ABSTRACT
Background. The COVID-19 pandemic has demonstrated the importance of pathogen genomic surveillance. At RKI, the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance. Methods. SARS-CoV-2 positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. This surveillance instrument enables (i) almost-real-time monitoring of SARS-CoV-2 genomic diversity and evolution, (ii) in vitro assessment of vaccine coverage against emerging variants and (iii) genome-based estimates of SARS-CoV-2-incidences. Results. We report the results of our analyses of 3623 SARS-CoV-2 genomes collected between 12/1/2020 and 12/31/2021. All variants of concern were identified, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Lineage distributions fluctuated over time, covering the rise of the Alpha and Delta, as well as the emergence of Omicron. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modelled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. Conclusion. This example illustrates that pathogen genomics enables a proactive approach to controlling a pandemic as the virus evolves. Molecular and genomic SARS-CoV-2 surveillance will be crucial during the post-pandemic future, informing public health policies including vaccination strategies. Of note, the IMS-SC2 infrastructure can be adapted to many other pathogens, serving as a blueprint for future efforts to increase genomic pathogen surveillance.
ABSTRACT
Background: As a standalone tertiary spinal cord rehabilitation program, our patients requiring diagnostic imaging during their inpatient stay need to be transported to an acute care hospital to receive these services. Over the course of inpatient rehabilitation, patients routinely travel to acute care hospitals for diagnostic imaging for surgical follow-up, musculoskeletal injuries, vascular complications such as deep vein thrombosis and other medical complications. Due to travel and wait time, patients typically miss at least a half day of therapy to attend imaging appointments. At the beginning of the COVID-19 pandemic, an urgent need arose to develop a new approach to diagnostic imaging due to a significant reduction in access to acute care diagnostic imaging and in order to reduce the risk of patient exposure to COVID-19. Objective: The goal of this initiative was to implement a new, mobile diagnostic imaging service that would minimize external travel during inpatient rehab, reduce risk of exposure to COVID-19, reduce lost therapy hours, while at least remaining cost-neutral. In order to evaluate this service, the costs and benefits associated with this mobile x-ray and ultrasound service were examined. Methods: With the support of Joint Department of Medical Imaging, our SCI rehab program partnered with STL Diagnostic Imaging to provide onsite x-ray and ultrasound imaging.The service began on May 11, 2020 and consisted of mobile x-ray imaging twice per week and mobile ultrasound scans once per week for two hours each. All imaging was conducted in patient rooms by STL technologists. Monthly STL billing costs were compared to estimated transportation costs for patients. Typical transportation costs range from $60-$284 depending on mode of transportation. Results: Between May 11, 2020 and January 28, 2021, 144 patients received 203 x-ray images over 67 x-ray days and 81 patients received 105 ultrasound scans over 37 ultrasound days. Over this timeframe, the approximate savings in transportation costs ranged from $7114 to $20,753. In addition, it is estimated that 225 - 450 lost therapy hours were avoided since patients did not have to travel for imaging and therefore avoided missing scheduled therapy appointments. Although not formally evaluated, physician, patient and nursing staff satisfaction regarding this new service has also been extremely positive. Conclusion: Although implemented out of necessity during the pandemic, this partnership to provide mobile diagnostic imaging has been cost-effective and beneficial to patients.
ABSTRACT
Objective: Percutaneous ultrasound-guided creation of an arteriovenous fistula (pAVF) for hemodialysis access is a relatively novel procedure with promising technical success and patency rates. The vascular surgery departments of two collaborating Swiss hospitals had decided to introduce the technique to their services. A surgeon experienced in the technique (AM) was supposed to come to Switzerland and proctor the first four procedures. Due to the SARS-CoV-2 pandemic and travel restrictions, this was not possible and we decided to perform the first four pAVF procedures tele-proctored via a video conference system. We present the setup and our experience with tele-proctoring. Methods: The setup relied on an all-in-one live video production device, video encoder, video streamer and video recorder (Pearl-2, Epiphan), which made it possible to simultaneously transmit the live image from the ultrasound device (GE Logiq S8, linear probe 9L-D) and a live image from a video camera (JVC Camcorder G/-HM440E, Japan), both connected via HDMI (Figure). The live stream was shared with the proctor in France and the device support team in the US, using an encrypted Swiss video client (www.vitimway.ch). The setup was tested with all parties three days in advance. Results: All 4 procedures started with a verbal briefing and a live ultrasound scan. All steps of the procedures were taken under the proctor's instruction and supervision. The proctor gave on average 21 instructions per procedure. An average 4 were device-related but these became less frequent as we proceeded. The operators consulted the proctor on average 5 times per procedure. The average duration of the procedure was 34 min. The pAVF creation was successful in all 4 patients, with an average fistula flow measured at the end of the procedure of 600ml/min. Conclusion: Our experience showed us that pAVF creation, which is a procedure performed entirely under sonographic guidance lends itself particularly well to tele-proctoring. The simultaneous transmission of the live sonographic image and the live image of the operators' hands allowed the proctor to supervise and correct the key steps of the procedures. The simplicity of the set-up and the quality of proctor-operator interaction was such a positive experience that we can well envisage a much wider use of tele-proctoring in the future.
ABSTRACT
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.