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1.
American Journal of Transplantation ; 22(Supplement 3):572, 2022.
Article in English | EMBASE | ID: covidwho-2063393

ABSTRACT

Purpose: To study the clinical application of metagenomic next-generation sequencing (mNGS) in the detection of viral infections in kidney transplant recipients (KTRs) during the COVID-19 pandemic. Method(s): Using mNGS techniques, 50 human fluid samples of KTRs were detected in Henan Province People's Hospital between May 2020 to May 2021, including 20 bronchoalveolar lavage fluid (BALF) samples, 21 urine samples and 9 blood samples. The detected nucleic acid sequences were compared and analyzed with the existing viral nucleic acid sequences in the database, and the virus infection spectrum of KTRs was drawn. Result(s): The viral nucleic acids of 15 types of viruses were detected in 96.00% (48/50) of the samples, of which 11 types of viruses were in BALF (95.00%, 19/20), and the dominant viruses were torque teno virus (TTV) (65.00%;13/20), cytomegalovirus (CMV) (45.00%;9/20) and human alphaherpesvirus 1 (25.00%;5/20). 12 viruses (95.24%, 20/21) were detected in the urine, and the dominant viruses were TTV (52.38%;11/21), JC polyomavirus (52.38%;11/21), BK polyomavirus (42.86%;9/21), CMV (33.33%;7/21) and human betaherpesvirus 6B (28.57%;6/21). 7 viruses were detected in the blood (100.00%, 9/9), and the dominant virus was TTV (100.00%;9/9). Four rare viruses were detected in BALF and urine, including WU polyomavirus, primate bocaparvovirus 1, simian virus 12, and volepox virus. Further analysis showed that TTV infection with high reads indicated a higher risk of acute rejection (P<0.05). Conclusion(s): mNGS detection reveals the rich virus spectrum of infected persons after kidney transplantation, and improves the detection rate of rare viruses. TTV may be a new biomarker for predicting rejection. (Figure Presented).

2.
Zhongguo Bingdubing Zazhi = Chinese Journal of Viral Diseases ; - (4):284, 2022.
Article in English | ProQuest Central | ID: covidwho-2040496

ABSTRACT

Objective To understand the genomic characteristics of SARS-CoV-2 from 40 imported cases with confirmed COVID-19 in Sichuan during January and March 2022. Methods Total viral RNA was extracted from respiratory samples of 182 confirmed COVID-19 cases who entered China through Chendu International Airport from January to March 2022.Mutation nucleic acid detection kit was used to identify the mutant strains and Illumina sequencing platform was applied for whole genome sequence(WGS) of virus.SARS-CoV-2 reference sequences were downloaded from NCBI database for genetic evolution and antigen variation analysis.The Nextclade and Pangolin online virus analysis platform were used to determine the virus family and type,and to analyze the mutation loci of the virus.The phylogenetic tree was constructed,along with the epidemiological data of cases to analyze the source and correlation of viruses. Results Among 182 imported COVID-19 cases,B.1.617.2 mutations were identified in 3 cases and B.1.1.529 mutations were detected in 57 cases.A total of 40 SARS-CoV-2 whole genome sequences with coverage>95% were obtained in this study.Nextclade typing analysis showed that 3 sequences belonged to 21J(Delta),5 sequences belonged to 21K(Omicron)and the remaining 32 sequences belonged to 21L(Omicron).Pangolin typing analysis showed that the 3 sequences of 21J(Delta)belonged to AY.4,AY.109and B.1.617.2,the 5sequences of 21K(Omicron)all belonged to BA.1.1,and the remaining 32 sequences of 21L(Omicron)belonged to BA.2.Our sequence results were99.7% consistency with the Omicron variants sequences in current GISAID database.Compared with the reference sequence strain Wuhan-Hu-1(NC_045512.2),45,47and 42nucleotide variation sites and 36,25 and 36amino acid variation sites were found in the 3 sequences of 21J(Delta).There were average 59(26-64)nucleotide mutation sites and 48(10-53)amino acid mutation sites in the 5sequences of 21K(Omicron).The median number of nucleotide mutation sites of 71(66-76)and amino acid mutation sites of 53(40-56)were identified in the 32sequences of 21L(Omicron).Phylogenetic tree analysis showed that 40SARS-CoV-2WGSs were all related to the current variants of concern(VOC). Conclusions Continuous sequencing of SARS-CoV-2whole genome from imported cases with confirmed COVID-19is of great significance for the prevention and control of the outbreak and prevalence of local epidemic caused by imported viruses in Sichuan.

3.
Canadian Entomologist ; 154(1), 2022.
Article in English | ProQuest Central | ID: covidwho-2040072

ABSTRACT

In the Canadian Maritimes, many beekeepers rent honey bee, Apis mellifera Linnaeus (Hymenoptera: Apidae), hives to growers of lowbush blueberry, Vaccinium angustifolium (Ericaceae), for pollination services. Anecdotally, hives have less vigour following pollination, potentially due to higher Nosema spp. (Nosematidae) spore loads, the microsporidian causing nosemosis. We undertook a study to determine whether sending honey bee hives to lowbush blueberry fields for pollination (blueberry hives) results in higher Nosema spp. spore loads relative to hives remaining in apiaries (home hives). Nosema spp. spore loads were quantified using light microscopy. Nosema apis and Nosema ceranae were differentiated using polymerase chain reaction and sequencing. Nosema spp. spore loads were greatest in April and May and declined to low levels from June to September. Ninety-eight per cent of Nosema detections were positive for N. ceranae. In April, blueberry hives had a lower spore load than home hives did;however, in June, spore loads were significantly higher in blueberry hives. No other differences in Nosema spp. spore loads were observed between hive types. We conclude that Nosema ceranae is the dominant Nosema species in the Canadian Maritimes and that using hives for lowbush blueberry pollination does not appear to influence long-term Nosema spp. spore loads.

4.
Journal of Hydrology ; 61(1):45-57, 2022.
Article in English | ProQuest Central | ID: covidwho-1970466

ABSTRACT

Surveillance of municipal wastewater for RNA of SARS-CoV-2, the causative agent of coronavirus disease (COVID-19), is well documented around the world. However, unlike most countries where wastewater surveillance was initially employed during 2020, New Zealand was in the fortunate position of having very few COVID-19 cases, generally confined to Managed Isolation and Quarantine facilities. As such, the prevalence of SARS-CoV-2 RNA in wastewater was likely much lower than seen in other countries. A nine-week pilot study was undertaken to assess the feasibility of detecting SARSCoV-2 RNA in wastewater in New Zealand. Wastewater from 18 catchments across New Zealand was monitored, including six that contained Managed Isolation and Quarantine facilities. Testing both in regions known to have COVID-19 cases and regions where detection was not expected (catchments not containing Managed Isolation and Quarantine facilities) allowed the sensitivity and specificity of detection methods to be assessed. SARS-CoV-2 RNA was detected in seven out of the nine weeks of this study in the Auckland South Western Interceptor catchment, which contained a dedicated isolation facility to which confirmed cases from Auckland, Hamilton and Rotorua were transferred. In weeks two and three of sampling, SARS-CoV-2 RNA was detected in the Christchurch catchment. This coincided with up to 14 COVID-19 cases likely to be shedding high levels of virus (PCR Cq value < 20) in the Managed Isolation and Quarantine facilities. Samples from the seven other weeks were negative despite up to 35 infected cases present at any one time. However, on any of these test dates eight cases or fewer had a PCR Cq value < 30 and were within 10 days of symptom onset or positive PCR test date. Sample inhibition and non-specificity were not observed to be issues. The results of this pilot study underpinned recommendations that wastewater monitoring for SARS-CoV-2 RNA be incorporated as a surveillance tool in New Zealand's COVID-19 response.

5.
Scopus; 2021.
Preprint in English | Scopus | ID: ppcovidwho-341348

ABSTRACT

Background: A recent bioinformatics technique involves changing nucleotide sequences into 2D speckles. This technique produces speckles called GB-speckles (Gene Based speckles). All classical strategies of speckle-optics, namely speckle-interferometry, subtraction of speckle-images as well as speckle-correlometry have been inferred for processing of GB-speckles. This indicates the considerable improvement in the present tools of bioinformatics.   Methods: Colour s-LASCA imaging of virtual laser GB-speckles, a new method of high discrimination and typing of pathogenic viruses, has been developed. This method has been adapted to the detecting of natural mutations in nucleotide sequences, related to the spike glycoprotein (coding the gene «S») of SARS-CoV-2 gene as the molecular target.    Results: The rate of the colouring images of virtual laser GB-speckles generated by s-LASCA can be described by the specific value of R. If the nucleotide sequences compared utilizing this approach the relevant images are completely identical, then the three components of the resulting colour image will be identical, and therefore the value of R will be equal to zero. However, if there are at least minimal differences in the matched nucleotide sequences, then the value of R will be positive.    Conclusion: The high effectiveness of an application of the colour images of GB-speckles that were generated by s-LASCA- has been demonstrated for discrimination between different variants of the SARS-CoV-2 spike glycoprotein gene. Copyright: © 2021 Ulianova O et al.

6.
Evolutionary Bioinformatics ; 18, 2022.
Article in English | EMBASE | ID: covidwho-1928021

ABSTRACT

Introduction: In an effort to combat SARS-CoV-2 through multi-subunit vaccine design, during studies using whole genome and immunome, ORF10, located at the 3′ end of the genome, displayed unique features. It showed no homology to any known protein in other organisms, including SARS-CoV. It was observed that its nucleotide sequence is 100% identical in the SARS-CoV-2 genomes sourced worldwide, even in the recent-most VoCs and VoIs of B.1.1.529 (Omicron), B.1.617 (Delta), B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma) lineages, implicating its constant nature throughout the evolution of deadly variants. Aim: The structure and function of SARS-CoV-2 ORF10 and the role it may play in the viral evolution is yet to be understood clearly. The aim of this study is to predict its structure, function, and understand evolutionary dynamics on the basis of mutations and likely heightened immune responses in the immunopathogenesis of this deadly virus. Methods: Sequence analysis, ab-initio structure modeling and an understanding of the impact of likely substitutions in key regions of protein was carried out. Analyses of viral T cell epitopes and primary anchor residue mutations was done to understand the role it may play in the evolution as a molecule with likely enhanced immune response and consequent immunopathogenesis. Results: Few amino acid substitution mutations are observed, most probably due to the ribosomal frameshifting, and these mutations may not be detrimental to its functioning. As ORF10 is observed to be an expressed protein, ab-initio structure modeling shows that it comprises mainly an α-helical region and maybe an ER-targeted membrane mini-protein. Analyzing the whole proteome, it is observed that ORF10 presents amongst the highest number of likely promiscuous and immunogenic CTL epitopes, specifically 11 out of 30 promiscuous ones and 9 out of these 11, immunogenic CTL epitopes. Reactive T cells to these epitopes have been uncovered in independent studies. Majority of these epitopes are located on the α-helix region of its structure, and the substitution mutations of primary anchor residues in these epitopes do not affect immunogenicity. Its conserved nucleotide sequence throughout the evolution and diversification of virus into several variants is a puzzle yet to be solved. Conclusions: On the basis of its sequence, structure, and epitope mapping, it is concluded that it may function like those mini-proteins used to boost immune responses in medical applications. Due to the complete nucleotide sequence conservation even a few years after SARS-CoV-2 genome was first sequenced, it poses a unique puzzle to be solved, in view of the evolutionary dynamics of variants emerging in the populations worldwide.

7.
10th International Congress on Advanced Applied Informatics, IIAI-AAI 2021 ; : 35-40, 2021.
Article in English | Scopus | ID: covidwho-1922696

ABSTRACT

A trim distance between two positions in the set of nucleotide sequences is a tree-based distance between the trimmed phylogenetic trees at two positions, each of which is obtained by applying the label-based closest-neighbor trimming method to the relabeled phylogenetic tree at the position that the index as a label of leaves is relabeled to the nucleotide occurring at the position. In this paper, as a tree-based distance, we adopt a label histogram distance and a depth histogram distance. Then, we introduce new trim distances that a label trim distance and a depth trim distance, respectively. Finally, by using the nucleotide sequences and the reconstructed phylogenetic tree from them provided from NCBI, we investigate the trim distances between the positions in the nucleotide sequences for structural proteins of spike, envelope, membrane and nucleocapsid proteins of SARS-CoV-2. © 2021 IEEE.

8.
Virologie ; 26(2):193-194, 2022.
Article in English | EMBASE | ID: covidwho-1913287

ABSTRACT

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has become one of the most studied viruses since its emergence. Two years after its outbreak, SARSCoV- 2 still represents a major public health priority as it keeps spreading at an alarming rate through the rise of many pathogenic variants. These latter can be a serious threat the more their genomic sequence diverge from the original strain, the less efficient the vaccine will remain. Therefore, it is critical for medical services to be able to determine straight out the strain they are dealing with, also as the location of the occurred genomic mutations and identify which viral protein has evolved. In this context, our main goal is to understand the nuances behind the mutations observed simultaneously in the genome and the proteome. To do so, we developed a user-friendly web-service software (Viral Instant Mutation Viewer or VIMVer) which allows an instant identification of new mutations and displayed them in both the nucleotide and protein sequences in comparison to a reference sequence (wuhan-1). Given a SARS-CoV-2 nucleotide sequence (as a newly sequenced genome), our software will instantly extract, analyse and visualize mutations on the genome and the proteome with the proper numbering and positioning. Additionally, the output is linked to Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin COVID-19) (2), which will thus allow an automatic identification of the Lineage or its position in relation to known lineage. We believe this tool will help many in their daily process to analyse their data. The source code is released under public licence and can be adapted for further development.

9.
Patterns (N Y) ; 3(9): 100562, 2022 Sep 09.
Article in English | MEDLINE | ID: covidwho-1914886

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome data are essential for epidemiology, vaccine development, and tracking emerging variants. Millions of SARS-CoV-2 genomes have been sequenced during the pandemic. However, downloading SARS-CoV-2 genomes from databases is slow and unreliable, largely due to suboptimal choice of compression method. We evaluated the available compressors and found that Nucleotide Archival Format (NAF) would provide a drastic improvement compared with current methods. For Global Initiative on Sharing Avian Flu Data's (GISAID) pre-compressed datasets, NAF would increase efficiency 52.2 times for gzip-compressed data and 3.7 times for xz-compressed data. For DNA DataBank of Japan (DDBJ), NAF would improve throughput 40 times for gzip-compressed data. For GenBank and European Nucleotide Archive (ENA), NAF would accelerate data distribution by a factor of 29.3 times compared with uncompressed FASTA. This article provides a tutorial for installing and using NAF. Offering a NAF download option in sequence databases would provide a significant saving of time, bandwidth, and disk space and accelerate biological and medical research worldwide.

10.
Applied Sciences ; 12(11):5329, 2022.
Article in English | ProQuest Central | ID: covidwho-1892762

ABSTRACT

Plants have evolved defense mechanisms to suppress viral transcription and replication by transcriptional and post-transcriptional gene silencing mediated by virus-derived small interfering RNAs (vsiRNAs). Based on this response, virus-induced gene silencing (VIGS)-based technology has been developed to silence target genes on either host plants or insect pests. This mechanism could also be used for the silencing of genes of interest in the medical field. We used the VIGS vector pEuMV-YP:Krt18, which was obtained by inserting the Mus musculus (M. musculus) Krt18 sequence into pEuMV-YP:ΔAV1. The objective was to evaluate the capacity of pEuMV-YP:Krt18 to induce Nicotiana benthamiana (N. benthamiana) production of vsiRNAs of a specific sequence that belongs to neither the plant genome nor the wild virus genome, which were used to induce cross-kingdom gene silencing between plants and mammals. The percentage of vsiRNA for each viral gene was calculated from an sRNA library of N. benthamiana plants infected by pEuMV-YP: Krt18. When the vsiRNAs were characterized, it was found that they corresponded to all the genes of the pEuMV-YP:Krt18 vector. These vsiRNAs induced the silencing of the Krt18 gene in M. musculus macrophages, supporting the ability to use VIGS vectors in plants as biofactories for the production of sRNAs that induce gene silencing in mammals.

11.
Archives of Virology ; 165(3):703-707, 2020.
Article in English | ProQuest Central | ID: covidwho-1877434

ABSTRACT

Using viral metagenomics, the complete genome sequence of an infectious bronchitis virus (IBV) strain (named ahysx-1) from a fecal sample from a healthy chicken in Anhui province, China, was determined. The genome sequence of ahysx-1 was found to be very similar to that of IBV strain ck/CH/LLN/131040 (KX252787), except for the spike gene region, which is similar to that of a turkey coronavirus strain (EU022526), suggesting that ahysx-1 is a recombinant. Recombination analysis and phylogenetic analysis based on the genomic sequences of ahysx-1 and other related strains confirmed that ahysx-1 appears to be a recombinant resulting from a recombination event that occurred between a chicken coronavirus and a turkey coronavirus. Further studies need to be performed to determine whether this recombinant IBV strain is pathogenic and whether it is transmitted between chickens and turkeys.

12.
PLoS Biology ; 18(4), 2020.
Article in English | ProQuest Central | ID: covidwho-1876907

ABSTRACT

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.

13.
Bioinformation ; 18(4):432, 2022.
Article in English | ProQuest Central | ID: covidwho-1876089

ABSTRACT

SARS-CoV-2 (Severe Acute Respiratory Syndrome), a causative agent of COVID-19 disease created a pandemic situation worldwide. Nsp15 is a uridine specific endoribonuclease encoded by the genome of SARS-CoV-2. It plays important role in processing viral RNA and, thus evades the host immune system. Therefore, it is of interest to identify mutants of nsp15 amongst Asian SARS-CoV-2 isolates, where a total of 1795 mutations, from 7793 sequences of Asia submitted till 31st January 2022, amongst which A231V, H234Y, K109N, K259R and S261A mutations were found frequent. Hence, we report data on the predicted secondary structure of wild type form followed by hydropathy plot, physiochemical properties, Ramachandran plot, B-cell epitopes prediction and protein modeling of wild type and mutant of nsp15 protein. Data shows that nsp15 of SARS-CoV-2 is a pontential candidate for the development of vaccine to control the infections of SARSCoV-2.

14.
Infektsionnye Bolezni ; 20(1):127-130, 2022.
Article in English | EMBASE | ID: covidwho-1863505

ABSTRACT

Objective. To study the prevalence of mutations causing resistance to macrolides in Mycoplasma pneumoniae in the Tula region and compare the data with similar studies from European and Asian countries. Material and methods. A retrospective study of 76 samples of biological materials (nasal and pharynx swabs) was conducted. The materials were collected from the patients with an established diagnosis: the lower respiratory tract infection (pneumonia, bronchitis). All the patients included in the study were treated in specialized infections units and clinics of the Tula region for the period 2017–2018. Antibiotic therapy was not conducted before the initial survey. All the samples contained M. pneumoniae DNA. A real-time polymerase chain reaction (real-time PCR) technology was used to detect the DNA of M. pneumoniae in the materials. The analysis of mutations in the 23S rRNA gene was performed at the Scientific Research Institute of Antimicrobial Chemotherapy in Smolensk. During the study, a modified real-time PCR technique with the effect of the fluorescence quenching of the probe with a primer (patent No. 2646123) was used. The statistical analysis was carried out with the MS Excel software package. Results. It was identified that 9 samples (11.84%) had mutations associated with resistance to macrolides. Two samples had the A2059G mutation, while seven samples had the A2058G mutation (numbering of nucleotide sequences in the M. pneumoniae rRNA gene was compiled following E. coli numbering). The data obtained by us are slightly higher than the mean values of European countries and are significantly lower according to the studies of Asian countries. Conclusions. Provided unique data on the prevalence and identification of mutations of macrolide-resistant strains of M. pneumoniae in one of the regions of the Central Federal District is a contribution to the study of antibiotic-resistant strains of M. pneumoniae in Russia and all over the world. There is a necessity to monitor antibiotic resistance in other regions and increase diligence on atypical forms of community-acquired pneumonia since the co-infection of M. pneumoniae patients with COVID-19 leads to a deterioration in the condition and an increase in the duration of treatment.

15.
Disease Surveillance ; 37(2):160-166, 2022.
Article in Chinese | GIM | ID: covidwho-1855880

ABSTRACT

Objective: To investigate the incidence, epidemiology and clinical characteristics of Creutzfeldt-Jakob disease (CJD) in China in 2020.

16.
Indian Veterinary Journal ; 98(12):22-29, 2021.
Article in English | EMBASE | ID: covidwho-1820592

ABSTRACT

Spike (S) proteins covering the outer surface of the Coronaviruses are the major hotspots of evolution and are also responsible for attaching the virus to the angiotensin-converting enzyme (ACE2) receptor on the host cells. In this study, we unveiled the evolutionary relics of the S-protein sequences of different beta Coronaviruses, namely, Severe Acute Respiratory Syndrome (SARS-CoV), SARS-CoV-2, and Middle East Respiratory Syndrome (MERSCoV). The present study aims at exploring the sequence divergence of the spike protein (S-protein) of nCov2 viruses to illuminate the evolutionary process. The nucleotide sequences of S-proteins of nCov2 viruses, namely, SARS, MERS and SARS-CoV2, representing different continents of the world, were downloaded from the NCBI Nucleotide databases. The conserved regions have been depicted through multiple sequence alignment (Clustal Omega, Jalview) and the molecular phylogeny has been studied. (using MEGA 7). Comparative analysis of the pairwise distance and selection pressure indicated that the SARS-CoV and SARS-CoV-2 are close to each other, however, distantly related to MERS-CoV and the SARS-CoV2 could have evolved from SARS (Severe Acute Respiratory Syndrome).

17.
Water ; 14(5):827, 2022.
Article in English | ProQuest Central | ID: covidwho-1742775

ABSTRACT

The sequestration and storage of carbon dioxide by marine macrophytes is called blue carbon;this ecosystem function of coastal marine ecosystems constitutes an important countermeasure to global climate change. The contribution of marine macrophytes to blue carbon requires a detailed examination of the organic carbon stock released by these macrophytes. Here, we introduce a quantitative real-time polymerase chain reaction (qPCR)-based environmental DNA (eDNA) system for the species-specific detection of marine macrophytes. and report its application in a field survey in Hiroshima Bay, Japan. A method of qPCR-based quantification was developed for mangrove, seagrass, Phaeophyceae, Rhodophyta and Chlorophyta species, or species-complex, collected from the Japanese coast to investigate their dynamics after they wither and die in the marine environment. A trial of the designed qPCR system was conducted using sediment samples from Hiroshima Bay. Ulva spp. were abundant in coastal areas of the bay, yet their eDNA in the sediments was scarce. In contrast, Zostera marina and the Sargassum subgenus Bactrophycus spp. were found at various sites in the bay, and high amounts of their eDNA were detected in the sediments. These results suggest that the fate of macrophyte-derived organic carbon after death varies among species.

18.
International Journal of Infectious Diseases ; 116:S86, 2022.
Article in English | EMBASE | ID: covidwho-1734445

ABSTRACT

Purpose: The origin of the current COVID-19 pandemic is unknown but horseshoe bats, of the family Rhinolophidae, are natural hosts to a suite of sarbecoviruses. Global surveillance is key to monitoring potentially pathogenic viral strains and improving the capacity for surveillance across Europe will bolster our understanding of viral populations within zoonotic reservoirs. Methods & Materials: Faecal samples were collected from Lesser horseshoe bats (Rhinolophus hipposideros) in the UK during annual population monitoring surveys, stored in RNAlater and frozen prior to genomic analysis. For metagenomic analysis, the Sequence-independent Single-Primer Amplification (SISPA) method was employed and sequencing completed using Illumina Nextera and the Oxford Nanopore GridION platforms. Results: A De novo hybrid assembly utilising shorter Illumina reads with longer Nanopore reads acting as a scaffold, generated a 29kb contig named RhGB01. Mapping raw reads against RhGB01 demonstrated a combined depth of 50x across the genome. Sequence alignment exhibits genomic organisation comparable to other sarbecoviruses isolated from animal and human hosts. Within the receptor binding domain, but excluding the receptor binding motif, RhGB01 has 77% and 81% amino acid homology compared to SARS-CoV-2 and SARS respectively. Maximum likelihood phylogenies inferred from the nucleotide sequence of RNA dependent RNA polymerase, spike glycoprotein and entire coding sequence exhibit clustering with the only other fully sequenced zoonotic Sarbecovirus from Europe which was isolated from Rhinolophus blasii. The structure of the receptor binding domain of RhGB01 was predicted by homology modelling using a crystal structure of the receptor binding domain of SARS-CoV as a template. This model was selected with a Global Model Quality Estimate (GMQE) > 0.7 and Quaternary Structure Quality Estimate (QMEAN) of -2.18. Structural comparisons between the predicted receptor binding domain of RhGB01 and SARS-CoV-2 highlight structurally different regions which house hACE2 contact residues. Conclusion: Phylogenetic inference and structural modelling suggest an absence of pathogenic potential for RhGB01. However, the discovery of a novel Sarbecovirus at the western limit of Lesser horseshoe bats demonstrates their presence throughout the entire horseshoe bat distribution and indicates the need for viral surveillance systems in Western Europe.

19.
Glob Food Sec ; 33: 100619, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1729785

ABSTRACT

Severe price spikes of the major grain commodities and rapid expansion of cultivated area in the past two decades are symptoms of a severely stressed global food supply. Scientific discovery and improved agricultural productivity are needed and are enabled by unencumbered access to, and use of, genetic sequence data. In the same way the world witnessed rapid development of vaccines for COVID-19, genetic sequence data afford enormous opportunities to improve crop production. In addition to an enabling regulatory environment that allowed for the sharing of genetic sequence data, robust funding fostered the rapid development of coronavirus diagnostics and COVID-19 vaccines. A similar level of commitment, collaboration, and cooperation is needed for agriculture.

20.
Kidney International Reports ; 7(2):S333-S334, 2022.
Article in English | EMBASE | ID: covidwho-1705211

ABSTRACT

Introduction: Diarrhea is common gastrointestinal problem in kidney transplant recipients. Numerous cases of post-transplant diarrhea in the past have been ascribed solely to the toxicity of immunosuppressive drugs, leading to diagnostic misconceptions. Noro Virus, one of the common cause of acute diarrhea in adult is emerging as important cause of persistent diarrhea in solid organ transplant recipients.Here, we are presenting our experience with chronic Noro virus infection in renal transplant recipients. Aim of the study was to determine the clinical significance of Noro virus infection in renal transplant recipients with persistent diarrhea. Methods: Between December’19 and November’20, renal transplant recipients presenting with persistent diarrhoea (≥3 stools/day for ≥14 consecutive days) were evaluated in a step wise manner including stool Noro virus RTPCR and were followed for 12 months. Stool specimen were collected in container (Cary-Blair Transport Media) and stored or at -94°F (-70°C). This tests were performed using TaqMan real-time reverse transcription-PCR assay ( Fast-track diagnostic). The detection and typing of Norovirus by conserved nucleotide sequences of the ORF1-ORF2 junction region of the Norovirus genome. Patients were followed up clinically. Repeat RTPCR Noro virus in stool were evaluated on follow up at 3, 6, 9 and 12 months. Because of COVID 19 pandemic, we were not able to collect repeat stool RTPCR samples for Noro virus on follow up in all patients. Telephonic follow up was obtained in patients who had not come for follow up during study period. Results: 29 out of 39 patients were positive for Noro virus RTPCR. Median time of presentation following transplant was 59 months (range 12 to 143 months). Median duration of diarrhoea was 69 days (range 14 to 365 days). Median weight loss on presentation was 6.4 kg (range 1.7 to 17.3 kg). Out of 20 patients who were on Tac/MMF/Prednisolone at presentation, MMF was withheld in 11;switched to Azathioprine in 3, switched to Everolimus in 3 and 3 were continued on same medications. Out of 7 patients receiving Tac/Azathioprine/Prednisolone, Azathiporine dose reduced in all;3 were switched to cyclosporine from tacrolimus. 2 patients receiving Tacrolimus & prednisolone only, were switched to cyclosporine. Diarrhoea responded in all. Out of 13 patients presenting with renal dysfunction;6 had worsening of renal function whereas 8 had steady or better renal function at 6 months. 15 patients gained weight at 6 months;8 had persistent weight loss. Conclusions: Noro virus infection is important cause of persistent diarrhea in renal transplant recipients. It is associated with significant weight loss, renal dysfunction and prolonged asymptomatic viral shedding. We should look for etiologies other than immunesuppression drugs as cause of persistent diarrhea. No conflict of interest

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