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Supplementary material 2 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245

Kavanaugh, David H. ; Maddison, David R. ; Simison, W. Brian ; [et al.]

Pensoft Publishers ; 2021

In: ZooKeys Vol. 1044 ( 2021-06-16), p. 41-152

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In: ZooKeys, Pensoft Publishers, Vol. 1044 ( 2021-06-16), p. 41-152

Abstract: The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK, and wingless ), and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI (“barcode” region) and COI (“Pat/Jer” region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted genera and subgenera (all except Notiokasis and Archileistobrius ), and eight outgroup taxa. Separate maximum likelihood (ML) analyses of individual genes, combined ML analyses of nuclear, nuclear protein-coding, and mitochondrial genes, and combined ML and Bayesian analyses of the eight-gene-fragment matrix resulted in a well-resolved phylogeny of the supertribe, with most nodes in the tree strongly supported. Within Nebriitae, 167 internal nodes of the tree (out of the maximum possible 255) are supported by maximum-likelihood bootstrap values of 90% or more. The tribes Notiophilini, Opisthiini, Pelophilini, and Nebriini are well supported as monophyletic but relationships among these are not well resolved. Nippononebria is a distinct genus more closely related to Leistus than Nebria . Archastes , Oreonebria , Spelaeonebria , and Eurynebria , previously treated as distinct genera by some authors, are all nested within a monophyletic genus Nebria. Within Nebria , four major clades are recognized: (1) the Oreonebria Series, including eight subgenera arrayed in two subgeneric complexes (the Eonebria and Oreonebria Complexes); (2) the Nebriola Series, including only subgenus Nebriola; (3) the Nebria Series, including ten subgenera arrayed in two subgeneric complexes, the Boreonebria and Nebria Complexes, with the latter further subdivided into three subgeneric subcomplexes (the Nebria , Epinebriola , and Eunebria Subcomplexes)); and (4) the Catonebria Series, including seven subgenera arrayed in two subgeneric complexes (the Reductonebria and Catonebria Complexes). A strong concordance of biogeography with the inferred phylogeny is noted and some evident vicariance patterns are highlighted. A revised classification, mainly within the Nebriini, is proposed to reflect the inferred phylogeny. Three genus-group taxa ( Nippononebria , Vancouveria and Archastes ) are given revised status and seven are recognized as new synonymies ( Nebriorites Jeannel, 1941 and Marggia Huber, 2014 = Oreonebria Daniel, 1903; Pseudonebriola Ledoux & amp; Roux, 1989 = Boreonebria Jeannel, 1937; Patrobonebria Bänninger, 1923, Paranebria Jeannel, 1937 and Barbonebriola Huber & amp; Schmidt, 2017 = Epinebriola Daniel & amp; Daniel, 1904; and Asionebria Shilenkov, 1982 = Psilonebria Andrewes, 1923). Six new subgenera are proposed and described for newly recognized clades: Parepinebriola Kavanaugh subgen. nov. (type species: Nebria delicata Huber & amp; Schmidt, 2017), Insulanebria Kavanaugh subgen. nov. (type species: Nebria carbonaria Eschscholtz, 1829), Erwinebria Kavanaugh subgen. nov. (type species Nebria sahlbergii Fischer von Waldheim, 1828), Nivalonebria Kavanaugh subgen. nov. (type species: Nebria paradisi Darlington, 1931), Neaptenonebria Kavanaugh subgen. nov. (type species: Nebria ovipennis LeConte, 1878), and Palaptenonebria Kavanaugh subgen. nov. (type species: Nebria mellyi Gebler, 1847). Future efforts to better understand relationships within the supertribe should aim to expand the taxon sampling of DNA sequence data, particularly within subgenera Leistus and Evanoleist us of genus Leistus and the Nebria Complex of genus Nebria .

Type of Medium: Online Resource

ISSN: 1313-2970 , 1313-2989

URL: Article

DOI: 10.3897/zookeys.1044.62245

DOI: 10.3897/zookeys.1044.62245.figure1

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DOI: 10.3897/zookeys.1044.62245.chart1

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DOI: 10.3897/zookeys.1044.62245.figure4

DOI: 10.3897/zookeys.1044.62245.figure411

DOI: 10.3897/zookeys.1044.62245.suppl1

DOI: 10.3897/zookeys.1044.62245.suppl2

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2021

detail.hit.zdb_id: 2445640-8

SSG: 12

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A highly virulent variant of HIV-1 circulating in the Netherlands

Wymant, Chris ; Bezemer, Daniela ; Blanquart, François ; [et al.]

American Association for the Advancement of Science (AAAS) ; 2022

In: Science Vol. 375, No. 6580 ( 2022-02-04), p. 540-545

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In: Science, American Association for the Advancement of Science (AAAS), Vol. 375, No. 6580 ( 2022-02-04), p. 540-545

Abstract: A cluster of HIV-infected individuals with high viral loads, rapid CD4 + cell declines, and increased infectivity has been detected in Europe.

Type of Medium: Online Resource

ISSN: 0036-8075 , 1095-9203

URL: Article

DOI: 10.1126/science.abk1688

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: American Association for the Advancement of Science (AAAS)

Publication Date: 2022

detail.hit.zdb_id: 128410-1

detail.hit.zdb_id: 2066996-3

detail.hit.zdb_id: 2060783-0

SSG: 11

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Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Matuozzo, Daniela ; Talouarn, Estelle ; Marchal, Astrid ; [et al.]

Springer Science and Business Media LLC ; 2023

In: Genome Medicine Vol. 15, No. 1 ( 2023-04-05)

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In: Genome Medicine, Springer Science and Business Media LLC, Vol. 15, No. 1 ( 2023-04-05)

Abstract: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. Methods We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Results No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7 , with an OR of 27.68 (95%CI 1.5–528.7, P = 1.1 × 10 −4 ) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], P = 2.1 × 10 −4 ). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 3.4 × 10 −3 ), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], P = 7.7 × 10 −8 ). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10 −5 ). Conclusions Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.

Type of Medium: Online Resource

ISSN: 1756-994X

URL: Article

DOI: 10.1186/s13073-023-01173-8

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2023

detail.hit.zdb_id: 2484394-5

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A second update on mapping the human genetic architecture of COVID-19

The COVID-19 Host Genetics Initiative ; Kanai, Masahiro ; Andrews, Shea J. ; [et al.]

Springer Science and Business Media LLC ; 2023

In: Nature Vol. 621, No. 7977 ( 2023-09-07), p. E7-E26

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In: Nature, Springer Science and Business Media LLC, Vol. 621, No. 7977 ( 2023-09-07), p. E7-E26

Type of Medium: Online Resource

ISSN: 0028-0836 , 1476-4687

URL: Article

DOI: 10.1038/s41586-023-06355-3

RVK:

TA 1000

RVK:

UA 1000

RVK:

WA 15000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2023

detail.hit.zdb_id: 120714-3

detail.hit.zdb_id: 1413423-8

SSG: 11

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Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths

Bastard, Paul ; Gervais, Adrian ; Le Voyer, Tom ; [et al.]

American Association for the Advancement of Science (AAAS) ; 2021

In: Science Immunology Vol. 6, No. 62 ( 2021-08-10)

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In: Science Immunology, American Association for the Advancement of Science (AAAS), Vol. 6, No. 62 ( 2021-08-10)

Abstract: Circulating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/ml; in plasma diluted 1:10) of IFN-α and/or IFN-ω are found in about 10% of patients with critical COVID-19 (coronavirus disease 2019) pneumonia but not in individuals with asymptomatic infections. We detect auto-Abs neutralizing 100-fold lower, more physiological, concentrations of IFN-α and/or IFN-ω (100 pg/ml; in 1:10 dilutions of plasma) in 13.6% of 3595 patients with critical COVID-19, including 21% of 374 patients 〉 80 years, and 6.5% of 522 patients with severe COVID-19. These antibodies are also detected in 18% of the 1124 deceased patients (aged 20 days to 99 years; mean: 70 years). Moreover, another 1.3% of patients with critical COVID-19 and 0.9% of the deceased patients have auto-Abs neutralizing high concentrations of IFN-β. We also show, in a sample of 34,159 uninfected individuals from the general population, that auto-Abs neutralizing high concentrations of IFN-α and/or IFN-ω are present in 0.18% of individuals between 18 and 69 years, 1.1% between 70 and 79 years, and 3.4% 〉 80 years. Moreover, the proportion of individuals carrying auto-Abs neutralizing lower concentrations is greater in a subsample of 10,778 uninfected individuals: 1% of individuals 〈 70 years, 2.3% between 70 and 80 years, and 6.3% 〉 80 years. By contrast, auto-Abs neutralizing IFN-β do not become more frequent with age. Auto-Abs neutralizing type I IFNs predate SARS-CoV-2 infection and sharply increase in prevalence after the age of 70 years. They account for about 20% of both critical COVID-19 cases in the over 80s and total fatal COVID-19 cases.

Type of Medium: Online Resource

ISSN: 2470-9468

URL: Article

DOI: 10.1126/sciimmunol.abl4340

Language: English

Publisher: American Association for the Advancement of Science (AAAS)

Publication Date: 2021

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The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies

Manry, Jérémy ; Bastard, Paul ; Gervais, Adrian ; [et al.]

Proceedings of the National Academy of Sciences ; 2022

In: Proceedings of the National Academy of Sciences Vol. 119, No. 21 ( 2022-05-24)

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 21 ( 2022-05-24)

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection fatality rate (IFR) doubles with every 5 y of age from childhood onward. Circulating autoantibodies neutralizing IFN-α, IFN-ω, and/or IFN-β are found in ∼20% of deceased patients across age groups, and in ∼1% of individuals aged 〈 70 y and in 〉 4% of those 〉 70 y old in the general population. With a sample of 1,261 unvaccinated deceased patients and 34,159 individuals of the general population sampled before the pandemic, we estimated both IFR and relative risk of death (RRD) across age groups for individuals carrying autoantibodies neutralizing type I IFNs, relative to noncarriers. The RRD associated with any combination of autoantibodies was higher in subjects under 70 y old. For autoantibodies neutralizing IFN-α2 or IFN-ω, the RRDs were 17.0 (95% CI: 11.7 to 24.7) and 5.8 (4.5 to 7.4) for individuals 〈 70 y and ≥70 y old, respectively, whereas, for autoantibodies neutralizing both molecules, the RRDs were 188.3 (44.8 to 774.4) and 7.2 (5.0 to 10.3), respectively. In contrast, IFRs increased with age, ranging from 0.17% (0.12 to 0.31) for individuals 〈 40 y old to 26.7% (20.3 to 35.2) for those ≥80 y old for autoantibodies neutralizing IFN-α2 or IFN-ω, and from 0.84% (0.31 to 8.28) to 40.5% (27.82 to 61.20) for autoantibodies neutralizing both. Autoantibodies against type I IFNs increase IFRs, and are associated with high RRDs, especially when neutralizing both IFN-α2 and IFN-ω. Remarkably, IFRs increase with age, whereas RRDs decrease with age. Autoimmunity to type I IFNs is a strong and common predictor of COVID-19 death.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.2200413119

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2022

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Benefits and risks of noninvasive oxygenation strategy in COVID-19: a multicenter, prospective cohort study (COVID-ICU) in 137 hospitals

COVID-ICU group, for the REVA network, COVID-ICU investigators ; Schmidt, Matthieu ; Demoule, Alexandre ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Critical Care Vol. 25, No. 1 ( 2021-12)

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In: Critical Care, Springer Science and Business Media LLC, Vol. 25, No. 1 ( 2021-12)

Abstract: To evaluate the respective impact of standard oxygen, high-flow nasal cannula (HFNC) and noninvasive ventilation (NIV) on oxygenation failure rate and mortality in COVID-19 patients admitted to intensive care units (ICUs). Methods Multicenter, prospective cohort study (COVID-ICU) in 137 hospitals in France, Belgium, and Switzerland. Demographic, clinical, respiratory support, oxygenation failure, and survival data were collected. Oxygenation failure was defined as either intubation or death in the ICU without intubation. Variables independently associated with oxygenation failure and Day-90 mortality were assessed using multivariate logistic regression. Results From February 25 to May 4, 2020, 4754 patients were admitted in ICU. Of these, 1491 patients were not intubated on the day of ICU admission and received standard oxygen therapy (51%), HFNC (38%), or NIV (11%) ( P 〈 0.001). Oxygenation failure occurred in 739 (50%) patients (678 intubation and 61 death). For standard oxygen, HFNC, and NIV, oxygenation failure rate was 49%, 48%, and 60% ( P 〈 0.001). By multivariate analysis, HFNC (odds ratio [OR] 0.60, 95% confidence interval [CI] 0.36–0.99, P = 0.013) but not NIV (OR 1.57, 95% CI 0.78–3.21) was associated with a reduction in oxygenation failure). Overall 90-day mortality was 21%. By multivariable analysis, HFNC was not associated with a change in mortality (OR 0.90, 95% CI 0.61–1.33), while NIV was associated with increased mortality (OR 2.75, 95% CI 1.79–4.21, P 〈 0.001). Conclusion In patients with COVID-19, HFNC was associated with a reduction in oxygenation failure without improvement in 90-day mortality, whereas NIV was associated with a higher mortality in these patients. Randomized controlled trials are needed.

Type of Medium: Online Resource

ISSN: 1364-8535

URL: Article

DOI: 10.1186/s13054-021-03784-2

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2051256-9

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Predicting 90-day survival of patients with COVID-19: Survival of Severely Ill COVID (SOSIC) scores

Schmidt, Matthieu ; Guidet, Bertrand ; Demoule, Alexandre ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Annals of Intensive Care Vol. 11, No. 1 ( 2021-12)

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In: Annals of Intensive Care, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-12)

Abstract: Predicting outcomes of critically ill intensive care unit (ICU) patients with coronavirus-19 disease (COVID-19) is a major challenge to avoid futile, and prolonged ICU stays. Methods The objective was to develop predictive survival models for patients with COVID-19 after 1-to-2 weeks in ICU. Based on the COVID–ICU cohort, which prospectively collected characteristics, management, and outcomes of critically ill patients with COVID-19. Machine learning was used to develop dynamic, clinically useful models able to predict 90-day mortality using ICU data collected on day (D) 1, D7 or D14. Results Survival of Severely Ill COVID (SOSIC)-1, SOSIC-7, and SOSIC-14 scores were constructed with 4244, 2877, and 1349 patients, respectively, randomly assigned to development or test datasets. The three models selected 15 ICU-entry variables recorded on D1, D7, or D14. Cardiovascular, renal, and pulmonary functions on prediction D7 or D14 were among the most heavily weighted inputs for both models. For the test dataset, SOSIC-7’s area under the ROC curve was slightly higher (0.80 [0.74–0.86]) than those for SOSIC-1 (0.76 [0.71–0.81] ) and SOSIC-14 (0.76 [0.68–0.83]). Similarly, SOSIC-1 and SOSIC-7 had excellent calibration curves, with similar Brier scores for the three models. Conclusion The SOSIC scores showed that entering 15 to 27 baseline and dynamic clinical parameters into an automatable XGBoost algorithm can potentially accurately predict the likely 90-day mortality post-ICU admission (sosic.shinyapps.io/shiny). Although external SOSIC-score validation is still needed, it is an additional tool to strengthen decisions about life-sustaining treatments and informing family members of likely prognosis.

Type of Medium: Online Resource

ISSN: 2110-5820

URL: Article

DOI: 10.1186/s13613-021-00956-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2617094-2

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Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome Associated with COVID-19: An Emulated Target Trial Analysis

Hajage, David ; Combes, Alain ; Guervilly, Christophe ; [et al.]

American Thoracic Society ; 2022

In: American Journal of Respiratory and Critical Care Medicine Vol. 206, No. 3 ( 2022-08-01), p. 281-294

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In: American Journal of Respiratory and Critical Care Medicine, American Thoracic Society, Vol. 206, No. 3 ( 2022-08-01), p. 281-294

Type of Medium: Online Resource

ISSN: 1073-449X , 1535-4970

URL: Article

DOI: 10.1164/rccm.202111-2495OC

RVK:

XA 21200

Language: English

Publisher: American Thoracic Society

Publication Date: 2022

detail.hit.zdb_id: 1468352-0

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X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19

Asano, Takaki ; Boisson, Bertrand ; Onodi, Fanny ; [et al.]

American Association for the Advancement of Science (AAAS) ; 2021

In: Science Immunology Vol. 6, No. 62 ( 2021-08-10)

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In: Science Immunology, American Association for the Advancement of Science (AAAS), Vol. 6, No. 62 ( 2021-08-10)

Abstract: Autosomal inborn errors of type I IFN immunity and autoantibodies against these cytokines underlie at least 10% of critical COVID-19 pneumonia cases. We report very rare, biochemically deleterious X-linked TLR7 variants in 16 unrelated male individuals aged 7 to 71 years (mean, 36.7 years) from a cohort of 1202 male patients aged 0.5 to 99 years (mean, 52.9 years) with unexplained critical COVID-19 pneumonia. None of the 331 asymptomatically or mildly infected male individuals aged 1.3 to 102 years (mean, 38.7 years) tested carry such TLR7 variants ( P = 3.5 × 10 −5 ). The phenotypes of five hemizygous relatives of index cases infected with SARS-CoV-2 include asymptomatic or mild infection ( n = 2) or moderate ( n = 1), severe ( n = 1), or critical ( n = 1) pneumonia. Two patients from a cohort of 262 male patients with severe COVID-19 pneumonia (mean, 51.0 years) are hemizygous for a deleterious TLR7 variant. The cumulative allele frequency for deleterious TLR7 variants in the male general population is 〈 6.5 × 10 −4 . We show that blood B cell lines and myeloid cell subsets from the patients do not respond to TLR7 stimulation, a phenotype rescued by wild-type TLR7 . The patients’ blood plasmacytoid dendritic cells (pDCs) produce low levels of type I IFNs in response to SARS-CoV-2. Overall, X-linked recessive TLR7 deficiency is a highly penetrant genetic etiology of critical COVID-19 pneumonia, in about 1.8% of male patients below the age of 60 years. Human TLR7 and pDCs are essential for protective type I IFN immunity against SARS-CoV-2 in the respiratory tract.

Type of Medium: Online Resource

ISSN: 2470-9468

URL: Article

DOI: 10.1126/sciimmunol.abl4348

Language: English

Publisher: American Association for the Advancement of Science (AAAS)

Publication Date: 2021

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