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1.
Sci Rep ; 12(1): 5856, 2022 Apr 07.
Article in English | MEDLINE | ID: covidwho-1784021

ABSTRACT

Rapid dissemination of SARS-CoV-2 sequencing data to public repositories has enabled widespread study of viral genomes, but studies of longitudinal specimens from infected persons are relatively limited. Analysis of longitudinal specimens enables understanding of how host immune pressures drive viral evolution in vivo. Here we performed sequencing of 49 longitudinal SARS-CoV-2-positive samples from 20 patients in Washington State collected between March and September of 2020. Viral loads declined over time with an average increase in RT-QPCR cycle threshold of 0.87 per day. We found that there was negligible change in SARS-CoV-2 consensus sequences over time, but identified a number of nonsynonymous variants at low frequencies across the genome. We observed enrichment for a relatively small number of these variants, all of which are now seen in consensus genomes across the globe at low prevalence. In one patient, we saw rapid emergence of various low-level deletion variants at the N-terminal domain of the spike glycoprotein, some of which have previously been shown to be associated with reduced neutralization potency from sera. In a subset of samples that were sequenced using metagenomic methods, differential gene expression analysis showed a downregulation of cytoskeletal genes that was consistent with a loss of ciliated epithelium during infection and recovery. We also identified co-occurrence of bacterial species in samples from multiple hospitalized individuals. These results demonstrate that the intrahost genetic composition of SARS-CoV-2 is dynamic during the course of COVID-19, and highlight the need for continued surveillance and deep sequencing of minor variants.


Subject(s)
COVID-19 , COVID-19/genetics , Genome, Viral , Humans , Metagenome , Metagenomics , SARS-CoV-2/genetics
2.
Commun Biol ; 5(1): 151, 2022 02 22.
Article in English | MEDLINE | ID: covidwho-1708032

ABSTRACT

A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit's taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases of Klebsiella pneumoniae and Neisseria gonorrhoeae infection, BugSplit's taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available at https://bugseq.com/academic .


Subject(s)
Algorithms , Bacteria/genetics , Computational Biology/methods , Metagenome/genetics , Metagenomics/methods , Nanopore Sequencing/methods , Bacteria/classification , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Humans , Internet , Pandemics/prevention & control , Reproducibility of Results , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/physiology
3.
Environ Int ; 161: 107146, 2022 03.
Article in English | MEDLINE | ID: covidwho-1689284

ABSTRACT

Microplastics (MPs) have been considered as a new vector for the long-distance transport of pathogens in aquatic ecosystems. However, the composition of viral communities attached on MPs and their environmental risk are largely unknown. Here, we profiled the viral diversity and potential risk in five different MPs collected from the Beilun River based on metagenomic analysis. Nearly 2863 million raw reads were produced and assembled, and annotation resulted in the identification of 1719 different species of viruses in MPs. Viruses in polypropylene (PP) displayed the highest diversity, with about 250 specific viruses detected. Source tracking of viruses in MPs by the fast expectation-maximization microbial source tracking method (FEAST) demonstrated that viruses in upstream and downstream MPs are two major sources of viruses in estuary. Furthermore, the MP-type-dependent potential environmental risk of viruses was significant based on both antibiotic resistance genes (ARGs) and virulence factors (VFs) detected in viral metagenomes, and PP was confirmed with the highest potential environmental risk. This study reveals the high diversity and potential environmental risk of viruses in different MPs, and provides an important guidance for future environmental monitoring and understanding the potential risks associated with both viral transmission and MPs pollution.


Subject(s)
Microplastics , Water Pollutants, Chemical , Ecosystem , Environmental Monitoring , Metagenome , Plastics , Rivers , Water Pollutants, Chemical/analysis , Water Pollutants, Chemical/toxicity
4.
Viruses ; 14(2)2022 01 28.
Article in English | MEDLINE | ID: covidwho-1662709

ABSTRACT

The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.


Subject(s)
Gastrointestinal Microbiome/genetics , Metagenome , Metagenomics/methods , Virome/genetics , Virus Diseases/drug therapy , Animals , COVID-19/therapy , Humans , Mice , Obesity/complications , SARS-CoV-2/genetics , Virus Diseases/therapy , Viruses/classification , Viruses/genetics
5.
Euro Surveill ; 26(27)2021 07.
Article in English | MEDLINE | ID: covidwho-1577032

ABSTRACT

BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.


Subject(s)
Cross Infection , Influenza, Human , Nanopores , Antiviral Agents/therapeutic use , Cross Infection/diagnosis , Cross Infection/drug therapy , Drug Resistance , Drug Resistance, Viral/genetics , Humans , Influenza A Virus, H3N2 Subtype/genetics , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Influenza, Human/epidemiology , Metagenome , Neuraminidase/genetics , Seasons , United Kingdom
6.
Front Cell Infect Microbiol ; 11: 706970, 2021.
Article in English | MEDLINE | ID: covidwho-1581382

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause gastrointestinal symptoms in the patients, but the role of gut microbiota in SARS-CoV-2 infection remains unclear. Thus, in this study, we aim to investigate whether SARS-CoV-2 infection affects the composition and function of gut microbiota. In this study, we demonstrated for the first time that significant shifts in microbiome composition and function were appeared in both SARS-CoV-2-infected asymptomatic and symptomatic cases. The relative abundance of Candidatus_Saccharibacteria was significantly increased, whereas the levels of Fibrobacteres was remarkably reduced in SARS-CoV-2-infected cases. There was one bacterial species, Spirochaetes displayed the difference between patients and asymptomatic cases. On the genus level, Tyzzerella was the key species that remarkably increased in both symptomatic and asymptomatic cases. Analyses of genome annotations further revealed SARS-CoV-2 infection resulted in the significant 'functional dysbiosis' of gut microbiota, including metabolic pathway, regulatory pathway and biosynthesis of secondary metabolites etc. We also identified potential metagenomic markers to discriminate SARS-CoV-2-infected symptomatic and asymptomatic cases from healthy controls. These findings together suggest gut microbiota is of possible etiological and diagnostic importance for SARS-CoV-2 infection.


Subject(s)
COVID-19 , Dysbiosis , Humans , Metagenome , Metagenomics , SARS-CoV-2
7.
Adv Sci (Weinh) ; 8(23): e2102593, 2021 12.
Article in English | MEDLINE | ID: covidwho-1559092

ABSTRACT

Fast and accurate identification of microbial pathogens is critical for the proper treatment of infections. Traditional culture-based diagnosis in clinics is increasingly supplemented by metagenomic next-generation-sequencing (mNGS). Here, RNA/cDNA-targeted sequencing (meta-transcriptomics using NGS (mtNGS)) is established to reduce the host nucleotide percentage in clinic samples and by combining with Oxford Nanopore Technology (ONT) platforms (meta-transcriptomics using third-generation sequencing, mtTGS) to improve the sequencing time. It shows that mtNGS improves the ratio of microbial reads, facilitates bacterial identification using multiple-strategies, and discovers fungi, viruses, and antibiotic resistance genes, and displaying agreement with clinical findings. Furthermore, longer reads in mtTGS lead to additional improvement in pathogen identification and also accelerate the clinical diagnosis. Additionally, primary tests utilizing direct-RNA sequencing and targeted sequencing of ONT show that ONT displays important potential but must be further developed. This study presents the potential of RNA-targeted pathogen identification in clinical samples, especially when combined with the newest developments in ONT.


Subject(s)
Bronchoalveolar Lavage Fluid/microbiology , High-Throughput Nucleotide Sequencing/methods , Infections/genetics , Metagenomics/methods , RNA/genetics , Sequence Analysis, RNA/methods , Aged , Bronchoalveolar Lavage/methods , Female , Humans , Male , Metagenome/genetics , Middle Aged
9.
Viruses ; 13(11)2021 10 26.
Article in English | MEDLINE | ID: covidwho-1526862

ABSTRACT

Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover-as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.


Subject(s)
Microalgae/virology , Phylogeny , Ponds , RNA Viruses/classification , Water Microbiology , Animals , Biodiversity , Biomass , Metagenome , Pilot Projects , RNA Viruses/genetics , Rotifera/virology , Seasons , Water
10.
NPJ Biofilms Microbiomes ; 7(1): 81, 2021 11 18.
Article in English | MEDLINE | ID: covidwho-1526078

ABSTRACT

The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.


Subject(s)
Microbiota/genetics , Saliva/microbiology , Adult , Bacteria/genetics , COVID-19/genetics , DNA/genetics , DNA, Bacterial/genetics , Female , Humans , Male , Metagenome/genetics , Metagenomics/methods , Middle Aged , RNA, Ribosomal, 16S/genetics , SARS-CoV-2/pathogenicity , Sequence Analysis, DNA/methods
11.
PLoS One ; 16(11): e0259712, 2021.
Article in English | MEDLINE | ID: covidwho-1523436

ABSTRACT

OBJECTIVES: The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification (SISPA) for the detection and characterization of SARS-CoV-2. METHODS: We performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies. RESULTS: Our assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-complete genomes from 20 specimens that were classified as positive by mNGS. Phylogenetic analysis revealed that 10/11 specimens from British Columbia had a closest relative to another British Columbian specimen. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern (VOC) PCR results. Our assay was able to distinguish between the Alpha and Gamma variants, which was not possible with the current standard VOC PCR being used in British Columbia. CONCLUSIONS: This study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.


Subject(s)
COVID-19/diagnosis , Metagenome , Nanopore Sequencing/methods , Pandemics , SARS-CoV-2/isolation & purification , Humans , Sensitivity and Specificity
12.
Int J Mol Sci ; 22(19)2021 Oct 05.
Article in English | MEDLINE | ID: covidwho-1463710

ABSTRACT

The present Special Issue focuses on the latest approaches to health and public health microbiology using multiomics [...].


Subject(s)
Bacteria/growth & development , Holistic Health/standards , Metabolome , Metagenome , Microbiota , Proteome , Public Health/standards , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Humans
13.
Viruses ; 13(10)2021 10 06.
Article in English | MEDLINE | ID: covidwho-1460085

ABSTRACT

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.


Subject(s)
Alphacoronavirus/isolation & purification , Betacoronavirus/isolation & purification , Chiroptera/virology , Genome, Viral/genetics , Metagenome/genetics , Alphacoronavirus/classification , Alphacoronavirus/genetics , Animals , Betacoronavirus/classification , Betacoronavirus/genetics , Chiroptera/genetics , Computational Biology/methods , Feces/virology , High-Throughput Nucleotide Sequencing , Metagenomics/methods , Moscow , Phycodnaviridae/classification , Phycodnaviridae/genetics , Phycodnaviridae/isolation & purification , Sequence Analysis, DNA
14.
Expert Rev Mol Diagn ; 21(11): 1139-1146, 2021 11.
Article in English | MEDLINE | ID: covidwho-1450340

ABSTRACT

INTRODUCTION: Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. AREAS COVERED: This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. EXPERT OPINION: The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.


Subject(s)
Genome, Viral/genetics , Meningoencephalitis/diagnosis , Meningoencephalitis/virology , Metagenome/genetics , Diagnostic Tests, Routine , Humans , Metagenomics/methods
15.
Infect Genet Evol ; 93: 104939, 2021 09.
Article in English | MEDLINE | ID: covidwho-1373189

ABSTRACT

The rise in human adenovirus (HAdV) infections poses a serious challenge to public health in China. Real-time (RT) sequencing provides solutions for achieving rapid pathogen identification during outbreaks, whereas high-throughput sequencing yields higher sequence accuracy. In the present study, we report the outcomes of applying nanopore and BGI platforms in the identification and genomic analysis of an HAdV outbreak in Hubei province, China in May of 2019. A mixed sample of nine nasopharyngeal swabs and one single sample were submitted to direct nanopore sequencing (MinION device), generating their first HAdV-55 reads within 13 and 20 min, respectively. The sequences were confirmed by RT-polymerase chain reaction (PCR). Ten HAdV-positive samples were further sequenced using next-generation high-throughput sequencing (BGISEQ-500 device). Phylogenetic analysis revealed that the outbreak strain had a close genetic relation to strains isolated in Sichuan province. Metagenomic analysis showed that HAdV-55 was not a dominant species in samples from which the whole HAdV-55 genome could not be assembled. The present results highlight the value of combining sequencing platforms and using mixed samples for nucleic acid enrichment in pathogen detection of infectious disease outbreaks.


Subject(s)
Adenovirus Infections, Human/diagnosis , Adenoviruses, Human/isolation & purification , Metagenome , Adenovirus Infections, Human/epidemiology , Adenovirus Infections, Human/virology , Adenoviruses, Human/genetics , China/epidemiology , Disease Outbreaks , High-Throughput Nucleotide Sequencing , Metagenomics , Phylogeny , Real-Time Polymerase Chain Reaction
17.
Microbiome ; 9(1): 130, 2021 06 05.
Article in English | MEDLINE | ID: covidwho-1257969

ABSTRACT

BACKGROUND: Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. METHODS: Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. RESULTS: LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. CONCLUSIONS: The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics. Video abstract.


Subject(s)
High-Throughput Nucleotide Sequencing , Microbiota , Metagenome , Microbiota/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
19.
Emerg Microbes Infect ; 10(1): 1418-1428, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1284839

ABSTRACT

Chlamydia psittaci infection in humans, also known as psittacosis, is usually believed to be an uncommon disease which mainly presents as community-acquired pneumonia (CAP). It is usually sporadic, but outbreaks of infection may occasionally occur. In outbreaks, diagnosis and investigations were usually hampered by the non-specificity of laboratory testing methods to identify C. psittaci. In this study, we use metagenomic next-generation sequencing (mNGS) in the diagnosis of a family outbreak of psittacosis under COVID-19. Three members of an extended family of 6 persons developed psittacosis with pneumonia and hepatic involvement with common symptoms of fever and weakness. Two newly purchased pet parrots, which had died successively, were probably the primary source of infection. Imagings show lung consolidations and infiltrates, which are difficult to be differentiated from CAP caused by other common pathogens. mNGS rapidly identified the infecting agent as C. psittaci within 48 h. The results of this work suggest that there are not characteristic clinical manifestations and imagings of psittacosis pneumonia which can differentiate from CAP caused by other pathogens. The use of mNGS can improve accuracy and reduce the delay in the diagnosis of psittacosis especially during the outbreak, which can shorten the course of the disease control. Family outbreak under COVID-19 may be related to the familial aggregation due to the epidemic. To our knowledge, this is the first reported family outbreak of psittacosis in China, and the first reported psittacosis outbreak identified by the method of mNGS in the world.


Subject(s)
Chlamydophila psittaci/genetics , Family , High-Throughput Nucleotide Sequencing , Metagenomics , Pneumonia/microbiology , Psittacosis/diagnostic imaging , Adult , Aged , Animals , COVID-19/epidemiology , China/epidemiology , Chlamydophila psittaci/isolation & purification , Disease Outbreaks , Female , Humans , Male , Metagenome , Middle Aged , Parrots/microbiology , Pneumonia/diagnostic imaging , Psittacosis/microbiology , Psittacosis/transmission , Retrospective Studies , Tomography, X-Ray Computed
20.
Sci Total Environ ; 793: 148494, 2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1284513

ABSTRACT

The ongoing COVID-19 pandemic has not only globally caused a high number of causalities, but is also an unprecedented challenge for scientists. False-positive virus detection tests not only aggravate the situation in the healthcare sector, but also provide ground for speculations. Previous studies have highlighted the importance of software choice and data interpretation in virome studies. We aimed to further expand theoretical and practical knowledge in bioinformatics-driven virome studies by focusing on short, virus-like DNA sequences in metagenomic data. Analyses of datasets obtained from different sample types (terrestrial, animal and human related samples) and origins showed that coronavirus-like sequences have existed in host-associated and environmental samples before the current COVID-19 pandemic. In the analyzed datasets, various Betacoronavirus-like sequences were detected that also included SARS-CoV-2 matches. Deepening analyses indicated that the detected sequences are not of viral origin and thus should not be considered in virome profiling approaches. Our study confirms the importance of parameter selection, especially in terms of read length, for reliable virome profiling. Natural environments are an important source of coronavirus-like nucleotide sequences that should be taken into account when virome datasets are analyzed and interpreted. We therefore suggest that processing parameters are carefully selected for SARS-CoV-2 profiling in host related as well as environmental samples in order to avoid incorrect identifications.


Subject(s)
COVID-19 , Pandemics , Animals , Humans , Metagenome , Metagenomics , SARS-CoV-2
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