Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations.

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, mutations arise that will allow the virus to evade immune defenses and therapeutics. Assays that can identify these mutations can be used to guide personalized patient treatment plans. Digital PCR (dPCR) is a fast and reliable complement to whole-genome sequencing that can be used to discriminate single nucleotide polymorphisms (SNPs) in template molecules. Here, we developed a panel of SARS-CoV-2 dPCR assays and demonstrate its applications for typing variant lineages and therapeutic monoclonal antibody resistance. We first designed multiplexed dPCR assays for SNPs located at residue 3395 in the orf1ab gene that differentiate the Delta, Omicron BA.1, and Omicron BA.2 lineages. We demonstrate their effectiveness on 596 clinical saliva specimens that were sequence verified using Illumina whole-genome sequencing. Next, we developed dPCR assays for spike mutations R346T, K444T, N460K, F486V, and F486S, which are associated with host immune evasion and reduced therapeutic monoclonal antibody efficacy. We demonstrate that these assays can be run individually or multiplexed to detect the presence of up to 4 SNPs in a single assay. We perform these dPCR assays on 81 clinical saliva SARS-CoV-2-positive specimens and properly identify mutations in Omicron subvariants BA.2.75.2, BM.1.1, BN.1, BF.7, BQ.1, BQ.1.1, and XBB. Thus, dPCR could serve as a useful tool to determine if clinical specimens contain therapeutically relevant mutations and inform patient treatment. IMPORTANCE Spike mutations in the SARS-CoV-2 genome confer resistance to therapeutic monoclonal antibodies. Authorization for treatment options is typically guided by general trends of variant prevalence. For example, bebtelovimab is no longer authorized for emergency use in the United States due to the increased prevalence of antibody-resistant BQ.1, BQ.1.1, and XBB Omicron subvariants. However, this blanket approach limits access to life-saving treatment options to patients who are otherwise infected with susceptible variants. Digital PCR assays targeting specific mutations can complement whole-genome sequencing approaches to genotype the virus. In this study, we demonstrate the proof of concept that dPCR can be used to type lineage defining and monoclonal antibody resistance-associated mutations in saliva specimens. These findings show that digital PCR could be used as a personalized diagnostic tool to guide individual patient treatment.

Operative Management of Acute Appendicitis Was Safe During the COVID-19 Pandemic Shutdown.

INTRODUCTION: In the spring of 2020, New York City was one of the first epicenters of the COVID outbreak. In this study, we evaluate the incidence and treatment of appendicitis in two New York City community hospitals during the COVID pandemic. METHODS: This retrospective study focused on the incidence and outcome of acute appendicitis in the adult population (>18 y old) during peak-COVID periods (March 16, 2020,-June 15, 2020) compared to pre-COVID and post-COVID periods. We compared the number of patients who underwent operative versus nonoperative management, patient demographics, length of stay (LOS), complications, and readmission rates within these time periods. Data are presented as mean ± standard deviation (analysis of variance). RESULTS: From January 1, 2020 to December 31, 2020, 393 patients presented with acute appendicitis and 321 (81.7%) were treated operatively, compared to 441 total and 366 treated operatively (83%) in 2019 (P = 0.88). During the COVID outbreak, fewer patients presented with appendicitis (mean 6.9 ± 1 pre-COVID case/week, 4.4 ± 2.4 peak-COVID cases/week and 7.6 ± 0.65 post-COVID cases/week, P = 0.018) with no significant difference in the pre-COVID and post-COVID period. There was no difference in LOS between the pre-, peak-, and post-COVID periods with a median of 1 for all the three, (interquartile range (IQR): 0.8-2, 0.6-2, 0.6-2, respectively, P = 0.43). Additionally, there was no difference in 30-day readmission rates (4.2%, 0%, 3.9%, P = 0.99) and postoperative complications (4.2%, 0%, 2.9%, P = 0.98). CONCLUSIONS: During peak-COVID, there was a significant reduction in the number of patients who presented with acute appendicitis without a post rebound increase in presentation. Those who presented during peak-COVID were able to undergo operative management safely, without affecting LOS or postoperative complications.

Operative Management of Acute Appendicitis is Safe During the COVID-19 Pandemic Shutdown

Background In the spring of 2020, New York City was one of the first epicenters of the COVID outbreak. In this study, we evaluate the incidence and treatment of appendicitis in two New York City community hospitals during the COVID pandemic. Methods This retrospective study focused on the incidence and outcome of acute appendicitis in the adult population (>18yo) during peak-COVID (3/16/20-6/15/20) compared to pre and post. We compared the number of patients who underwent operative vs non-operative management, patient demographics, length of stay (LOS), complications, and readmission rates within these time periods. Data is presented as mean ± SD (ANOVA). Results From 1/1/2020 to 12/31/2020, 393 patients presented with acute appendicitis and 321 (81.7%) were treated operatively, compared to 441 total and 366 treated operatively (83%) in 2019 (p=0.88). During the COVID outbreak, fewer patients presented with appendicitis (mean 6.9±1 pre-, 4.4±2.4 peak- and 7.6±0.65 post-COVID cases/week, p=0.018) with no significant difference pre and post. There was no difference in LOS between the pre, peak, and post periods with median of 1 for all three, (IQR 0.8-2, 0.6-2, 0.6-2 respectively p = 0.43). Additionally, there was no difference in 30-day readmission rates (4.2%, 0%, 3.9%, p=0.99) and post-operative complications (4.2%, 0%, 2.9%, p=0.98). Conclusion During peak-COVID, there was significant reduction in the number of patients who presented with acute appendicitis without a post-rebound increase in presentation. Those who presented during peak-COVID were able to undergo operative management safely, without affecting length of stay or post-operative complications.

Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA.

The adaptive evolution of SARS-CoV-2 variants is driven by selection for increased viral fitness in transmissibility and immune evasion. Understanding the dynamics of how an emergent variant sweeps across populations can better inform public health response preparedness for future variants. Here, we investigated the state-level genomic epidemiology of SARS-CoV-2 through baseline genomic sequencing surveillance of 27,071 public testing specimens and 1,125 hospital inpatient specimens diagnosed between November 1, 2021, and January 31, 2022, in Arizona. We found that the Omicron variant rapidly displaced Delta variant in December 2021, leading to an "Omicron surge" of COVID-19 cases in early 2022. Wastewater sequencing surveillance of 370 samples supported the synchronous sweep of Omicron in the community. Hospital inpatient COVID-19 cases of Omicron variant presented to three major hospitals 10.51 days after its detection from public clinical testing. Nonsynonymous mutations in nsp3, nsp12, and nsp13 genes were significantly associated with Omicron hospital cases compared to community cases. To model SARS-CoV-2 transmissions across the state population, we developed a scalable sequence network methodology and showed that the Omicron variant spread through intracounty and intercounty transmissions. Finally, we demonstrated that the temporal emergence of Omicron BA.1 to become the dominant variant (17.02 days) was 2.3 times faster than the prior Delta variant (40.70 days) or subsequent Omicron sublineages BA.2 (39.65 days) and BA.5 (35.38 days). Our results demonstrate the uniquely rapid sweep of Omicron BA.1. These findings highlight how integrated public health surveillance can be used to enhance preparedness and response to future variants. IMPORTANCE SARS-CoV-2 continues to evolve new variants throughout the pandemic. However, the temporal dynamics of how SARS-CoV-2 variants emerge to become the dominant circulating variant is not precisely known. Genomic sequencing surveillance offers unique insights into how SARS-CoV-2 spreads in communities and the lead-up to hospital cases during a surge. Specifically, baseline sequencing surveillance through random selection of positive diagnostic specimens provides a representative outlook of the virus lineages circulating in a geographic region. Here, we investigated the emergence of the Omicron variant of concern in Arizona by leveraging baseline genomic sequence surveillance of public clinical testing, hospitals, and community wastewater. We tracked the spread and evolution of the Omicron variant as it first emerged in the general public, and its rapid shift in hospital admissions in the state health system. This study demonstrates the timescale of public health preparedness needed to respond to an antigenic shift in SARS-CoV-2.

Operative Shutdown and Recovery: Restructuring Surgical Operations During the SARS-CoV-2 Pandemic.

BACKGROUND: During the 2020 SARS-CoV-2 outbreak in New York City, hospitals canceled elective surgeries to increase capacity for critically ill patients. We present case volume data from our community hospital to demonstrate how this shutdown affected surgical care. METHODS: Between March 16 and June 14, 2020, all elective surgeries were canceled at our institution. All procedures performed during this operating room shutdown (ORS) were logged, as well as those 4 weeks before (PRE) and 4 weeks after (POST) for comparison. RESULTS: A total of 2,475 cases were included in our analysis, with 754 occurring during shutdown. Overall case numbers dropped significantly during ORS and increased during recovery (mean 245.0 ± 28.4 PRE versus 58.0 ± 30.9 ORS versus 186.0±19.4 POST cases/wk, P< 0.001). Emergency cases predominated during ORS (26.4% PRE versus 59.3% ORS versus 31.5% POST, P< 0.001) despite decreasing in frequency (mean 64.5 ± 7.9 PRE versus 34.4 ± 12.1 ORS versus 58.5 ± 4.0 POST cases/wk, P< 0.001). Open surgeries remained constant in all three phases (52.2-54.1%), whereas laparoscopic and robotic surgeries decreased (-3.4% and -3.0%, P< 0.001). General and/or vascular surgery, urology, and neurosurgery comprised a greater proportion of caseload (+9.5%, +3.0%, +2.8%), whereas orthopedics, gynecology, and otolaryngology/plastic surgery all decreased proportionally (-5.0%, -4.4%, -5.9%, P< 0.001). CONCLUSION: Operative volume significantly decreased during the SARS-CoV-2 outbreak. Emergency cases predominated during this time, although there were fewer emergency cases overall. General/vascular surgery became the most active service and open surgeries became more common. This reallocation of resources may be useful for future crisis planning among community hospitals.

Utility of d-dimer for diagnosis of deep vein thrombosis in coronavirus disease-19 infection.

OBJECTIVE: The objective of this study was to investigate the clinical usefulness of d-dimer in excluding a diagnosis of deep vein thrombosis (DVT) in patients with coronavirus disease (COVID-19) infection, potentially limiting the need for venous duplex ultrasound examination. METHODS: We retrospectively reviewed consecutive patients admitted to our institution with confirmed COVID-19 status by polymerase chain reaction between March 1, 2020, and May 13, 2020, and selected those who underwent both d-dimer and venous duplex ultrasound examination. This cohort was divided into two groups, those with and without DVT based on duplex ultrasound examination. These groups were then compared to determine the value of d-dimer in establishing this diagnosis. RESULTS: A total of 1170 patients were admitted with COVID-19, of which 158 were selected for this study. Of the 158, there were 52 patients with DVT and 106 without DVT. There were no differences in sex, age, race, or ethnicity between groups. Diabetes and routine hemodialysis were less commonly seen in the group with DVT. More than 90% of patients in both groups received prophylactic anticoagulation, but the use of low-molecular-weight heparin or subcutaneous heparin prophylaxis was not predictive of DVT. All patients had elevated acute-phase d-dimer levels using conventional criteria, and 154 of the 158 (97.5%) had elevated levels with age-adjusted criteria (mean d-dimer 16,163 ± 5395 ng/mL). Those with DVT had higher acute-phase d-dimer levels than those without DVT (median, 13,602 [interquartile range, 6616-36,543 ng/mL] vs 2880 [interquartile range, 1030-9126 ng/mL], P < .001). An optimal d-dimer cutoff of 6494 ng/mL was determined to differentiate those with and without DVT (sensitivity 80.8%, specificity 68.9%, negative predictive value 88.0%). Wells DVT criteria was not found to be a significant predictor of DVT. Elevated d-dimer as defined by our optimal metric was a statistically significant predictor of DVT in both univariate and multivariable analyses when adjusting for other factors (odds ratio, 6.12; 95% confidence interval, 2.79-13.39; P < .001). CONCLUSIONS: d-dimer levels are uniformly elevated in patients with COVID-19. Although standard predictive criteria failed to predict DVT, our analysis showed a d-dimer of less than 6494 ng/mL may exclude DVT, potentially limiting the need for venous duplex ultrasound examination.