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Article ; Online: Benchmarking Metagenomics Tools for Taxonomic Classification.

Ye, Simon H / Siddle, Katherine J / Park, Daniel J / Sabeti, Pardis C

2019 Volume 178, Issue 4, Page(s) 779–794

Abstract: Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the ... ...

Abstract	Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Benchmarking/methods ; Databases, Genetic ; Fungi/classification ; Fungi/genetics ; Metagenome/genetics ; Metagenomics/methods ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Software ; Viruses/classification ; Viruses/genetics
Language	English
Publishing date	2019-08-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2019.07.010
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Article ; Online: High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection.

Normandin, Erica / Rudy, Melissa / Barkas, Nikolaos / Schaffner, Stephen F / Levine, Zoe / Padera, Robert F / Babadi, Mehrtash / Mukerji, Shibani S / Park, Daniel J / MacInnis, Bronwyn L / Siddle, Katherine J / Sabeti, Pardis C / Solomon, Isaac H

Nature communications

2023 Volume 14, Issue 1, Page(s) 574

Abstract: SARS-CoV-2 distribution and circulation dynamics are not well understood due to challenges in assessing genomic data from tissue samples. We develop experimental and computational workflows for high-depth viral sequencing and high-resolution genomic ... ...

Abstract	SARS-CoV-2 distribution and circulation dynamics are not well understood due to challenges in assessing genomic data from tissue samples. We develop experimental and computational workflows for high-depth viral sequencing and high-resolution genomic analyses from formalin-fixed, paraffin-embedded tissues and apply them to 120 specimens from six subjects with fatal COVID-19. To varying degrees, viral RNA is present in extrapulmonary tissues from all subjects. The majority of the 180 viral variants identified within subjects are unique to individual tissue samples. We find more high-frequency (>10%) minor variants in subjects with a longer disease course, with one subject harboring ten such variants, exclusively in extrapulmonary tissues. One tissue-specific high-frequency variant was a nonsynonymous mutation in the furin-cleavage site of the spike protein. Our findings suggest adaptation and/or compartmentalized infection, illuminating the basis of extrapulmonary COVID-19 symptoms and potential for viral reservoirs, and have broad utility for investigating human pathogens.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Mutation ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2023-02-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-34256-y
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Article ; Online: Viral Lineages in the 2022 RSV Surge in the United States.

The New England journal of medicine

2023 Volume 388, Issue 14, Page(s) 1335–1337

MeSH term(s)	Humans ; Infant ; Respiratory Syncytial Virus Infections/epidemiology ; Respiratory Syncytial Virus Infections/genetics ; Respiratory Syncytial Virus Infections/virology ; Seasons ; United States/epidemiology ; Disease Outbreaks ; Respiratory Syncytial Viruses/genetics
Language	English
Publishing date	2023-02-22
Publishing country	United States
Document type	Letter
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc2216153
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Article ; Online: Neuropathological features of SARS-CoV-2 delta and omicron variants.

Normandin, Erica / Valizadeh, Navid / Rudmann, Emily A / Uddin, Rockib / Dobbins, Sabrina T / MacInnis, Bronwyn L / Padera, Robert F / Siddle, Katherine J / Lemieux, Jacob E / Sabeti, Pardis C / Mukerji, Shibani S / Solomon, Isaac H

Journal of neuropathology and experimental neurology

2023 Volume 82, Issue 4, Page(s) 283–295

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continually evolving resulting in variants with increased transmissibility, more severe disease, reduced effectiveness of treatments or vaccines, or diagnostic detection failure. The SARS- ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continually evolving resulting in variants with increased transmissibility, more severe disease, reduced effectiveness of treatments or vaccines, or diagnostic detection failure. The SARS-CoV-2 Delta variant (B.1.617.2 and AY lineages) was the dominant circulating strain in the United States from July to mid-December 2021, followed by the Omicron variant (B.1.1.529 and BA lineages). Coronavirus disease 2019 (COVID-19) has been associated with neurological sequelae including loss of taste/smell, headache, encephalopathy, and stroke, yet little is known about the impact of viral strain on neuropathogenesis. Detailed postmortem brain evaluations were performed for 22 patients from Massachusetts, including 12 who died following infection with Delta variant and 5 with Omicron variant, compared to 5 patients who died earlier in the pandemic. Diffuse hypoxic injury, occasional microinfarcts and hemorrhage, perivascular fibrinogen, and rare lymphocytes were observed across the 3 groups. SARS-CoV-2 protein and RNA were not detected in any brain samples by immunohistochemistry, in situ hybridization, or real-time quantitative PCR. These results, although preliminary, demonstrate that, among a subset of severely ill patients, similar neuropathological features are present in Delta, Omicron, and non-Delta/non-Omicron variant patients, suggesting that SARS-CoV-2 variants are likely to affect the brain by common neuropathogenic mechanisms.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Neuropathology ; Stroke
Language	English
Publishing date	2023-02-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	3088-0
ISSN	1554-6578 ; 0022-3069
ISSN (online)	1554-6578
ISSN	0022-3069
DOI	10.1093/jnen/nlad015
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Article ; Online: Population variation in miRNAs and isomiRs and their impact on human immunity to infection.

Rotival, Maxime / Siddle, Katherine J / Silvert, Martin / Pothlichet, Julien / Quach, Hélène / Quintana-Murci, Lluis

Genome biology

2020 Volume 21, Issue 1, Page(s) 187

Abstract: Background: MicroRNAs (miRNAs) are key regulators of the immune system, yet their variation and contribution to intra- and inter-population differences in immune responses is poorly characterized.: Results: We generate 977 miRNA-sequencing profiles ... ...

Abstract	Background: MicroRNAs (miRNAs) are key regulators of the immune system, yet their variation and contribution to intra- and inter-population differences in immune responses is poorly characterized. Results: We generate 977 miRNA-sequencing profiles from primary monocytes from individuals of African and European ancestry following activation of three TLR pathways (TLR4, TLR1/2, and TLR7/8) or infection with influenza A virus. We find that immune activation leads to important modifications in the miRNA and isomiR repertoire, particularly in response to viral challenges. These changes are much weaker than those observed for protein-coding genes, suggesting stronger selective constraints on the miRNA response to stimulation. This is supported by the limited genetic control of miRNA expression variability (miR-QTLs) and the lower occurrence of gene-environment interactions, in stark contrast with eQTLs that are largely context-dependent. We also detect marked differences in miRNA expression between populations, which are mostly driven by non-genetic factors. On average, miR-QTLs explain approximately 60% of population differences in expression of their cognate miRNAs and, in some cases, evolve adaptively, as shown in Europeans for a miRNA-rich cluster on chromosome 14. Finally, integrating miRNA and mRNA data from the same individuals, we provide evidence that the canonical model of miRNA-driven transcript degradation has a minor impact on miRNA-mRNA correlations, which are, in our setting, mainly driven by co-transcription. Conclusion: Together, our results shed new light onto the factors driving miRNA and isomiR diversity at the population level and constitute a useful resource for evaluating their role in host differences of immunity to infection.
MeSH term(s)	Black People ; Genome, Human ; Humans ; Immunity ; Infections/immunology ; Infections/metabolism ; MicroRNAs/immunology ; MicroRNAs/metabolism ; Monocytes/metabolism ; Quantitative Trait Loci ; RNA Isoforms/immunology ; RNA Isoforms/metabolism ; White People
Chemical Substances	MicroRNAs ; RNA Isoforms
Language	English
Publishing date	2020-07-30
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-020-02098-w
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Article ; Online: Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing.

Nature communications

2024 Volume 15, Issue 1, Page(s) 747

Abstract: The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical ... ...

Abstract	The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
MeSH term(s)	Humans ; Senegal/epidemiology ; Cross-Sectional Studies ; Malaria/diagnosis ; Malaria/epidemiology ; Plasmodium ; Fever/epidemiology ; Borrelia/genetics
Language	English
Publishing date	2024-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-44800-7
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Article: The 2022 RSV surge was driven by multiple viral lineages.

medRxiv : the preprint server for health sciences

2023

Abstract: The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether viral ... ...

Abstract	The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether viral characteristics contributed to the extent or severity of the surge, we sequenced 105 RSV-positive specimens from symptomatic patients diagnosed with RSV who presented to the Massachusetts General Hospital (MGH) and its outpatient practices in the Greater Boston Area. Genomic analysis of the resulting 77 genomes (54 with >80% coverage, and 23 with >5% coverage) demonstrated that the surge was driven by multiple lineages of RSV-A (91%; 70/77) and RSV-B (9%; 7/77). Phylogenetic analysis of all US RSV-A revealed 12 clades, 4 of which contained Massachusetts and Washington genomes. These clades individually had times to most recent common ancestor (tMRCA) between 2014 and 2017, and together had a tMRCA of 2009, suggesting that they emerged well before the COVID-19 pandemic. Similarly, the RSV-B genomes had a tMRCA between 2016 and 2019. We found that the RSV-A and RSV-B genomes in our sample did not differ statistically from the estimated clock rate of the larger phylogenetic tree (10.6 and 12.4 substitutions per year, respectively). In summary, the polyphyletic nature of viral genomes sequenced in the US during the autumn 2022 surge is inconsistent with the emergence of a single, highly transmissible causal RSV lineage.
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.04.23284195
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Article ; Online: Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques.

Santus, Luisa / Sopena-Rios, Maria / García-Pérez, Raquel / Lin, Aaron E / Adams, Gordon C / Barnes, Kayla G / Siddle, Katherine J / Wohl, Shirlee / Reverter, Ferran / Rinn, John L / Bennett, Richard S / Hensley, Lisa E / Sabeti, Pardis C / Melé, Marta

Nature communications

2023 Volume 14, Issue 1, Page(s) 3866

Abstract: Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from ... ...

Abstract	Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies.
MeSH term(s)	Animals ; Hemorrhagic Fever, Ebola/genetics ; RNA, Long Noncoding/genetics ; Macaca mulatta ; Ebolavirus/genetics ; Virus Internalization
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2023-06-30
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39627-7
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Article ; Online: Population variation in miRNAs and isomiRs and their impact on human immunity to infection

Maxime Rotival / Katherine J. Siddle / Martin Silvert / Julien Pothlichet / Hélène Quach / Lluis Quintana-Murci

Genome Biology, Vol 21, Iss 1, Pp 1-

2020 Volume 31

Abstract: Abstract Background MicroRNAs (miRNAs) are key regulators of the immune system, yet their variation and contribution to intra- and inter-population differences in immune responses is poorly characterized. Results We generate 977 miRNA-sequencing profiles ...

Abstract	Abstract Background MicroRNAs (miRNAs) are key regulators of the immune system, yet their variation and contribution to intra- and inter-population differences in immune responses is poorly characterized. Results We generate 977 miRNA-sequencing profiles from primary monocytes from individuals of African and European ancestry following activation of three TLR pathways (TLR4, TLR1/2, and TLR7/8) or infection with influenza A virus. We find that immune activation leads to important modifications in the miRNA and isomiR repertoire, particularly in response to viral challenges. These changes are much weaker than those observed for protein-coding genes, suggesting stronger selective constraints on the miRNA response to stimulation. This is supported by the limited genetic control of miRNA expression variability (miR-QTLs) and the lower occurrence of gene-environment interactions, in stark contrast with eQTLs that are largely context-dependent. We also detect marked differences in miRNA expression between populations, which are mostly driven by non-genetic factors. On average, miR-QTLs explain approximately 60% of population differences in expression of their cognate miRNAs and, in some cases, evolve adaptively, as shown in Europeans for a miRNA-rich cluster on chromosome 14. Finally, integrating miRNA and mRNA data from the same individuals, we provide evidence that the canonical model of miRNA-driven transcript degradation has a minor impact on miRNA-mRNA correlations, which are, in our setting, mainly driven by co-transcription. Conclusion Together, our results shed new light onto the factors driving miRNA and isomiR diversity at the population level and constitute a useful resource for evaluating their role in host differences of immunity to infection.
Keywords	miRNAs ; Isoforms ; Population ; miR-QTLs ; Immunity ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Subject code	570
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection

Erica Normandin / Melissa Rudy / Nikolaos Barkas / Stephen F. Schaffner / Zoe Levine / Robert F. Padera / Mehrtash Babadi / Shibani S. Mukerji / Daniel J. Park / Bronwyn L. MacInnis / Katherine J. Siddle / Pardis C. Sabeti / Isaac H. Solomon

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 12

Abstract: Here, by high-resolution SARS-CoV-2 sequencing, genomic and transcriptomic analyses from tissue samples, Normandin et al. investigate viral dynamics in fatal cases of COVID-19, revealing persistent infection in distinct anatomical sites, including the ... ...

Abstract	Here, by high-resolution SARS-CoV-2 sequencing, genomic and transcriptomic analyses from tissue samples, Normandin et al. investigate viral dynamics in fatal cases of COVID-19, revealing persistent infection in distinct anatomical sites, including the heart and testis.
Keywords	Science ; Q
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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