Complete Genome Sequence of Bacteriophage Fizzles, Isolated from Microbacterium foliorum

Microbacteriophage Fizzles has a 62,078-bp linear double-stranded DNA genome sequence, predicted to contain 104 protein-coding genes. Fizzles is a Siphoviridae actinobacteriophage isolated from an ant hill soil sample collected in Stephenville, TX. Microbacteriophage Fizzles has >83.6% nucleotide identity with microbacteriophages Squash and Nike.

First Report on Co-isolation and Whole-genomic Characterization of Mammalian Orthorubulavirus 5 and Mammalian Orthoreovirus Type-3 From Domestic Pigs in India

During a surveillance study to monitor porcine epidemic diarrohoea virus and transmissible gastroenteritis virus in India, a total of 1043 swine samples including faeces (n=264) and clotted blood (n=779) were collected and tested. Five samples (four faecal and one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infective cell supernatant revealed the presence of two types of virions. Next generation sequencing (de novo) enabled complete genome assembly of Mammalian orthorubulavirus 5 (MRuV5; 15246 bp) and all 10 gene segments of Mammalian orthoreovirus (MRV; 22219 bp and 20512 bp). Genetic analysis of the MRuV5 revealed grouping of the Indian MRuV5 with those isolated from various mammalian species in South Korea and China, sharing more than 99% nucleotide identity. Deduced amino acid sequences of the HN, NP and F genes of MRuV5 isolates showed three (92L, 111R, 447H), two (86S, 121S) and two (139T, 246T) amino acid substitutions, respectively, compared to previously reported virus strains. The Indian MRV isolates were identified as MRV type-3 based on genetic analysis of S1 gene, showing the highest nucleotide identity (97.73%) with the MRV3 strain ZJ2013 isolated from pigs in China. Deduced amino acid sequences of MRV3 S1 gene revealed amino acid residues 198-204NLAIRLP, 249I, 340D, 419E known for sialic acid binding and neurotropism. We report the co-isolation and whole-genomic characterization of MRuV5 and MRV3 recorded incidentally for the first time from domestic pigs in India. It attracts attention to perform detailed surveillance studies and continuous monitoring of evolution and spread of emerging viruses, which may have pathogenic potential in animal and human hosts.

Smilax auriculata: A new host for Orchid fleck dichorhavirusvirus identified in Florida, USA

In June 2020, Orchid fleck virus (OFV) was detected in a species of Liriope in Leon and Alachua County, Florida (Fife et al; 2021). In October of the same year, four adjacent dune/ear-leaf greenbrier vines, Smilax auriculata (Smilaceae: Liliales), showed yellowing and mottling symptoms (Figure 1). Infected and healthy S. auriculata leaves samples were collected in Alachua County by the Florida Department of Agriculture and Consumer Services, Gainesville, Florida. OFV primers successfully detected in four Smilax samples by conventional RT-PCR assay. Amplicon sequences (Acc. No. MZ645935 and MZ645938) shared 99% nucleotide identity with OFV infecting orchids (LC222629) and citrus (MK522804). The OFV subgroup I (OFV-Orc1) and subgroup II (OFV-Orc2) specific primers (Kondo et al 2017) were utilized to confirm the presence of OFV type strains infecting Smilax. Sanger sequencing of subgroup I specific amplicons (MZ645934) shared 99% nucleotide identity with OFV-Orc1 (LC222629) whereas subgroup II specific amplicon sequence (MZ645930) shared 98-99 % nucleotide identity with OFV-Orc2 (AB244417). Further confirmation was done by USDA-APHIS-PPQ-Plant Pathogen Confirmatory Diagnostics Laboratory utilizing optimized conventional RT-PCR protocols (Roy et al. 2020) and deep sequencing on a on a NextSeq550 Illumina platform. Assembled reads identified seven non-overlapping viral contigs. Five RNA1 and two RNA2 contigs covered more than 97% of the bipartite OFV genome with average coverage depth of 5297.61 and 5186.04, respectively. Contigs of RNA1 and RNA2 shared 98-99% nt identity to OFV-Orc2-RNA1 (AB244417) and OFV-Orc-RNA2 (AB244418 and LC222630). No other pathogen sequences were identified. This is the first time the genus Smilax has been identified as a natural host of OFV. Very recent findings of OFV-Orc in Florida in Liriope, Aspidistra, and Ophiopogon among the Asparagaceae family members (Fife et al; 2021) and now in the Smilacaceae suggest a broader host range of the virus than previously known; further research should be conducted to better characterize the potential risk of introduction into citrus in Florida.

First report of cucurbit chlorotic yellows virus infecting watermelon and zucchini in the Canary Islands, Spain

In July 2019, eleven watermelon (Citrullus lanatus) plants, six ‘Augusta negra’ and five ‘Kasmira’, and seven zucchini (Cucurbita pepo) ‘Marcado’ plants showing yellowing and vein clearing on the leaves were collected in Arico, in Tenerife Island of the Canary Islands. Analysis with enzyme-linked immunosorbent assay (ELISA) with polyclonal antibodies using kits from (LOEWE® Biochemica GmbH, Sauerlach, Germany) detected cucurbit chlorotic yellows virus (CCYV) in four watermelon (two ‘Augusta negra’ and two ‘Kasmira’) plants and one zucchini plant. Reverse transcription-polymerase chain reaction (RT-PCR) with primers CCYV-CPs (5'-ATGGAGAAGACTGACAATAAACAA-3’) and CCYV-CPas (5'-TTTACTACAACCTCCCGGTG-3’) (Hamed et al. 2011) yielded 750 bp DNA fragments, which were purified, and directly sequenced by Sanger sequencing. The four CCYV sequences obtained from watermelon plants were identical and showed a 99.6% nucleotide identity with the CCYV isolate from Zucchini. The nucleotide sequences of CCYV isolates 351/19 from watermelon and 361/19 from zucchini were deposited in GenBank under accessions OK562588 and OK562589, respectively. BLASTn analysis showed high nucleotide identity, greater than 99 % with most worldwide CCYV isolates (AB523789, HM581658, JF502222, JF807053, JN126045-6, JQ904629, JX014262, KC990503-5, KC990507, KJ735450, KJ149806, KT946809, KT946816, KU507602, KX118632, KY400632-4, KY618799, LT716000, LT716003-4, MH477612, MH806868, MH819191, MN529560, MN815012-3, MT396249 MT048669, MW033301, MW584337, MW251342, MW521380, MW521381, MW584335-6, MW629380, MZ325848-9 and MZ405664), about 98% with two Saudi Arabian isolates (KT946810 and KT946815) and about 95 % with three Iranian isolates (KC577201-3). These genetic relationships were confirmed with a phylogenetic tree (Supplementary Fig. 1) inferred with the maximum likelihood method with 500 bootstrap replicates and the nucleotide substitution model HKY+G implemented in the program MEGA-X (Kumar et al., 2018). There is no correlation between geographic distance and genetic distance. CCYV is related to viruses in the genus Crinivirus, family Closteroviridae (Okuda et al., 2010). It is widespread and causes high economic losses (yield reduction and unmarketable fruits) in cucurbit crops from East Asia: Japan, China, Taiwan and South Korea; North America (the USA states of California, Texas, Georgia and Alabama); Middle East: Sudan, Saudi Arabia and Iran; and the Mediterranean basin: Egypt, Israel, Lebanon, Turkey, Greece, Algeria and peninsular Spain (Kheireddine et al., 2020; Chynoweth et al., 2021; Jailani, et al., 2021; Kwak et al., 2021). This is the first report of CCYV infecting cucurbits in the Canary Islands. The emergence of this virus poses a threat to the cucurbit crops in the Canary Islands and requires control measures to prevent its spread in Tenerife and the other Canary Islands.

Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.

Whole-genome based strain identification of fowlpox virus directly from cutaneous tissue and propagated virus

Fowlpox (FP) is an economically important viral disease of commercial poultry. The fowlpox virus (FPV) is primarily characterised by immunoblotting, restriction enzyme analysis in combination with PCR, and/or nucleotide sequencing of amplicons. Whole-genome sequencing (WGS) of FPV directly from clinical specimens prevents the risk of potential genome modifications associated with in vitro culturing of the virus. Only one study has sequenced FPV genomes directly from clinical samples using Nanopore sequencing, however, the study didn’t compare the sequences against Illumina sequencing or laboratory propagated sequences. Here, the suitability of WGS for strain identification of FPV directly from cutaneous tissue was evaluated, using a combination of Illumina and Nanopore sequencing technologies. Sequencing results were compared with the sequence obtained from FPV grown in chorioallantoic membranes (CAMs) of chicken embryos. Complete genome sequence of FPV was obtained directly from affected comb tissue using a map to reference approach. FPV sequence from cutaneous tissue was highly similar to that of the virus grown in CAMs with a nucleotide identity of 99.8%. Detailed polymorphism analysis revealed the presence of a highly comparable number of single nucleotide polymorphisms (SNPs) in the two sequences when compared to the reference genome, providing essentially the same strain identification information. Comparative genome analysis of the map to reference consensus sequences from the two genomes revealed that this field isolate had the highest nucleotide identity of 99.5% with an FPV strain from the USA (Fowlpox virus isolate, FWPV-MN00.2, MH709124) and 98.8% identity with the Australian FPV vaccine strain (FWPV-S, MW142017). Sequencing results showed that WGS directly from cutaneous tissues is not only rapid and cost-effective but also provides essentially the same strain identification information as in-vitro grown virus, thus circumventing in vitro culturing.

Chryseobacterium lecithinasegens sp. nov., a siderophore-producing bacterium isolated from soil at the bottom of a pond

Bacterial strain PAGU 2197T, which was isolated from soil collected from the bottom of a pond in Japan, is characterized in this study. Cells of strain PAGU 2197T were aerobic, Gram-negative, short rod-shaped, non-motile, flexirubin-producing, oxidase-positive, catalase-positive and lecithinase-negative. A phylogenetic study based on 16S rRNA gene sequences and multilocus sequence analysis (gyrB, rpoB and rpoD) indicated that strain PAGU 2197T belongs to the genus Chryseobacterium and is a member of an independent lineage including Chryseobacterium tructae CCUG 60111T (sequence similarity, 95.9 %), Chryseobacterium lactis CCUG 60566T (93.4 %) and Chryseobacterium viscerum CCUG 60103T (91.6 %). The average nucleotide identity values were 80.83–85.04 %. Because average nucleotide identity values of 95–96 % exceed the 70 % DNA–DNA hybridization cutoff value for species discrimination, strain PAGU 2197T represents a novel species in the genus Chryseobacterium . The genome of strain PAGU 2197T was 4 967 738 bp with a G+C content of 35.5 mol%. The sole respiratory quinone of strain PAGU 2197T was MK-6; the major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl); and the major polar lipids were phosphoglycolipids and phosphatidylethanolamine. These results indicate that strain PAGU 2197T should be classified as representing a novel species in the genus Chryseobacterium , for which the name Chryseobacterium lecithinasegens sp. nov. is proposed, with strain PAGU 2197T (=NBRC 114264T=CCUG 75150T) as the type strain.

Vineibacter terrae gen. nov., sp. nov., an ammonium-assimilating and nitrate-reducing bacterium isolated from vineyard soil

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640T, isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640T were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °С and pH 7. Strain CC-CFT640T showed highest 16S rRNA gene sequence similarity to members of the genus Enhydrobacter (90.0 %, n=1) followed by Hypericibacter (89.4–90.0 %, n=2), Reyranella (88.8–89.8 %, n=5) and Nitrospirillum (89.2–89.4 %, n=2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated Reynerella species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % (n=1), 74.0–74.6 % (n=2), 67.5–68.3 % (n=2) when compared within the type strains of the genera Enhydrobacter , Reyranella and Niveispirillum , respectively. The dominant cellular fatty acids (>5 %) included C16 : 0, iso-C17 : 1 ω10c, C19 : 0 cyclo ω8c, C18 : 1 2-OH and C18 : 1 ω7c/C18 : 1 ω6c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA–DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640T is considered to represent a novel genus and species of the family Rhodospirillaceae , for which the name Vineibacter terrae gen. nov., sp. nov. is proposed. The type strain is CC-CFT640T (=BCRC 81219T=JCM 33507T).

First Report of Cirsium arvense (Canada thistle) as a New Host of Orobanche cumana Wallr. in Xinjiang, China

Cirsium arvense (Canada thistle) is a perennial herb native to Eurasia that has been introduced to temperate regions of the world where it is considered one of the serious weeds for arable and pastoral agriculture (Schröder et al. 1993). C. arvense reproduces both clonally and sexually. The weed is highly competitive, causes yield reductions in crops such as wheat, alfalfa, sugarbeet, and can reduce forage availability and production (Wilson 1981). Canada thistle is also a harbour for plant pathogens such as plant-parasitic nematodes (Tenuta et al. 2014). Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant species with a restricted range of hosts both in the wild, where it mainly parasitizes a few species of the Asteraceae, and in agricultural fields, where it is exclusively found growing on sunflower (Fernández-Martínez et al. 2015). O. cumana infection can cause up to 80% of the yield loss in sunflower, which is a serious threat for sunflower production in Xinjiang and Inner Mongolia, China (Parker 2009). In July 2019, broomrape was observed parasitizing C. arvense in the greenhouse used for sunflower resistance identification (Shihezi, 86° 3' 36" E, 44° 18' 36" N, 500 m elevation) in Xinjiang, China. Fifty percent of the plants were parasitized by broomrape in the greenhouse and the host had an average of 1-2 broomrape shoots per plant. For molecular analysis, total genomic DNA was extracted from the flowers of broomrape and the rps2, rbcL, trnL-F genes, and ribosomal DNA internal transcribed spacer (ITS) region were amplified by PCR using the primer pairs rps2F/rps2R, rbcLF/rbcLR, C/F, ITS1/ITS4, respectively (Park et al. 2007; Manen et al. 2004; Taberlet et al. 1991; Anderson et al. 2004). The ITS (659bp), rps2 (451 bp), trnL-F (914 bp), and rbcL (961 bp) gene sequences of the broomrape were deposited in GenBank, the accession numbers are MT856745, MW809407, MW809408, and MW809409. The results of BLAST analysis showed that ITS sequence shared 100% similarity with O. cumana (659/659 nucleotide identity, MK567978), the rps2 sequence shared 99% similarity with O. cumana (449/451 nucleotide identity, KT387722), trnL-F sequence shared 99% similarity with O. cumana (907/911 nucleotide identity, MT027325), rbcL sequence shared 99% similarity with O. cumana (956/964 nucleotide identity, MK577840). The morphological characteristics such as stem, inflorescence, corolla, bracts, calyx, stamens, gynoecium are consistent with O. cumana described by Pujadas-Salvá and Velasco (2000). Morphological and molecular identification strongly support that the broomrape parasitic on C. arvense belonged to the O. cumana. Greenhouse pot experiments were carried out to assess the parasitic relationship between sunflower broomrape and C. arvense (Fernández-Martínez et al. 2000). In January 2020, C. arvense roots were harvested from an extant field of C. arvense in the greenhouse at Shihezi University (Supplementary Figure S1A). The soil was dug to 30-40 cm depth and C. arvense roots were removed and carefully washed in water. The healthy and living C. arvense roots were selected and cut into 10-11 cm pieces. Four C. arvense root pieces were grown (buried at a depth of 10-12 cm) in 8-L pots containing a mixture of sand-vermiculite-compost (1:1:1 v:v:v) and O. cumana seeds (50 mg of O. cumana seeds per 1 kg of the substrate) with 5 replicates. Three non-infected plants were grown and evaluated in parallel. Approximately 80 days after planting, at the flowering stage of the O. cumana, C. arvense plants were uprooted from the soil. Compared to non-infected plants, the hosts’ symptoms were slow growth, leaf wilting, and chlorosis, and similiar to the broomrape-infected C. arvense plants observed in the greenhouse field. The roots of C. arvense and broomrape were carefully washed in water and observed the parasitism of O. cumana. The infection was confirmed by observation of the attachment of the O. cumana to the C. arvense roots (Supplementary Figure S1D). To the best of our knowledge, this is the first report of O. cumana parasitizing C. arvense in Xinjiang, China. C. arvense as a new host of O. cumana indicates that sunflower broomrape can also propagate and survive in a host such as Canada thistle grown in sunflower fields. This finding suggests that it may be more difficult to control sunflower broomrape by rotation. 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A novel SARS-CoV-2 related coronavirus in bats from Cambodia

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identifies nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a region of the spike, which is not compatible with human ACE2-mediated entry. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously reported, and suggests that Southeast Asia represents a key area to consider for future surveillance for coronaviruses.