Relationship between serum phosphorus and mortality in non-dialysis chronic kidney disease patients: evidence from NHANES 2001-2018.

BACKGROUND: Hyperphosphatemia is common in chronic kidney disease (CKD), associated with higher mortality in dialysis patients. Its impact in non-dialysis patients, especially those with preserved kidney function, remains uncertain. METHODS: A prospective cohort study was conducted using data from the National Health and Nutrition Examination Survey (2001-2008). Serum phosphorus was analyzed as a continuous variable, or categorized into three groups: < 3.5 mg/dL, 3.5 to < 4.5 mg/dL, and ≥ 4.5 mg/dL. Cox proportional hazards models were used to analyze the association between phosphorus with all-cause and cardiovascular disease (CVD) mortality, with or without adjustment for age, sex, race, hemoglobin, estimated glomerular filtration rate (eGFR), serum albumin, serum calcium, 25(OH)D, obesity, hypertension, diabetes, and CVD. RESULTS: A total of 7694 participants were included in the analysis, representing 28 million CKD patients in the United States. During mean 92 months of follow up, 2708 all-cause deaths (including 969 CVD deaths) were observed. Per 1 mg/dL increase in phosphorus was associated with a 13% and 24% increased risk of all-cause mortality (hazard ratio [HR], 1.13; 95%CI, 1.02-1.24) and CVD mortality (HR, 1.24; 95%CI, 1.07-1.45), respectively. Compared with the < 3.5 mg/dL, phosphorus ≥ 4.5 mg/dL was associated with a 28% and 57% increased risk of all-cause mortality (HR, 1.28; 95%CI, 1.05-1.55) and CVD mortality (HR, 1.57; 95CI, 1.19-2.08), respectively. In participants with eGFR < 60 ml/min/1.73m2, elevated phosphorus (≥ 4.5 mg/ dL) were significantly associated with increased risk of all-cause mortality (HR, 1.36; 95%CI, 1.07-1.72). No significant association was observed in eGFR ≥ 60 ml/min/1.73m2 group (HR, 1.31; 95%CI, 0.86-1.99). This correlation does not differ significantly between subgroups defined by eGFR level (P for interaction = 0.889). CONCLUSION: Serum phosphorus above 4.5 mg/dL is significantly associated with a 28% and 57% increased risk of all-cause and CVD death in non-dialysis CKD patients, respectively. This relationship still demonstrated in patients with eGFR < 60 ml/min/1.73m2. However, for population with eGFR ≥ 60 ml/min/1.73m2, further verification is needed.

L-shaped association of serum 25-hydroxyvitamin D with all-cause and cardiovascular mortality in older people with chronic kidney disease: results from the NHANES database prospective cohort study.

BACKGROUND: This study was conducted to assess the association of serum 25-hydroxyvitamin D [25(OH)D] concentrations with all-cause and cardiovascular disease (CVD) mortality in older people with chronic kidney disease (CKD) in the United States. METHODS: We identified 3230 CKD participants aged ≥ 60 years from the National Health and Nutrition Examination Survey (2001-2018). CKD was defined as an estimated glomerular filtration rate (eGFR) < 60 ml/min/1.73 m2. Mortality outcomes were determined by linkage to National Death Index (NDI) records through December 31, 2019. Restricted cubic spline based on Cox regression models were utilized to elucidate the nonlinear relationship between serum 25(OH)D concentrations and mortality in patients with CKD. RESULTS: During median 74 months of follow-up, 1615 all-cause death and 580 CVD death were recorded. We found an L-shaped association between serum 25(OH)D concentrations and all-cause and CVD mortality, reaching a plateau at 90 nmol/L. Accordingly, per one-unit increment in natural log-transformed 25(OH)D was associated with a 32% and 33% reduced risk of all-cause mortality (hazard ratio [HR] 0.68; 95%CI, 0.56 to 0.83) and CV mortality (HR 0.69; 95%CI, 0.49 to 0.97) in participants with serum 25(OH)D < 90 nmol/L, but no considerable difference was observed in participants with serum 25(OH)D ≥ 90 nmol/L. Compared with those in the deficiency group (< 50 nmol/L), insufficient (50 to < 75 nmol/L) and sufficient group (≥ 75 nmol/L) were significantly associated with lower all-cause mortality (HR,0.83; 95%CI, 0.71 to 0.97 and HR, 0.75; 95%CI, 0.64 to 0.89) and CV mortality (HR,0.87; 95%CI, 0.68 to 1.10 and HR, 0.77; 95%CI, 0.59 to < 1.0), respectively. CONCLUSION: An L-shaped relationship between serum 25(OH)D levels with all-cause and CVD mortality was observed in elderly CKD patients in the United States. A 25(OH)D concentration of 90 nmol/L may be the target to reduce the risk of premature death.

Association between serum creatinine and type 2 diabetes in the Chinese population: a retrospective cohort study.

The relationship between serum creatinine and type 2 diabetes is limited. We aimed to investigate the association of baseline serum creatinine and new-onset type 2 diabetes in Chinese population. This retrospective cohort study was conducted using data from the health screening program in China. The population were divided into four groups based on serum creatinine levels, and the outcome of interest was the occurrence of a diabetic event. Cox proportional risk model was used to assess the independent effect of baseline serum creatinine level on future diabetes risk. Sensitivity and subgroup analysis were used to verify the reliability of the results. After an average follow-up of 3.12 years, among 201,298 individuals aged ≥ 20 years, 3389 patients developed diabetes. Compared with participants in quartile 2-4 (> 51.6umol/L for female, > 71.8umol/L for male,), a significantly higher risk of new-onset Type 2 Diabetes (OR, 1.15; 95%CI: 1.07-1.23) was found in those in quartile 1 (< 51.6umol/L for female, < 71.8umol/L for male). Moreover, Similar results were found in various subgroups stratified by age, BMI, TG, TC, FPG and family history group. Low serum creatinine is independently associated with increased risk of type 2 diabetes in Chinese adults. It was also stable in various subgroups stratified.

Lower serum chloride concentrations are associated with an increased risk of death in ICU patients with acute kidney injury: an analysis of the MIMIC-IV database.

BACKGROUND: The association between baseline serum chloride levels and mortality in patients with severe acute kidney injury (AKI) is unknown. Our aim was to investigate the relationship between baseline blood chloride levels and 28-day mortality in patients with AKI admitted to the ICU and to detect possible effect modifiers in this population. METHODS: AKI patients with severe critical illness were extracted from the MIMIC-IV. During ICU admission, chloride levels were measured for the first time. Our primary outcome was 28-day mortality in patients with AKI after 24 hours in the ICU. Multivariable logistic regression was used to examine the association between three groups of chloride levels and 28-day mortality, and logistic regression with restricted cubic spline was applied to detect the non-linear trendy. RESULTS: A total of 24,166 patients with critically ill AKI were included in this retrospective cohort study. The total 28-day mortality rate in the ICU was 15.9%. Overall, there was a U-shaped relationship between baseline serum chloride levels and 28-day mortality (non-linear P<0.001). Accordingly, patients with low serum chloride (<96 mEq/L) had a significantly increased risk of death compared to patients with normal serum chloride (96-108 meq/L) (adjusted OR=1.94, 95% CI: 1.68-2.24, P<0.001). None of the variables, including age, gender, 24-hour fluid intake, continuous renal replacement therapy, ventilation, Atrial fibrillation, Sequential Organ Failure Assessment score, whether to measure lactate and AKI stage, significantly modified the association between lower chloride levels and 28-day mortality. CONCLUSIONS: Low serum chloride levels at baseline were associated with death at 28 days in intensive illnesses with AKI.

Complete Genome Sequences of Tomato Leaf Curl Guam Virus, a Novel Tomato-Infecting Begomovirus from Guam, USA.

Genome sequences of a novel begomovirus infecting tomato on Guam were obtained using primer-walking and sequencing. The complete genome sequences are 2,750 nucleotides long with a typical monopartite organization and display less than 91% nucleotide sequence identity to other begomoviruses. A provisional name, tomato leaf curl Guam virus (ToLCGuV), is proposed.

Understanding the Transmissibility of Cucumber Green Mottle Mosaic Virus in Watermelon Seeds and Seed Health Assays.

Cucumber green mottle mosaic virus (CGMMV), an emerging tobamovirus, has caused serious disease outbreaks to cucurbit crops in several countries, including the United States. Although CGMMV is seed-borne, the mechanism of its transmission from a contaminated seed to germinating seedling is still not fully understood, and the most suitable seed health assay method has not been well established. To evaluate the mechanism of seed transmissibility, using highly contaminated watermelon seeds collected from CGMMV-infected experimental plants, bioassays were conducted in a greenhouse through seedling grow-out and by mechanical inoculation. Through natural seedling grow-out, we did not observe seed transmission of CGMMV to germinating seedlings. However, efficient transmission of CGMMV was observed using bioassays on melon plants through mechanical inoculation of seed extract prepared from CGMMV-contaminated seeds. Understanding the seed-borne property and the ease of mechanical transmission of CGMMV from a contaminated seed to seedling is an important finding. In comparative evaluation of various laboratory techniques for seed health assays, we found that enzyme-linked immunosorbent assay and loop-mediated isothermal amplification were the most sensitive and reliable methods to detect CGMMV on cucurbit seeds. Because CGMMV is a seed-borne and highly contagious virus, a new infection might not result in a natural seedling grow-out; it could occur through mechanical transmission from contaminated seeds. Therefore, a sensitive seed health test is necessary to ensure CGMMV-free seed lots are used for planting.

Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses.

Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5'- and 3'-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining. The analytical results of the features in the detected siRNA duplexes were consistent with those from previous studies. The investigation of siRNA duplexes is useful for a better understanding of the RNA interference (RNAi) mechanism. It can also help to improve the virus detection based on the small RNA sequencing (sRNA-seq) technologies and to rationally design siRNAs for RNAi experiments.

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.

Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline that can efficiently analyze large-scale small RNA (sRNA) datasets for both known and novel virus identification. VirusDetect performs both reference-guided assemblies through aligning sRNA sequences to a curated virus reference database and de novo assemblies of sRNA sequences with automated parameter optimization and the option of host sRNA subtraction. The assembled contigs are compared to a curated and classified reference virus database for known and novel virus identification, and evaluated for their sRNA size profiles to identify novel viruses. Extensive evaluations using plant and insect sRNA datasets suggest that VirusDetect is highly sensitive and efficient in identifying known and novel viruses. VirusDetect is freely available at http://bioinfo.bti.cornell.edu/tool/VirusDetect/.

A single base pair in the right terminal domain of tomato planta macho viroid is a virulence determinant factor on tomato.

Tomato planta macho viroid (TPMVd), including isolates previously designated as Mexican papita viroid (MPVd), causes serious disease on tomatoes in North America. Two predominant variants, sharing 93.8% sequence identity, incited distinct severe (MPVd-S) or mild (MPVd-M) symptoms on tomato. To identify virulence determinant factor, a series of chimeric infectious clones were generated using synthetic DNA approach to progressively replace each structural domain between the two variants. In bioassays on tomato 'Rutgers', three chimeras containing Terminal Left and Pathogenicity (MPVd-H1), Central (MPVd-H2), or Variable (MPVd-H3) of MPVd-S, incited mild to intermediate symptoms. However, a chimera containing Terminal Right (TR) of MPVd-S (MPVd-H4) incited severe symptoms. Only one base-pair mutation in the TR domain between MPVd-M (176U:A185) and MPVd-S (174G:C183) was identified. A reciprocal mutant (MPVd-H5) rendered the chimeric viroid mild on tomato. This single base-pair in the TR domain was determined as the virulence determinant factor for TPMVd.

Molecular and Biological Characterization of Tomato mottle mosaic virus and Development of RT-PCR Detection.

Tomato mottle mosaic virus (ToMMV) was first identified in 2013 as a novel tobamovirus infecting tomatoes in Mexico. In just a few years, ToMMV has been identified in several countries around the world, including the United States. In the present study, we characterized the molecular, serological, and biological properties of ToMMV and developed a species-specific RT-PCR to detect three tomato-infecting tobamoviruses: Tobacco mosaic virus (TMV), Tomato mosaic virus (ToMV), and ToMMV. Previously, ToMMV has been reported in Florida and New York. In this study, we made two new reports on the occurrences of ToMMV on tomatoes in California and South Carolina. Their complete genome sequences were obtained and their genetic relationships to other tobamoviruses evaluated. In host range studies, some differential responses in host plants were also identified between ToMMV and ToMV. To alleviate cross-serological reactivity among the tomato-infecting tobamoviruses, a new multiplex RT-PCR was developed to allow for species-specific detection and identification of TMV, ToMV, and ToMMV. In addition, we observed resistance breaking by ToMMV on selected tomato cultivars that were resistant to ToMV. This has caused serious concerns to tomato growers worldwide. In conclusion, the characterization in molecular and biological properties of ToMMV would provide us with fundamental knowledge to manage this emerging virus on tomato and other solanaceous crops in the U.S. and around the world.

A Duplex Real-Time RT-PCR System with an Internal Control Offers Sensitive and Reliable Broad-Spectrum Detection of Squash mosaic virus Variants.

Squash mosaic virus (SqMV), a seedborne virus, belongs to the genus Comovirus in the subfamily Comovirinae of the family Secoviridae. SqMV has a bipartite single-stranded RNA genome (RNA1 and RNA2) encapsidated separately with two capsid proteins. With the recent identification of a third genotype in SqMV, a greater genetic diversity with only 88 to 89% sequence identity among them are recognized. With the existence of genetic diversity, a previously developed quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) failed to detect isolates in this new genotype. Therefore, it was necessary to create a new qRT-PCR that would react with all SqMV isolates in three different genotypes. From a multiple sequence alignment of the available SqMV sequences in GenBank, a conserved sequence segment in the 3' untranslated region of RNA2 was identified for primer and probe design. A new qRT-PCR was developed, which provided broad-spectrum reactions to SqMV isolates, including those from the newly recognized third genotype. To improve the reliability in determining the sample quality and result interpretation, an internal amplification control with an endogenous gene sequence (18S ribosomal RNA) was successfully incorporated to develop a duplex qRT-PCR system that was useful for seed health test.

Complete Genome Sequence of a Tomato-Infecting Tomato Mottle Mosaic Virus in New York.

The complete genome sequence of an isolate of tomato mottle mosaic virus (ToMMV) infecting tomatoes in New York was obtained using small RNA (sRNA) deep sequencing. ToMMV_NY-13 shared 99% sequence identity with isolates from Mexico and Florida. Broader distribution of this emerging virus is a cause for concern to the tomato industry.

Complete Genome Sequence of Southern tomato virus Identified in China Using Next-Generation Sequencing.

The complete genome sequence of Southern tomato virus (STV), a double-stranded RNA virus that affects tomato in China, was determined using small RNA deep sequencing. This Chinese isolate shares 99% sequence identity to other isolates from Mexico, France, Spain, and the United States. This is the first report of STV infecting tomatoes in Asia.

Complete Genome Sequence of an Emerging Melon Necrotic Spot Virus Isolate Infecting Greenhouse Cucumber in North America.

The complete genome sequence (4,267 nt) of a Melon necrotic spot virus (MNSV) isolate (ABCA13-01) infecting greenhouse cucumber in Canada was determined through deep sequencing of small RNAs. Its genome sequence was most closely related to MNSV-N (97%) but lacked a 55-nucleotide insertion at the 3' untranslated region for resistance breaking.

First complete genome sequence of an emerging cucumber green mottle mosaic virus isolate in north america.

The complete genome sequence (6,423 nucleotides [nt]) of an emerging cucumber green mottle mosaic virus (CGMMV) isolate on cucumber in North America was determined through deep sequencing of small (sRNA) and rapid amplification of cDNA ends. The virus shares 99% nucleotide sequence identity with the Asian genotype but only 90% with the European genotype.

Complete genome sequence of a novel genotype of squash mosaic virus infecting squash in Spain.

The complete genome sequence of a new isolate of squash mosaic virus (SqMV) infecting squash plants in Spain was obtained using deep sequencing of small RNAs. The low nucleotide sequence identities, with only 87 to 88% for RNA1 and 84 to 86% for RNA2 to known SqMV isolates, suggested that this isolate belongs to a novel genotype.

Evaluation of disinfectants to prevent mechanical transmission of viruses and a viroid in greenhouse tomato production.

BACKGROUND: In recent years, a number of serious disease outbreaks caused by viruses and viroids on greenhouse tomatoes in North America have resulted in significant economic losses to growers. The objectives of this study were to evaluate the effectiveness of commercial disinfectants against mechanical transmission of these pathogens, and to select disinfectants with broad spectrum reactivity to control general virus and viroid diseases in greenhouse tomato production. METHODS: A total of 16 disinfectants were evaluated against Pepino mosaic virus (PepMV), Potato spindle tuber viroid (PSTVd), Tomato mosaic virus (ToMV), and Tobacco mosaic virus (TMV). The efficacy of each disinfectant to deactivate the pathogen's infectivity was evaluated in replicate experiments from at least three independent experiments. Any infectivity that remained in the treated solutions was assessed through bioassays on susceptible tomato plants through mechanical inoculation using inocula that had been exposed with the individual disinfectant for three short time periods (0-10 sec, 30 sec and 60 sec). A positive infection on the inoculated plant was determined through symptom observation and confirmed with enzyme-linked immunosorbent assay (PepMV, ToMV, and TMV) and real-time reverse transcription-PCR (PSTVd). Experimental data were analyzed using Logistic regression and the Bayesian methodology. RESULTS: Statistical analyses using logistic regression and the Bayesian methodology indicated that two disinfectants (2% Virkon S and 10% Clorox regular bleach) were the most effective to prevent transmission of PepMV, PSTVd, ToMV, and TMV from mechanical inoculation. Lysol all-purpose cleaner (50%) and nonfat dry milk (20%) were also effective against ToMV and TMV, but with only partial effects for PepMV and PSTVd. CONCLUSION: With the broad spectrum efficacy against three common viruses and a viroid, several disinfectants, including 2% Virkon S, 10% Clorox regular bleach and 20% nonfat dry milk, are recommend to greenhouse facilities for consideration to prevent general virus and viroid infection on tomato plants.

Complete Genome Sequence of Southern tomato virus Naturally Infecting Tomatoes in Bangladesh.

The complete genome sequence of a Southern tomato virus (STV) isolate on tomato plants in a seed production field in Bangladesh was obtained for the first time using next-generation sequencing. The identified isolate, STV_BD-13, shares a high degree of sequence identity (99%) with several known STV isolates worldwide.

Complete genome sequence of an emerging genotype of tobacco streak virus in the United States.

We report here the complete genome sequence of an emerging genotype of tobacco streak virus (TSV) infecting zucchini squash in Florida (TSV_FL13-07), obtained using deep sequencing of short RNAs (sRNAs) and validation by Sanger sequencing. TSV_FL13-07 shares only <90% sequence identity in all three genomic RNAs to several known U.S. isolates.

Development of reverse transcription loop-mediated isothermal amplification assay for rapid detection of an emerging potyvirus: tomato necrotic stunt virus.

Tomato necrotic stunt virus (ToNStV) is an emerging potyvirus that causes severe stunting to infected tomato plants. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for sensitive detection of ToNStV. The sensitivity of RT-LAMP was comparable to that of conventional RT-PCR, with detection of ToNStV in a reaction containing only 8 pg of total tomato RNA or with 1:20,000 dilution of crude tissue extract. This assay was able to detect ToNStV in a broad range of solanaceous plant species. The RT-LAMP for ToNStV was specific with no cross-reactivity to other potyviruses (i.e. Potato virus Y and Tobacco etch virus), as well as several other common tomato viruses. RT-LAMP should complement RT-PCR and real-time RT-PCR assays reported previously, with a potential to provide a simple, rapid, and sensitive field diagnostic method for ToNStV.