred to plates containing potato dextrose agar (PDA). Cultures were maintained in an incubator at 25°C with a 12 h dark/light photoperiod for 5 to 7 days. On PDA, colonies were white with yellow areas, floccose, dense, and moderately fast growing, attaining a diameter of 3.9 mm after 5 days and 9.0 mm after 14 days. Finally, large black stromata appeared after 28 days at 25°C. The conidiomata pycnidia were black, stomatic, globose, length 83.6 to 232 μm, width 37.9 to 146.3 μm and produced α-conidia that were unicellular, hyaline, sometimes two-guttulate, length 4.75 to 8.25 μm, width 1.50 to 3.00 μm. β-Conidia were not observed. To confirm the morphological identification, the ribosomal internal transcribed spacers (ITS1-5.8S-ITS2) from isolates were sequenced (GenBank Accession No. KC460334). The PCR products were cloned into a pMD-19T Cloning Vector (Sangon Biotech, Shanghai, China). The clones were purified with TIANprep Mini Plasmid Kit (Tiangen Biotech, Beijing, China) to get the full-length ITS sequence. BLAST analysis of the isolates showed 100% nucleotide sequence identity with Phomopsis longicolla (AY745021). Four additional primer pairs—large subunit (NL1/NL4), beta-tublin gene (Bt2a/Bt2b), translation elongation factor 1α gene(EF1-728F/EF1-986R), and act gene(ACT-512F/ACT-783R) (1,2)—were amplified and sequenced as described above. The large subunit gene, β-tubulin gene, and translation elongation factor 1α gene from isolates were sequenced (Sangon Biotech). BLAST analysis indicated that the isolates had 100% nucleotide sequence identity with P. longicolla (AB107259, HQ333514, and AF398896). Because the act gene sequence of P. longicolla was not in the NCBI database, this sequence had 94% nucleotide sequence identity with P. cuppatea (JN230389). To fulfill Koch's postulates, five leaves on five healthy soybean plants were inoculated with a conidial suspension (106/ml). Plants inoculated with sterile water served as the noninoculated controls. Plants were incubated in the greenhouse at 25°C. All the inoculated leaves developed pinhead spots on the leaves, gradually increasing to large brown spots. Spots were irregularly shaped, brown and necrotic in the center, and surrounded by a yellow halo. Black pycnidia appeared after 10 days, whereas the noninoculated control plants remained asymptomatic. P. longicolla was consistently recovered from all inoculated plants, except the control. Morphological description of isolates was similar to that of Hobbs (3). However, as described by Hobbs and others, P. longicolla conidiomata pycnidia have prominent necks more than 200 μm long, opening by apical ostioles; locules are uniostiolate or multiostiolate, globose, up to 500 μm wide. The pycnidia size of isolates by frozen section method was smaller than that of Hobbs. Based on morphological and sequence comparisons, the pathogen of leaf spot disease is caused by P. longicolla. This is the first reported leaf spot caused by P. longicolla on soybean in China. References: (1) T. Boekhou et al. Stud. Mycol. 38:75, 1995. (2) P. W. Crous et al. Stud. Mycol. 75:37, 2013. (3) T. W. Hobbs et al. Mycologia 77:535, 1985.


Author(s):  
Jane E. Sykes ◽  
Louise M. Ball ◽  
Nathan L. Bailiff ◽  
Michael M. Fry

A novel small haemoplasma was detected following cytological examination of blood smears from a splenectomized dog with haemic neoplasia. The 16S rRNA and rnpB genes of the organism were partially sequenced and a phylogenetic tree constructed. The organism was most closely related to the small feline haemoplasma, ‘Candidatus Mycoplasma haemominutum’ (94 % 16S rRNA gene nucleotide sequence identity; 75 % rnpB) and was only distantly related to Mycoplasma haemocanis (78 % 16S rRNA gene nucleotide sequence identity; 65 % rnpB). As this organism has not been cultured in vitro, the candidate species name ‘Candidatus Mycoplasma haematoparvum’ is proposed.


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