The CanMars Mars Sample Return analogue mission

The return of samples from known locations on Mars is among the highest priority goals of the international planetary science community. A possible scenario for Mars Sample Return (MSR) is a series of 3 missions: sample cache, fetch, and retrieval. The NASA Mars 2020 mission represents the first cache mission and was the focus of the CanMars analogue mission described in this paper. The major objectives for CanMars included comparing the accuracy of selecting samples remotely using rover data versus a traditional human field party, testing the efficiency of remote science operations with periodic pre-planned strategic observations (Strategic Traverse Days), assessing the utility of realistic autonomous science capabilities to the remote science team, and investigating the factors that affect the quality of sample selection decision-making in light of returned sample analysis. CanMars was conducted over two weeks in November 2015 and continued over three weeks in October and November 2016 at an analogue site near Hanksville, Utah, USA, that was unknown to the Mission Control Team located at the University of Western Ontario (Western) in London, Ontario, Canada. This operations architecture for CanMars was based on the Phoenix and Mars Exploration Rover missions together with previous analogue missions led by Western with the Mission Control Team being divided into Planning and Science sub-teams. In advance of the 2015 operations, the Science Team used satellite data, chosen to mimic datasets available from Mars-orbiting instruments, to produce a predictive geological map for the landing ellipse and a set of hypotheses for the geology and astrobiological potential of the landing site. The site was proposed to consist of a series of weakly cemented multi-coloured sedimentary rocks comprising carbonates, sulfates, and clays, and sinuous ridges with a resistant capping unit, interpreted as inverted paleochannels. Both the 2015 CanMars mission, which achieved 11 sols of operations, and the first part of the 2016 mission (sols 12–21), were conducted with the Mars Exploration Science Rover (MESR) and a series of integrated and hand-held instruments designed to mimic the payload of the Mars 2020 rover. Part 2 of the 2016 campaign (sols 22–39) was implemented without the MESR rover and was conducted exclusively by the field team as a Fast Motion Field Test (FMFT) with hand-carried instruments and with the equivalent of three sols of operations being executed in a single actual day. A total of 8 samples were cached during the 39 sols from which the Science Team prioritized 3 for “return to Earth”. Various science autonomy capabilities, based on flight-proven or near-future techniques intended for actual rover missions, were tested throughout the 2016 CanMars activities, with autonomous geological classification and targeting and autonomous pointing refinement being used extensively during the FMFT. Blind targeting, contingency sequencing, and conditional sequencing were also employed. Validation of the CanMars cache mission was achieved through various methods and approaches. The use of dedicated documentarians in mission control provided a detailed record of how and why decisions were made. Multiple separate field validation exercises employing humans using traditional geological techniques were carried out. All 8 of the selected samples plus a range of samples from the landing site region, collected out-of-simulation, have been analysed using a range of laboratory analytical techniques. A variety of lessons learned for both future analogue missions and planetary exploration missions are provided, including: dynamic collaboration between the science and planning teams as being key for mission success; the more frequent use of spectrometers and micro-imagers having remote capabilities rather than contact instruments; the utility of strategic traverse days to provide additional time for scientific discussion and meaningful interpretation of the data; the benefit of walkabout traverse strategies along with multi-sol plans with complex decisions trees to acquire a large amount of contextual data; and the availability of autonomous geological targeting, which enabled complex multi-sol plans gathering large suites of geological and geochemical survey data. Finally, the CanMars MSR activity demonstrated the utility of analogue missions in providing opportunities to engage and educate children and the public, by providing tangible hands-on linkages between current robotic missions and future human space missions. Public education and outreach was a priority for CanMars and a dedicated lead coordinated a strong presence on social media (primarily Twitter and Facebook), articles in local, regional, and national news networks, and interaction with the local community in London, Ontario. A further core objective of CanMars was to provide valuable learning opportunities to students and post-doctoral fellows in preparation for future planetary exploration missions. A learning goals survey conducted at the end of the 2016 activities had 90% of participants “somewhat agreeing” or “strongly agreeing” that participation in the mission has helped them to increase their understanding of the four learning outcomes

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission and is a key element in safely reopening society. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

ABSTRACT The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission 1, 2 . Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens

Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples.

Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

ABSTRACT The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission 1, 2 . Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens

Detection of COVID-19 using multimodal data from a wearable device: results from the first TemPredict Study.

Early detection of diseases such as COVID-19 could be a critical tool in reducing disease transmission by helping individuals recognize when they should self-isolate, seek testing, and obtain early medical intervention. Consumer wearable devices that continuously measure physiological metrics hold promise as tools for early illness detection. We gathered daily questionnaire data and physiological data using a consumer wearable (Oura Ring) from 63,153 participants, of whom 704 self-reported possible COVID-19 disease. We selected 73 of these 704 participants with reliable confirmation of COVID-19 by PCR testing and high-quality physiological data for algorithm training to identify onset of COVID-19 using machine learning classification. The algorithm identified COVID-19 an average of 2.75 days before participants sought diagnostic testing with a sensitivity of 82% and specificity of 63%. The receiving operating characteristic (ROC) area under the curve (AUC) was 0.819 (95% CI [0.809, 0.830]). Including continuous temperature yielded an AUC 4.9% higher than without this feature. For further validation, we obtained SARS CoV-2 antibody in a subset of participants and identified 10 additional participants who self-reported COVID-19 disease with antibody confirmation. The algorithm had an overall ROC AUC of 0.819 (95% CI [0.809, 0.830]), with a sensitivity of 90% and specificity of 80% in these additional participants. Finally, we observed substantial variation in accuracy based on age and biological sex. Findings highlight the importance of including temperature assessment, using continuous physiological features for alignment, and including diverse populations in algorithm development to optimize accuracy in COVID-19 detection from wearables