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Author(s):  
Qunfang Yu ◽  
Yanxiang Qi ◽  
Jinji Pu

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-2T, was isolated from coastal sediment sampled in Jiangsu Province and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 28 °C (range 4–38 °C) and pH 7 (pH 6–10). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YQF-2T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera pacifica KMM 1406T (98.6%), followed by Rheinheimera aestuarii H29T (98.4%), Rheinheimera japonica KMM 9513T (98.3%), Rheinheimera aquimaris SW-353T (98.3%), Rheinheimera hassiensis E48T (97.8%) and Rheinheimera muenzenbergensis E49T (97.7%). The 16S rRNA gene sequence identities between strain YQF-2T and other members of the genus Rheinheimera were below 97.2%. The digital DNA–DNA hybridization value between strain YQF-2T and R. pacifica KMM 1406T was 23.3±2.3%. The average nucleotide identity value between strain YQF-2T and R. pacifica KMM 1406T was 79.7%. The unique respiratory quinone was ubiquinone-8. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The strain had summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C12:0 3-OH and iso-C17:0 3-OH as major fatty acids. The G+C content of the genomic DNA was 50.0 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-2T represents a novel species of the genus Rheinheimera , for which the name Rheinheimera lutimaris sp. nov. is proposed, with the type strain YQF-2T (=KCTC 72184T=MCCC 1K03663T).


Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2194
Author(s):  
Kerry Gainor ◽  
Anne A. M. J. Becker ◽  
Yashpal S. Malik ◽  
Souvik Ghosh

Using a broad-range nested PCR assay targeting the DNA-dependent DNA polymerase (pol) gene, we detected adenoviruses in 17 (20.48%) out of 83 fecal samples from small Indian mongooses (Urva auropunctata) on the Caribbean island of St. Kitts. All 17 PCR amplicons were sequenced for the partial pol gene (~300 bp, hereafter referred to as Mon sequences). Fourteen of the 17 Mon sequences shared maximum homology (98.3–99.6% and 97–98.9% nucleotide (nt) and deduced amino acid (aa) sequence identities, respectively) with that of bovine adenovirus-6 (species Bovine atadenovirus E). Mongoose-associated adenovirus Mon-39 was most closely related (absolute nt and deduced aa identities) to an atadenovirus from a tropical screech owl. Mon-66 shared maximum nt and deduced aa identities of 69% and 71.4% with those of atadenoviruses from a spur-thighed tortoise and a brown anole lizard, respectively. Phylogenetically, Mon-39 and Mon-66 clustered within clades that were predominated by atadenoviruses from reptiles, indicating a reptilian origin of these viruses. Only a single mongoose-associated adenovirus, Mon-34, was related to the genus Mastadenovirus. However, phylogenetically, Mon-34 formed an isolated branch, distinct from other mastadenoviruses. Since the fecal samples were collected from apparently healthy mongooses, we could not determine whether the mongoose-associated adenoviruses infected the host. On the other hand, the phylogenetic clustering patterns of the mongoose-associated atadenoviruses pointed more towards a dietary origin of these viruses. Although the present study was based on partial pol sequences (~90 aa), sequence identities and phylogenetic analysis suggested that Mon-34, Mon-39, and Mon-66 might represent novel adenoviruses. To our knowledge, this is the first report on the detection and molecular characterization of adenoviruses from the mongoose.


Plant Disease ◽  
2021 ◽  
Author(s):  
Yameng Luan ◽  
Lili Zhang ◽  
Ting Sun ◽  
Xue Jiang ◽  
Xiaoyun Wu ◽  
...  

Mountain celery (Heracleum moellendorffii Hance), an edible perennial herb of Northeast Asia, is sporadically cultivated as a vegetable crop or for medicinal purposes in Northeast China and Korea [1]. In July 2019, a small field of mountain celeries showing chlorotic spots was found in Wangkui, Heilongjiang, China. A small-RNA (sRNA) library was constructed with equal amounts of leaf tissues of a diseased mountain celery and a tomato sample showing mottling symptom from a nearby field using the TruSeq small RNA library preparation kit (Illumina). The library was sequenced by the HiSeq 4000 sequencer at Lianchuan Biotechnology Co., Ltd (Hangzhou, China). After trimming adaptor sequences and discarding low quality reads by Cutadapt [2], the remaining 6,949,946 reads of 17 to 27 nucleotides (nt) were de novo assembled as described [3]. The resulting 395 contigs were searched against the GenBank viral sequence database using the BLASTn and BLASTx algorithms. Twenty-three contigs showed high nt sequence similarities (89-100%) to the genomic sequence of tomato mosaic virus (ToMV). The deduced amino acid (aa) sequences of thirty contigs had 22-96% aa sequence identities to viruses in the family Secoviridae, e.g., surrounding non-legume associated secovirus (snLaSV) and lettuce secovirus 1 (LSV-1). No contig homologous to the genomic sequences of other plant viruses was identified. Total RNAs were extracted from the mountain celery and tomato separately and reverse transcribed into cDNAs by random hexamer plus Oligo-dT(18) using the Super® IV Reverse Transcriptase (Invitrogen, Shanghai, China). Polymerase chain reactions (PCR) showed that the secovirus was derived from the mountain celery, whereas the tomato was infected by ToMV. The genome of this secovirus was determined by reverse transcription (RT)-PCR and rapid amplification of cDNA ends (RACE). Amplicons were cloned and Sanger sequenced with at least three independent clones per amplicon. Sequences were assembled by the SeqMan Pro 7.1.0 in the Lasergene (DNASTAR, Madison, WI). The genome of this virus is composed of two RNAs of 6,616 and 5,356 nt (excluding the polyadenylic acid tails) (GenBank accession nos. MW143070 and MW143071, respectively). The thirty contigs assembled from sRNAs could be mapped to the genome. Pairwise sequence analyses showed that RNA1 and RNA2 and their encoded polyproteins shared the highest nt (82.7% and 82.2%) and aa (93.4% and 91.8%) sequence identities with the respective RNAs (GenBank accession nos. MN412739 and MN412740) and their encoded polyproteins of snLaSV [4]. In the phylogenetic trees, this virus sequence clustered with snLaSV and LSV-1 in a separate branch neighboring viruses of the subgenus Stramovirus or Satsumavirus in the genus Sadwavirus. These results suggest that this virus is an isolate of the unclassified snLaSV and was referred as snLaSV-CHN. RT-PCR with primers SecoR1-3700F and SecoR1-5100R confirmed the presence of snLaSV-CHN in other mountain celeries (11 of 23 tested) showing chlorotic spots symptoms but not in healthy ones from the same field. To the best of our knowledge, this is the first report of snLaSV infecting mountain celery in China and a more orthodox name, mountain celery chlorotic spot virus (MCCSV), is tentatively proposed. Our findings provide a better insight of the distribution and host range of this virus and further surveys are necessary to determine its incidence and damage in mountain celery. Funding: This study is financial supported by the Program for the Scientific Activities of Selected Returned Overseas Professionals in Heilongjiang Province (Grant No. 2018QD0002) and the China National Funds for Excellent Young Scientists (Grant No. 32022071). References Son, H. J. 2020. Food Sci Nutr. 9:514. Martin, M. 2011. EMBnet J. 17:10. Che, X., et al. 2020. Plant Dis. 104: 3085. Gaafar, Y. Z. A., et al. 2020. Front Microbiol. 11: 583242.


2021 ◽  
Vol 12 ◽  
Author(s):  
Tianze Zhang ◽  
Chenyang Li ◽  
Mengji Cao ◽  
Dan Wang ◽  
Qi Wang ◽  
...  

Picornaviruses cause diseases in a wide range of vertebrates, invertebrates and plants. Here, a novel picornavirus was identified by RNA-seq technology from rice plants showing dwarfing and curling symptoms, and the name rice curl dwarf-associated virus (RCDaV) is tentatively proposed. The RCDaV genome consists of an 8,987 nt positive-stranded RNA molecule, excluding a poly(A) tail, that encodes two large polyproteins. Using in vitro cleavage assays, we have identified that the RCDaV 3C protease (3Cpro) as a serine protease recognizes the conserved EPT/S cleavage site which differs from the classic Q(E)/G(S) sites cleaved by most picornaviral 3C chymotrypsin-like cysteine proteases. Therefore, we comprehensively deciphered the RCDaV genome organization and showed that the two polyproteins of RCDaV can be cleaved into 12 mature proteins. We found that seven unclassified picornaviruses also encode a 3Cpro similar to RCDaV, and use the highly conserved EPT/S as the cleavage site. The precise genome organizations of these viruses were illustrated. Moreover, RCDaV and the seven unclassified picornaviruses share high sequence identities and similar genome organizations, and cluster into a distinct clade in the order Picornavirales. Our study provides valuable information for the understanding of picornaviral 3Cpros, deciphers the genome organization of a few relatively obscure picornaviruses, and lays the foundation for further pathogenesis research on these viruses.


Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1969
Author(s):  
Marta Canuti ◽  
Émilie Bouchard ◽  
Bruce Rodrigues ◽  
Hugh G. Whitney ◽  
Marti Hopson ◽  
...  

The genus Protoparvovirus (family Parvoviridae) includes several viruses of carnivores. We describe a novel fox protoparvovirus, which we named Newlavirus as it was discovered in samples from Newfoundland and Labrador, Canada. Analysis of the full non-structural protein (NS1) sequence indicates that this virus is a previously uncharacterized species. Newlavirus showed high prevalence in foxes from both the mainland (Labrador, 54/137, 39.4%) and the island of Newfoundland (22/50, 44%) but was not detected in samples from other carnivores, including coyotes (n = 92), lynx (n = 58), martens (n = 146), mink (n = 47), ermines (n = 17), dogs (n = 48), and ringed (n = 4), harp (n = 6), bearded (n = 6), and harbor (n = 2) seals. Newlavirus was found at similar rates in stool and spleen (24/80, 30% vs. 59/152, 38.8%, p = 0.2) but at lower rates in lymph nodes (2/37, 5.4%, p < 0.01). Sequencing a fragment of approximately 750 nt of the capsid protein gene from 53 samples showed a high frequency of co-infection by more than one strain (33.9%), high genetic diversity with 13 genotypes with low sequence identities (70.5–87.8%), and no geographic segregation of strains. Given the high prevalence, high diversity, and the lack of identification in other species, foxes are likely the natural reservoir of Newlavirus, and further studies should investigate its distribution.


2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Nina Wang ◽  
Lichao Yang ◽  
Guohui Li ◽  
Xu Zhang ◽  
Jianwei Shao ◽  
...  

Abstract Background Wenzhou virus (WENV), a newly discovered mammarenavirus in rodents, is associated with fever and respiratory symptoms in humans. This study was aimed to detect and characterize the emerging virus in rodents in Guangzhou, China. Results A total of 100 small mammals, including 70 Rattus norvegicus, 22 Suncus murinus, 4 Bandicota indica, 3 Rattus flavipectus, and 1 Rattus losea, were captured in Guangzhou, and their brain tissues were collected and pooled for metagenomic analysis, which generated several contigs targeting the genome of WENV. Two R. norvegicus (2.9%) were further confirmed to be infected with WENV by RT-PCR. The complete genome (RnGZ37-2018 and RnGZ40-2018) shared 85.1–88.9% nt and 83.2–96.3% aa sequence identities to the Cambodian strains that have been shown to be associated with human disease. Phylogenetic analysis showed that all identified WENV could be grouped into four different lineages, and the two Guangzhou strains formed an independent clade. We also analyzed the potential recombinant events occurring in WENV strains. Conclusions Our study showed a high genetic diversity of WENV strains in China, emphasizing the relevance of surveillance of this emerging mammarenavirus in both natural reservoirs and humans.


Plant Disease ◽  
2021 ◽  
Author(s):  
Mingfu Zhao ◽  
LU CHEN ◽  
Jianwei Guo ◽  
Rex Frimpong Anane ◽  
Zhe Wang ◽  
...  

Capsicum chlorosis virus (CaCV) is a negative sense ssRNA virus belonging to the genus Orthotospovirus in the family Tospoviridae. It was first discovered in Australia, and then reported in other places including Thailand, China, India, Greece, and United States (Zheng et al.2011; Melzer et al.2014; Chrysoula et al. 2018; Abudurexiti et al. 2019). CaCV infects plants of the families Amaranthaceae, Apocynaceae, Chenopodiaceae, Cucurbitaceae, Amaryllidaceae, Fabaceae and Solanaceae (Basavaraj et al. 2017; Basavaraj et al. 2020). Chromolaena odorata L. (commonly known as Feiji cao in China) is an invasive weedy herb that belongs to the genus Eupatorium (family Asteraceae), and is native to Central America. In May 2020, serrated chlorotic ring and chlorotic ringspots resembling symptoms of orthotospovirus infection (Supplementary Figure 1) was observed on the leaves of C. odorata plants in Honghe County, Yunnan. Three symptomatic leaf samples were collected and double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) was performed using antisera targeting Tomato spotted wilt virus (TSWV), Calla lily chlorotic spot virus (CCSV), Capsicum chlorosis virus (CaCV), and Tomato zonate spot virus (TZSV) (Proteintech Group, Inc., China). Buffer solution and healthy leaves were used as a blank and negative controls, respectively. All three symptomatic samples showed positive reactions with only CaCV antiserum (OD450 of 0.315-0.345 relative to 0.078 and 0.076 for healthy plants and the blank control, respectively. The total RNA extracted from the positive samples were further analyzed by reverse transcription-polymerase chain reaction (RT-PCR) using generic primers gL3637 (CCTTTAACAGTDGAAACAT) and gL4435c (CATDGCRCAAGARTGRTARACAGA) which were designed to amplify partial L segment encoding the RNA-dependent RNA polymerase (RdRP) of orthotospoviruses (Chu, et al. 2001). The expected ~800 bp DNA fragment was amplified from all three positive samples by RT-PCR. The amplified DNA was cloned and sequenced. BLAST search of the partial L RNA sequence (GenBank acc. nos. MW964378 to MW964380) revealed that they shared 86.2-97.4% nucleotide (nt) and 97.2-100% amino acid (aa) sequence identities with different isolates of CaCV available in GenBank with CaCV chili isolates (KU941834 to KU941836) from India sharing the highest aa identity of 100%. This confirmed the presence of CaCV in the symptomatic C. odorata plants. The 825 bp complete nucleocapsid protein (NP) of CaCV was also amplified from the samples using primers CaCV-F: ATGTCTAMCGTYAGGCAAC and CaCV-R: TYACACYTCWATAGAWGTACTAG) (Basavaraj et al. 2020), cloned, and sequenced to obtain complete S fragment-nucleocapsid protein (NP) with a size of 825 bp (MW964381 to MW964383). The pairwise comparisons of three fragments showed 85.1-98.3% nt and 87.6-99.6% aa sequence identities with different isolates of CaCV. Maximum-Likelihood phylogenetic trees inferred from the partial RdRP and complete NP aa sequences showed that the C. odorata isolates (CaCV-YN) clustered closely with CaCV tomato isolate from Taiwan and tomato (Yuxi-2013) isolate from China, respectively (Supplementary Figure 1). To our knowledge, this is the first time CaCV has been detected in C. odorata. This study will serve as an important reference for the study of host range of CaCV. Further studies will be required to determine whether thrips could transmit CaCV between C. odorata and other hosts of the virus.


2021 ◽  
Vol 44 (02) ◽  
Author(s):  
THI-HUYEN TRAN ◽  
NGOC-TUAN NGUYEN ◽  
LIN-WOO KANG

Xanthomonas oryzae pv. oryzae (Xoo) is causal agent of bacterial blight (BB) in rice. Many genes in Xoo have been identified in recently years. One of these genes, a gene coded for uridine diphosphate (UDP)-MurNAc-tripeptide ligase (MurE), catalyses the addition of meso-diaminopimelic acid (m-DAP) into peptidoglycan by coupled to the hydrolysis of ATP has more popular interest. However, there are no experimental data to confirm hypothesis of this enzyme in Xoo. A significant overview at the ATP binding site of most the MurE ligases demonstrated much more variable with amino acid sequence identities in this part, variable percentage around 22 to 26%. Besides, a refined homology structural feature between EcMurE and XooMurE will very important for determining possible involvement of the MurE ligase activity in Xoo. Therefore, a new recombinant protein named XooMurE from Xoo was purified with the N-terminal His-tagged form through a Ni-NTA column in this study. After purification, the Histag was removed then out of the N-terminal His-tagged XooMurE by TEV protease. Purification effectiveness of XooMurE over 95% in this study could produce an essential material for e studies about mechanism of XooMurE and consequently available direction for discovering novel anti-bacterial compounds against Xanthomonas oryzae pv. oryzae (xoo).  


2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Taotao Yang ◽  
Lingqian Zhang ◽  
Yingmei Lu ◽  
Minhong Guo ◽  
Zhibang Zhang ◽  
...  

Abstract Background Porcine sapelovirus (PSV) infection can lead severe polioencephalomyelitis with high morbidity and mortality, which result in significant economic losses. Infection with the PSV is believed to be common yet limited information is available on the prevalence and molecular characterization of PSV in China. Therefore, the objective of this study was to characterize the prevalence and genome of PSV strains identified in the western Jiangxi province of China. Results A high specificity and sensitivity SYBR Green I-based RT-PCR method for PSV detection was developed. Two hundred and ninety four fecal samples were collected from December 2018 to March 2019 in 4 farms. An overall PSV-positivity rate of 11.22% (33/294) was detected with the real-time RT-PCR method, and a high infection rate and viral load of PSV were found in nursery pigs. In total, complete VP1 gene sequences of 11 PSV strains (PSV-YCs) were obtained. Homology comparisons of the VP1 gene of the 11 PSV-YCs with previously reported PSVs revealed nucleotide sequence identities ranging from 63% to 96.8%, and deduced amino acid sequence identities from 61.4% to 99.7%. Phylogenetic analyses based on the VP1 gene exhibited 2 main clades corresponding to PSV-1 and PSV-2, and all PSV-YCs prevalent in western Jiangxi belonged to the traditional genotype (PSV-1). In addition, the pairwise distances of VP1 gene sequences between PSV-YCs ranged from 0.009 to 0.198, which indicating that substantial genetic diversity among the PSVs in western Jiangxi. Conclusions To the authors’ knowledge, this is the first description of PSV in the Jiangxi province pig herds in China, and it is crucial to understand the epidemiology of the viruses in China. The results also provide an important theoretical foundation for diagnosis and early warning of epidemic diseases caused by PSVs prevailing in this region.


Plant Disease ◽  
2021 ◽  
Author(s):  
Naomi Mumo ◽  
Elijah Miinda Ateka ◽  
Edward Mamati ◽  
Fredah Karambu Rimberia ◽  
George Ochieng' Asudi ◽  
...  

The potyvirus Moroccan watermelon mosaic virus (MWMV) naturally infects and severely threatens production of cucurbits and papaya. In this study, we identified and characterized MWMV isolated from pumpkin (Cucurbita moschata) intercropped with MWMV-infected papaya plants through next generation and Sanger sequencing approaches. Complete MWMV genome sequences were obtained from two pumpkin samples through NGS and validated using Sanger sequencing. The isolates share 83.4-83.7 % nucleotide (nt) and 92.3-95.1 % amino acid (aa) sequence identities in the coat protein and 79.5-79.9 % nt and 89.2-89.7 % aa identities in the polyprotein with papaya isolates of MWMV. Phylogenetic analysis using complete polyprotein nt sequences revealed the clustering of both pumpkin isolates of MWMV with corresponding sequences of cucurbit isolates of the virus from other parts of Africa and the Mediterranean regions, distinct from a clade formed by papaya isolates. Through sap inoculation, a pumpkin isolate of MWMV was pathogenic on zucchini (Cucurbita pepo), watermelon (Citrullus lanatus), and cucumber (Cucumis sativus), but not on papaya. Conversely, the papaya isolate of MWMV was non-pathogenic on pumpkin, watermelon, and cucumber, but infected zucchini. The results suggest occurrence of two strains of MWMV in Kenya having different biological characteristics associated with the host specificity.


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