Rapid Lineage Assignment of Severe Acute Respiratory Syndrome Coronavirus 2 Cases through Automated Library Preparation, Sequencing, and Bioinformatic Analysis

The coronavirus disease 2019 (COVID-19) pandemic has provided a stage to illustrate that there is considerable value in obtaining rapid, whole-genome-based information about pathogens. This article describes the utility of a commercially available, automated severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) library preparation, genome sequencing, and a bioinformatics analysis pipeline to provide rapid, near-real-time SARS-CoV-2 variant description. This study evaluated the turnaround time, accuracy, and other quality-related parameters obtained from commercially available automated sequencing instrumentation, from analysis of continuous clinical samples obtained from January 1, 2021, to October 6, 2021. This analysis included a base-by-base assessment of sequencing accuracy at every position in the SARS-CoV-2 chromosome using two commercially available methods. Mean turnaround time, from the receipt of a specimen for SARS-CoV-2 testing to the availability of the results, with lineage assignment, was <3 days. Accuracy of sequencing by one method was 100%, although certain sites on the genome were found repeatedly to have been sequenced with varying degrees of read error rate.

Use of wastewater surveillance for early detection of Alpha and Epsilon SARS-CoV-2 variants of concern and estimation of overall COVID-19 infection burden

A decline in diagnostic testing for SARS-CoV-2 is expected to delay the tracking of COVID-19 variants of concern and interest in the United States. We hypothesize that wastewater surveillance programs provide an effective alternative for detecting emerging variants and assessing COVID-19 incidence, particularly when clinical surveillance is limited. Here, we analyzed SARS-CoV-2 RNA in wastewater from eight locations across Southern Nevada between March 2020 and April 2021. Trends in SARS-CoV-2 RNA concentrations (ranging from 4.3 log₁₀ gc/L to 8.7 log₁₀ gc/L) matched trends in confirmed COVID-19 incidence, but wastewater surveillance also highlighted several limitations with the clinical data. Amplicon-based whole genome sequencing (WGS) of 86 wastewater samples identified the B.1.1.7 (Alpha) and B.1.429 (Epsilon) lineages in December 2020, but clinical sequencing failed to identify the variants until January 2021, thereby demonstrating that 'pooled' wastewater samples can sometimes expedite variant detection. Also, by calibrating fecal shedding (11.4 log₁₀ gc/infection) and wastewater surveillance data to reported seroprevalence, we estimate that ~38% of individuals in Southern Nevada had been infected by SARS-CoV-2 as of April 2021, which is significantly higher than the 10% of individuals confirmed through clinical testing. Sewershed-specific ascertainment ratios (i.e., X-fold infection undercounts) ranged from 1.0 to 7.7, potentially due to demographic differences. Our data underscore the growing application of wastewater surveillance in not only the identification and quantification of infectious agents, but also the detection of variants of concern that may be missed when diagnostic testing is limited or unavailable.

Optimal management of an aneurysmal subarachnoid hemorrhage in a patient with known factor XI deficiency: a case report

The authors report a rare case of an acute cerebral aneurysm rupture in a patient with a known factor XI deficiency. Aneurysmal subarachnoid hemorrhage (SAH) accounts for a high mortality and morbidity rate. When SAH is associated with an inherited coagulation disorder such as hemophilia C, an unexpected and possible increase in hemorrhagic stroke and increase in bleeding during surgery and in the postoperative period could lead to an extremely bad outcome. Clinical management consists of rapid correction of the coagulation disorder before undergoing any invasive intracranial procedure. Such an optimal therapeutic strategy must be under the care of a multidisciplinary medical and surgical team. Human factor XI concentrate (Hemoleven, Laboratoire Français du Fractionnement et des Biotechnologies [LFB], Les Ulis, France) was used successfully in this case report. New treatment using recombinant factor VIIa is discussed.

Capnography monitoring during neurosurgery: reliability in relation to various intraoperative positions

In neurosurgery, estimation of PaCO2 from PETCO2 has been questioned. The aim of this study was to reevaluate the accuracy of PETCO2 in estimating PaCO2 during neurosurgical procedures lasting >3 h and to measure the effect of surgical positioning on arterial to end-tidal CO2 gradient (P[a-ET]CO2) over time. One hundred four neurosurgical patients classified into four groups (supine [SP], lateral [LT], prone [PR], sitting [ST]) were included in a prospective study. PaCO2, PETCO2, and P(a-ET)CO2 were measured after induction of anesthesia (T0), after positioning (T1), each following hour (T2, T3, T4), and at the end of the procedure after return to the SP position (T5). Data are expressed as the mean +/- SD, and statistical analysis used linear regression, the Bland-Altman method, and analysis of variance. The mean durations of positioning and surgery were 4.1+/-1 h and 3.7+/-1.3 h, respectively. We performed 624 simultaneous measurements of PaCO2 (33+/-5 mm Hg) and PETCO2 (27+/-4 mm Hg), leading to a mean P(a-ET)CO2 of 6+/-4 mm Hg. P(a-ET)CO2 of the LT group (7+/-3 mm Hg) was larger (compared with the SP, PR, and ST groups) because of a lower PETCO2 (26+/-4 mm Hg). Negative P(a-ET)CO2 (PETCO2 > PaCO2) occurred 22 times, only in the SP (n = 9) and ST groups (n = 13). Changes in opposite directions of PETCO2 and PaCO2 between two successive measurements were found in 26% of the cases. Correlation coefficients in the four groups (PaCO2 versus PETCO2) were not in good agreement (0.46 to 0.62; P < 0.001). The mean bias was between 5 and 7 mm Hg. The superior (13-15 mm Hg) and inferior (-5 to 0 mm Hg) limits of agreement were too large to expect PETCO2 to replace PaCO2. In conclusion, during neurosurgical procedures of >3 h, capnography should be performed with regular analysis of arterial blood gases for optimal ventilator adjustment.

IMPLICATIONS

This study, which aimed to reevaluate the ability of PETCO2 to estimate PaCO2 during neurosurgical procedures according to surgical position, indicates that PETCO2 cannot replace PaCO2 for the following reasons: scattering of individual values; occurrence of negative arterial to end-tidal CO2 gradient (P[a-ET]CO2; PaCO2 and PETCO2 variations in opposite directions; large changes in P(a-ET)CO2 between two samples; and instability of P(a-ET)CO2 over time.

Paediatric day case anaesthesia: estimate of its quality at home

The aim of this clinical audit was to evaluate the home recovery and complications of 104 daycase anaesthetized children, as well as parent satisfaction. A questionnaire, explained at the time of preoperative visit, was given to parents at hospital discharge and returned by mail. Opioids were administered in 19% of the children whereas regional anaesthesia was performed in 28% of cases. In the recovery room, 8% of them suffered pain. At home, pain was the main problem (25%) and vomiting and agitation were found in 9% and 6% of the cases respectively. Parents reported anxiety in 45% of cases, and 14% called their general practitioner. Nevertheless, 94% were satisfied with the anaesthetic. A clinical audit is useful in detecting management deficiencies. Quality of home recovery may be improved by: wider use of perioperative analgesia, systematic prescription of take-home analgesia, designation of a hospital practitioner for advice, and closer collaboration with general practitioners.

A new device for the detection of sponges and other foreign objects left accidentally in the operative field

A new cost-effective device for the detection of sponges and other instruments left accidentally in the surgical field is presented. This device has 100 per cent sensitivity rate in the initial tests. It is extremely simple and rapid and does not require the use of radiation or other harmful techniques.

A discordant sibship analysis between beta-NGF and neurofibromatosis

A new restriction fragment length polymorphism 5' to the beta-nerve growth factor (beta-NGF) gene has been found in proximity to the BglII polymorphism, and both polymorphisms are detectable with an EcoRI 7-kilobase (kb) subclone. Absence of the TaqI recognition site lengthens the 4.3-kb and 1.7-kb hybridizing fragments to 6 kb, and the alleles are in Hardy-Weinberg equilibrium with frequencies of 83% and 17%, respectively. Previous research has suggested that NGF is involved in disseminated neurofibromatosis (NF). We found four informative disseminated NF families with the two beta-NGF polymorphisms and have provided clearcut evidence against beta-NGF gene alteration in these families. If disseminated NF is found to be heterogeneous at a molecular level, more families should be tested to further rule out any role for beta-NGF in this syndrome.