decreasing the levels of intracellular dNTPs 14,15 , which apparently compete with the 47 thymidine analog triphosphates for incorporation into HIV-1 cDNA during reverse 48 transcription 16 . We postulated that SAMHD1 could have a similar effect on nucleoside 49analog-based therapy in leukemia 6 . 50To investigate whether SAMHD1 expression enhances Ara-C cytotoxicity in AML 51 cells, we tested whether Ara-C sensitivity in 13 AML cell lines, determined by the half 52 maximal inhibitory concentration (IC 50 ), is correlated with SAMHD1 protein and mRNA 53 levels. Both SAMHD1 expression (Fig. 1a and Supplementary Fig. 1) and Ara-C sensitivity 54 (Supplementary Table 1) varied considerably among these cell lines. Unexpectedly, 55 SAMHD1 levels inversely correlated with Ara-C cytotoxicity (p=0.0037, Fig. 1b and 56 Supplementary Fig. 2a,b), as well as with the levels of early (Caspase 3 and 7 activity, 57 p=0.02, Supplementary Fig. 3a,b) and late (sub-G1 cells, apoptotic DNA fragmentation, 58 p=0.029, Supplementary Fig. 3c,d) markers of apoptosis. In contrast, no significant 59 correlation could be established between Ara-C IC 50 values and the expression of cellular 60 4 proteins previously implicated in Ara-C uptake or its conversion to Ara-CTP 1 , including 61 equilibrative nucleoside transporter (ENT1/SLC29A1), deoxycytidine kinase (DCK), cytidine 62 deaminase (CDA), deoxycytidilate deaminase (DCTD), or 5'-nucleotidase (NT5C2) (Fig. 63 1a,c-g). 64To further investigate its role in Ara-C resistance, we tested the effects of SAMHD1 65 deficiency by a number of approaches: (i) depletion of SAMHD1 in AML cell lines 66 expressing high endogenous SAMHD1 levels using either lentiviral vectors encoding 67 SAMHD1-specific shRNA or transfection with SAMHD1-specific siRNA; (ii) CRISPR/Cas9-68 mediated disruption of the SAMHD1 gene; and (iii) targeted degradation of SAMHD1 using 69 virus-like particles (VLPs) which shuttle the SAMHD1-interacting lentiviral Vpx protein 70 (Vpx-VLPs) into cells 7,8,17 (Fig. 2a and Supplementary Fig. 4). Vpx recruits SAMHD1 to a 71 cullin4A-RING E3 ubiquitin ligase (CRL4 DCAF1 ), which targets the enzyme for proteasomal 72 degradation 7,8 . 73SAMHD1 depletion in AML cell lines by RNA interference (OCI-AML3, THP-1), 74 SAMHD1 knockout (THP-1 -/-), or transduction with Vpx-VLPs (MonoMac6 cells, THP-1) 75 markedly sensitized AML cell lines to Ara-C toxicity relative to the respective controls (Fig. 76 2a,b and Supplementary Fig. 4). In contrast, SAMHD1 siRNA had only a marginal effect on 77 Ara-C toxicity in low SAMHD1-expressing HEL cells (Fig. 2a,b). Interestingly, we observed 78 SAMHD1 dependency, although less pronounced, for the purine analog fludarabine 79 ( Supplementary Fig. 5a); however, the IC 50 values for the topoisomerase II inhibitors 80 etoposide and daunorubicin, as well as for dFdC (2',2'-difluorodeoxycytidine; gemcitabine), 81were not consistently affected by SAMHD1 down-modulation ( Supplementary Fig. 5b-d), 82 indicating a certain degree of drug specificity. 83 5In HEL...

Since autumn 2020, rapid antigen tests (RATs) have been implemented in several countries as an important pillar of the national testing strategy to rapidly screen for infections on site during the SARS-CoV-2 pandemic. The current surge in infection rates around the globe is driven by the variant of concern (VoC) omicron (B.1.1.529). Here, we evaluated the performance of nine SARS-CoV-2 RATs in a single-centre laboratory study. We examined a total of 115 SARS-CoV-2 PCR-negative and 166 SARS-CoV-2 PCR-positive respiratory swab samples (101 omicron, 65 delta (B.1.617.2)) collected from October 2021 until January 2022 as well as cell culture-expanded clinical isolates of both VoCs. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 1.77 × 106 to 7.03 × 107 RNA copies subjected to the RAT for omicron compared to 1.32 × 105 to 2.05 × 106 for delta. To score positive in these point-of-care tests, up to 10-fold (LoD50) or 101-fold (LoD95) higher virus loads were required for omicron- compared to delta-containing samples. The rates of true positive test results for omicron samples in the highest virus load category (Ct values < 25) ranged between 31.4 and 77.8%, while they dropped to 0–8.3% for samples with intermediate Ct values (25–30). Of note, testing of expanded virus stocks suggested a comparable RAT sensitivity of both VoCs, questioning the predictive value of this type of in vitro-studies for clinical performance. Given their importance for national test strategies in the current omicron wave, awareness must be increased for the reduced detection rate of omicron infections by RATs and a short list of suitable RATs that fulfill the minimal requirements of performance should be rapidly disclosed.

DCs express intrinsic cellular defense mechanisms to specifically inhibit HIV-1 replication. Thus, DCs are productively infected only at very low levels with HIV-1, and this non-permissiveness of DCs is suggested to go along with viral evasion. We now illustrate that complement-opsonized HIV-1 (HIV-C) efficiently bypasses SAMHD1 restriction and productively infects DCs including BDCA-1 DCs. Efficient DC infection by HIV-C was also observed using single-cycle HIV-C, and correlated with a remarkable elevated SAMHD1 T592 phosphorylation but not SAMHD1 degradation. If SAMHD1 phosphorylation was blocked using a CDK2-inhibitor HIV-C-induced DC infection was also significantly abrogated. Additionally, we found a higher maturation and co-stimulatory potential, aberrant type I interferon expression and signaling as well as a stronger induction of cellular immune responses in HIV-C-treated DCs. Collectively, our data highlight a novel protective mechanism mediated by complement opsonization of HIV to effectively promote DC immune functions, which might be in the future exploited to tackle HIV infection.

No abstract

No abstract

A versatile portfolio of diagnostic tests is essential for the containment of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Besides nucleic acid-based test systems and point-of-care (POCT) antigen (Ag) tests, quantitative, laboratory-based nucleocapsid Ag tests for SARS-CoV-2 have recently been launched. Here, we evaluated four commercial Ag tests on automated platforms and one POCT to detect SARS-CoV-2. We evaluated PCR-positive (n = 107) and PCR-negative (n = 303) respiratory swabs from asymptomatic and symptomatic patients at the end of the second pandemic wave in Germany (February–March 2021) as well as clinical isolates EU1 (B.1.117), variant of concern (VOC) Alpha (B.1.1.7) or Beta (B.1.351), which had been expanded in a biosafety level 3 laboratory. The specificities of automated SARS-CoV-2 Ag tests ranged between 97.0 and 99.7% (Lumipulse G SARS-CoV-2 Ag (Fujirebio): 97.03%, Elecsys SARS-CoV-2 Ag (Roche Diagnostics): 97.69%; LIAISON® SARS-CoV-2 Ag (Diasorin) and SARS-CoV-2 Ag ELISA (Euroimmun): 99.67%). In this study cohort of hospitalized patients, the clinical sensitivities of tests were low, ranging from 17.76 to 52.34%, and analytical sensitivities ranged from 420,000 to 25,000,000 Geq/ml. In comparison, the detection limit of the Roche Rapid Ag Test (RAT) was 9,300,000 Geq/ml, detecting 23.58% of respiratory samples. Receiver-operating-characteristics (ROCs) and Youden’s index analyses were performed to further characterize the assays’ overall performance and determine optimal assay cutoffs for sensitivity and specificity. VOCs carrying up to four amino acid mutations in nucleocapsid were detected by all five assays with characteristics comparable to non-VOCs. In summary, automated, quantitative SARS-CoV-2 Ag tests show variable performance and are not necessarily superior to a standard POCT. The efficacy of any alternative testing strategies to complement nucleic acid-based assays must be carefully evaluated by independent laboratories prior to widespread implementation.

Guanylate binding proteins (GBPs) are paramount in the host immunity by providing defense against invading pathogens. Multigene families related to the immune system usually show that the duplicated genes can either undergo deletion, gain new functions, or become non-functional. Here, we show that in muroids, the Gbp genes followed an unusual pattern of gain and loss of genes. Muroids present a high diversity and plasticity regarding Gbp synteny, with most species presenting two Gbp gene clusters. The phylogenetic analyses revealed seven different Gbps groups. Three of them clustered with GBP2, GBP5 and GBP6 of primates. Four new Gbp genes that appear to be exclusive to muroids were identified as Gbpa, b, c and d. A duplication event occurred in the Gbpa group in the common ancestor of Muridae and Cricetidae (~20 Mya), but both copies were deleted from the genome of Mus musculus, M. caroli and Cricetulus griseus. The Gbpb gene emerged in the ancestor of Muridae and Cricetidae and evolved independently originating Gbpb1 in Muridae, Gbpb2 and Gbpb3 in Cricetidae. Since Gbpc appears only in three species, we hypothesize that it was present in the common ancestor and deleted from most muroid genomes. The second Gbp gene cluster, Gbp6, is widespread across all muroids, indicating that this cluster emerged before the Muridae and Cricetidae radiation. An expansion of Gbp6 occurred in M. musculus and M. caroli probably to compensate the loss of Gbpa and b. Gbpd is divided in three groups and is present in most muroids suggesting that a duplication event occurred in the common ancestor of Muridae and Cricetidae. However, in Grammomys surdaster and Mus caroli, Gbpd2 is absent, and in Arvicanthis niloticus, Gbpd1 appears to have been deleted. Our results further demonstrated that primate GBP1, GBP3 and GBP7 are absent from the genome of muroids and showed that the Gbp gene annotations in muroids were incorrect. We propose a new classification based on the phylogenetic analyses and the divergence between the groups. Extrapolations to humans based on functional studies of muroid Gbps should be re-evaluated. The evolutionary analyses of muroid Gbp genes provided new insights about the evolution and function of these genes.

No abstract