TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling.

BACKGROUND: Previously developed TaME-seq method for deep sequencing of HPV, allowed simultaneous identification of the human papillomavirus (HPV) DNA consensus sequence, low-frequency variable sites, and chromosomal integration events. The method has been successfully validated and applied to the study of five carcinogenic high-risk (HR) HPV types (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline. The HR-HPV type repertoire was expanded with HPV51, 52, and 59. As a proof-of-concept, TaME-seq2 was applied on SARS-CoV-2 positive samples showing the method's flexibility to a broader range of viruses, both DNA and RNA. RESULTS: Compared to TaME-seq version 1, the bioinformatics pipeline of TaME-seq2 is approximately 40× faster. In total, 23 HPV-positive samples and seven SARS-CoV-2 clinical samples passed the threshold of 300× mean depth and were submitted to further analysis. The mean number of variable sites per 1 kb was ~ 1.5× higher in SARS-CoV-2 than in HPV-positive samples. Reproducibility and repeatability of the method were tested on a subset of samples. A viral integration breakpoint followed by a partial genomic deletion was found in within-run replicates of HPV59-positive sample. Identified viral consensus sequence in two separate runs was > 99.9% identical between replicates, differing by a couple of nucleotides identified in only one of the replicates. Conversely, the number of identical minor nucleotide variants (MNVs) differed greatly between replicates, probably caused by PCR-introduced bias. The total number of detected MNVs, calculated gene variability and mutational signature analysis, were unaffected by the sequencing run. CONCLUSION: TaME-seq2 proved well suited for consensus sequence identification, and the detection of low-frequency viral genome variation and viral-chromosomal integrations. The repertoire of TaME-seq2 now encompasses seven HR-HPV types. Our goal is to further include all HR-HPV types in the TaME-seq2 repertoire. Moreover, with a minor modification of previously developed primers, the same method was successfully applied for the analysis of SARS-CoV-2 positive samples, implying the ease of adapting TaME-seq2 to other viruses.

PERCEPTION OF THE BENEFITS AND LIMITATIONS OF TELEVISIT IN A GROUP OF PATIENTS WITH CHRONIC HEART FAILURE

Telemedicine (T) has now become an indispensable operational tool for the management of patients with chronic conditions, in particular for patients with chronic heart failure (HF). The current COVID 19 pandemic has accelerated the development and application oh this method in daily clinical practice. Up to now, the evaluation of he advantage and disadvantage of televisit by cardiological patients have been very limited. In order to assess the satisfaction and criticalities of this method, we administered a satisfaction questionnaire to 74 patients (49 males and 25 females with an average of 75) followed in our clinic. Of the 74 questionnaire administered, 70 were received. When asked whether the inclusion of T had improved the quality of service 43 patients (61%) answered a lot, 24 patients (34%) sufficiently and 3 patients (4%) not at all. When asked if the organization of the T had been adequate, 50 patients (71%) responded adequately, 19 patients (27%) sufficiently adequate and 1 patient (1%) not at all adequate. When asked about the modalities of connection to the T for 54 patients (77%) they were found to be sìmple, for 13 patients (18%) a little complicated and for 3 patients (4%) difficult, very complicated. When asked what would be proposed to improve the service 7 patients (10%) answered the possible extension of hours also in the afternoon, 3 patients (4%) the provision by the ASL of electromedical devices, 14 patients (20%) the ability to directly request an appointment in T and 38 patients (54%) all options. In detail, 1 patient (1%) requested both the extension of the afternoon schedule and the provision of electromedicals, 4 patients (6%) requested both the extension of the afternoon schedule and the direct request for an appointment, 2 patients (2%) required both electromedical equipment and direct request for an appointment, 1 patient (1%) did not indicate any option. Finally, as regards the degree of satisfaction, 45 patients (64%) were considered totally satisfied, 22 patients (31%) partially satisfied and 3 patients (4%) dissatisfied. Conclusions: The televisit in the setting of patients with chronic HF, despite the limitations of a limited series, was generally well accepted, easy to access and with some useful operational proposal for public administration.

Increased Comorbidity Burden Among Hip Fracture Patients During the COVID-19 Pandemic in New York City.

BACKGROUND: The coronavirus disease 19 (COVID-19) pandemic had a devastating effect on New York City in the spring of 2020. Several global reports suggested worse early outcomes among COVID-positive patients with hip fractures. However, there is limited data comparing baseline comorbidities among patients treated during the pandemic relative to those treated in non-pandemic conditions. MATERIALS AND METHODS: A multicenter retrospective cohort study was performed at two Level 1 Trauma centers and one orthopedic specialty hospital to assess demographics, comorbidities, and outcomes among 67 hip fracture patients treated (OTA/AO 31, 32.1) during the peak of the COVID-19 pandemic in New York City (March 20, 2020 to April 24, 2020), including 9 who were diagnosed with COVID-19. These patients were compared to a cohort of 76 hip fracture patients treated 1 year prior (March 20, 2019 to April 24, 2019). Baseline demographics, comorbidities, treatment characteristics, and respiratory symptomatology were evaluated. The primary outcome was inpatient mortality. RESULTS: Relative to patients treated in 2019, patients with hip fractures during the pandemic had worse Charlson Comorbidity Indices (median 5.0 vs 6.0, P = .03) and American Society of Anesthesiologists (ASA) scores (mean 2.4 vs 2.7, P = .04). Patients during the COVID-19 pandemic were more likely to have decreased ambulatory status (P<.01) and a smoking history (P = .04). Patients in 2020 had longer inpatient stays (median 5 vs 7 days, P = .01), and were more likely to be discharged home (61% vs 9%, P<.01). Inpatient mortality was significantly increased during the COVID-19 pandemic (12% vs 0%, P = .002). CONCLUSIONS: Patients with hip fractures during the COVID-19 pandemic had worse comorbidity profiles and decreased functional status compared to patients treated the year prior. This information may be relevant in negotiations regarding reimbursement for cost of care of hip fracture patients with COVID-19, as these patients may require more expensive care.

Techno-solutionism and the standard human in the making of the COVID-19 pandemic

Quantification is particularly seductive in times of global uncertainty. Not surprisingly, numbers, indicators, categorizations, and comparisons are central to governmental and popular response to the COVID-19 pandemic. This essay draws insights from critical data studies, sociology of quantification and decolonial thinking, with occasional excursion into the biomedical domain, to investigate the role and social consequences of counting broadly defined as a way of knowing about the virus. It takes a critical look at two domains of human activity that play a central role in the fight against the virus outbreak, namely medical sciences and technological innovation. It analyzes their efforts to craft solutions for their user base and explores the unwanted social costs of these operations. The essay argues that the over-reliance of biomedical research on “whiteness” for lab testing and the techno-solutionism of the consumer infrastructure devised to curb the social costs of the pandemic are rooted in a distorted idea of a “standard human” based on a partial and exclusive vision of society and its components, which tends to overlook alterity and inequality. It contends that to design our way out of the pandemic, we ought to make space for distinct ways of being and knowing, acknowledging plurality and thinking in terms of social relations, alterity, and interdependence. © The Author(s) 2020.

Hip Fracture Outcomes During the COVID-19 Pandemic: Early Results From New York.

OBJECTIVE: To evaluate inpatient outcomes among patients with hip fracture treated during the COVID-19 pandemic in New York City. DESIGN: Multicenter retrospective cohort study. SETTING: One Level 1 trauma center and one orthopaedic specialty hospital in New York City. PATIENTS/PARTICIPANTS: Fifty-nine consecutive patients (average age 85 years, range: 65-100 years) treated for a hip fracture (OTA/AO 31, 32.1) over a 5-week period, March 20, 2020, to April 24, 2020, during the height of the COVID-19 crisis. MAIN OUTCOME MEASUREMENTS: COVID-19 infection status was used to stratify patients. The primary outcome was inpatient mortality. Secondary outcomes were admission to the intensive care unit, unexpected intubation, pneumonia, deep vein thrombosis, pulmonary embolus, myocardial infarction, cerebrovascular accident, urinary tract infection, and transfusion. Baseline demographics, comorbidities, treatment characteristics, and COVID-related symptomatology were also evaluated. RESULTS: Ten patients (15%) tested positive for COVID-19 (COVID+) (n = 9; 7 preoperatively and 2 postoperatively) or were presumed positive (n = 1), 40 (68%) patients tested negative, and 9 (15%) patients were not tested in the primary hospitalization. American Society of Anesthesiologists' scores were higher in the COVID+ group (d = -0.83; P = 0.04); however, the Charlson Comorbidity Index was similar between the study groups (d = -0.17; P = 0.63). Inpatient mortality was significantly increased in the COVID+ cohort (56% vs. 4%; odds ratio 30.0, 95% confidence interval 4.3-207; P = 0.001). Including the one presumed positive case in the COVID+ cohort increased this difference (60% vs. 2%; odds ratio 72.0, 95% confidence interval 7.9-754; P < 0.001). CONCLUSIONS: Hip fracture patients with concomitant COVID-19 infection had worse American Society of Anesthesiologists' scores but similar baseline comorbidities with significantly higher rates of inpatient mortality compared with those without concomitant COVID-19 infection. LEVEL OF EVIDENCE: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.