48 Background. Nucleic acid amplification tests (NAATs) are the primary means of 49 identifying acute infections caused by severe acute respiratory syndrome coronavirus 2 50 (SARS-CoV-2). Accurate and fast test results may permit more efficient use of protective and 51 isolation resources and allow for rapid therapeutic interventions. 52 Methods. We evaluated the analytical and clinical performance characteristics of the Xpert ® 53 Xpress SARS-CoV-2 (Xpert) test, a rapid, automated molecular test for SARS-CoV-2. 54 Analytical sensitivity and specificity/interference were assessed with infectious SARS-CoV-2, 55 other infectious coronavirus species including SARS-CoV, and 85 nasopharyngeal swab 56 specimens positive for other respiratory viruses including endemic human coronaviruses 57 (hCoVs). Clinical performance was assessed using 483 remnant upper and lower respiratory 58 specimens previously analyzed by standard of care (SOC) NAATs. 59 Results. The limit of detection of the Xpert test was 0.01 plaque forming units (PFU)/mL. 60 Other hCoVs, including Middle East Respiratory Syndrome coronavirus, were not detected by 61 the Xpert test. SARS-CoV, a closely related species in the Sarbecovirus subgenus, was 62 detected by a broad-range target (E) but was distinguished from SARS-CoV-2 (SARS-CoV-2-63 specific N2 target). Compared to SOC NAATs, the positive agreement of the Xpert test was 64 219/220 (99.5%) and the negative agreement was 250/261 (95.8%). A third tie-breaker 65 NAAT resolved all but three of the discordant results in favor the Xpert test. 66 Conclusions. The Xpert test provided sensitive and accurate detection of SARS-CoV-2 in a 67 variety of upper and lower respiratory tract specimens. The high sensitivity and fast time to 68 results of approximately 45 minutes may impact patient management. 69 70 Laboratory diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 72 (SARS-CoV-2) is usually accomplished by performing nucleic acid amplification tests 73 (NAATs) on respiratory tract specimens. An antibody response is often not detected in the 74 first week to ten days of symptoms and antibody testing is therefore generally unhelpful for 75 acute diagnosis(1-3), with virus isolation in culture presenting significant biosafety risks. 76 Upper respiratory tract (URT) specimens such as nasopharyngeal swabs (NPS) and 77 oropharyngeal swabs (OPS) generally have high SARS-CoV-2 viral loads upon symptom 78 onset.(2, 4-6) URT specimens may also have detectable RNA during the pre-symptomatic 79 period(7), and pediatric patients who remain asymptomatic through the entire course of 80 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 4 infection can persistently shed RNA in URT specimens for two weeks or longer.(4, 8) 81 Importantly, NPS may have higher viral loads than OPS.(6) Lower respiratory tract (LRT) 82 specimens including sputum(7, 9) and tracheal aspirates(10) (TA) are often positive for RNA 83 early in disease and remain positive longer than URT sources.(5) 84 NAATs are...
Since SARS-CoV-2-based disease (COVID-19) spreads as a pandemic, the necessity of a highly sensitive molecular diagnosis that can drastically reduce false negatives reverse transcription PCR (rtPCR) results, raises as a major clinical need. Here we evaluated the performance of a ddPCR-based assay to quantify SARS-CoV-2 titer in 55 suspected COVID-19 cases with negative rtPCR results thanks to in-house ddPCR assay (targeting RdRp and host RNaseP). Samples were collected at ASST-GOM Niguarda between February and May 2020 at hospital admission. Clinical and imaging data were obtained for clinical staging and definition of disease severity. Patients were mainly female (45.5%) with a median age of 73 (57-84) years. ddPCR-based assay detected SARS-CoV-2 genome in nasopharyngeal samples of 19 (34.5%) patients (median viral-load: 128 copies/mL, IQR: 72-345). In 15 of them (78.9%), chest CT showed a classical COVID-19 bilateral interstitial pneumonia; 14 patients (73.7%) showed severe COVID-19 manifestations. ddPCR did not identify any trace of SARS-CoV-2 genome in the respiratory samples of the remaining 36 patients. The serological assay performed in a subgroup of 34 patients at the later stage of illness (from 3 days to 90 days after) confirmed the presence of SARS-CoV-2 antibodies in all patients tested positive for SARS-CoV-2 in ddPCR (100%). Contrariwise, negative tests were observed in 95.0% ddPCR negative patients (P<0.001). Thanks to a ddPCR-based assay, we achieved a rapid and accurate SARS-CoV-2 diagnosis in rtPCR-negative respiratory
Cervical tissue explants (CTE) from 22 HIV-1 seronegative women were exposed to R5 HIV-1 ex vivo. Eight CTE were productively infected in terms of HIV-1 p24Gag release in culture supernatants whereas 14 were not. Nonetheless, both accumulation of HIV-1gag DNA and of p24Gag+ CD4+ T cells and macrophages occurred in both productive and, at lower levels, in nonproductive CTE. Nonproductive CTE differed from productive CTE for higher secretion of CCL3 and CCL5. A post-hoc analysis revealed that all productive CTE were established from women in their secretory phase of the menstrual cycle, whereas nonproductive CTE derived from women either in their secretory (28%) or proliferative (36%) menstrual cycle phases or with an atrophic endometrium (36%). Thus, our results support the epidemiological observation that sexual HIV-1 transmission from males to women as well as from women to men is more efficient during their secretory phase of the menstrual cycle.
Research letters GREAT Network. Clinical picture and risk prediction of short-term mortality in cardiogenic shock.
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