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Biosurveillance

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From Molecupedia, the encyclopedia of very small things
Monitoring of populations and environments for disease and biological threats

Biosurveillance is the monitoring of people, animals, plants and the environment for signs of disease and biological threats, with the aim of warning before the cases are counted. The United States defined it in 2007 as "the process of active data-gathering with appropriate analysis and interpretation of biosphere data that might relate to disease activity and threats to human or animal health ... in order to achieve early warning of health threats, early detection of health events, and overall situational awareness of disease activity".[1] The data come from clinics and laboratories, from news reports, from filters in the air and, since 2020 especially, from sewage.

Molecular Reality Corporation proposes one more stream, molecular sensors in the drains and toilets of ordinary buildings, which has not been built.

History

Counting cases is the oldest method and the slowest, since a case is counted only after a person has been ill, seen, tested and reported. Two services of the 1990s went around that chain. ProMED-mail, an Internet service for finding and circulating reports of outbreaks in humans, animals and plants, was in its eleventh year in 2005.[2] The Canadian Global Public Health Intelligence Network (GPHIN) reads the world's news, and its authors described it as "exiting the pyramid of official reporting".[3] In late November 2002 GPHIN picked up media reports of an influenza outbreak in mainland China. Retrospective case finding suggests that two respiratory outbreaks were under way in Guangdong Province that month, influenza and what appears to have been a first wave of SARS, and the World Health Organization office in Beijing received an email about the disease on February 10, 2003, saying that it had caused more than 100 deaths.[4]

In 1939 Paul and colleagues reported poliovirus recovered from sewage,[5] and in 1940 they wrote that in two of three large urban epidemics of poliomyelitis the virus had been found in samples of sewage, repeatedly at one of the sites. Both positive sites were near isolation hospitals, and they concluded that the virus could be carried "for short distances at least" by flowing sewage.[6] Air was sampled from 2003, when the first generation of BioWatch samplers was deployed in United States cities to give "an early indication of an aerosolized biological weapon attack". The filters are collected by hand every day and tested; the second-generation system could take up to 36 hours to detect and confirm a pathogen, and in April 2014 the Department of Homeland Security cancelled the acquisition of a successor system that could have analyzed samples in under 6 hours.[7][8]

Wastewater

Main article: Wastewater surveillance

In the spring of 2020 a group measured SARS-CoV-2 RNA in the primary sewage sludge of the New Haven, Connecticut, area for more than ten weeks. Allowing for time lags, the RNA tracked the clinical test results and hospital admissions, and it was 0 to 2 days ahead of positive tests by date of specimen collection, 1 to 4 days ahead of admissions and 6 to 8 days ahead of positive tests by date of reporting.[9] In The Netherlands, sewage from six cities and the airport showed no viral RNA on February 6, 2020, three weeks before the first Dutch case was reported, and RNA at three sites on March 4 and 5; at Amersfoort it appeared six days before the first cases.[10]

Reported lead times of signals in wastewater
Signal Place and year Compared with Lead
SARS-CoV-2 RNA in sludge New Haven, 2020 Hospital admissions 1 to 4 days[9]
SARS-CoV-2 RNA in sewage Amersfoort, 2020 First reported cases 6 days[10]
Sabin-like type 2 poliovirus Rockland and Orange counties, New York, 2022 Symptom onset of a paralytic case Up to 25 days[11]
Variants of SARS-CoV-2, by sequencing University of California San Diego campus, 2020 to 2021 Clinical genomic surveillance Up to 14 days[12]

The poliovirus in the New York samples had been collected for SARS-CoV-2 monitoring.[11] The lead times are retrospective and belong to particular places and strains; the Dutch result also shows the other side, a sewer with no signal in it three weeks before the first case.

Frequency and speed

A model of repeated screening for COVID-19 found that its effectiveness depended largely on how often people were tested and how fast the results came back, and that it was "only marginally improved by high test sensitivity".[13] Sensitivity has a physical limit as well. Calculations of the flux of analyte onto nanoscale sensors in unmixed fluids concluded that without directed transport they would be "limited to picomolar-order sensitivity for practical time scales", a limit set by how molecules get to the sensor.[14] See Capture rate (nanopore).

Nanopores in the field

Sequencing with nanopores has been used where laboratories are not. In April 2015 a nanopore sequencer was carried in standard airline luggage to Guinea, and it gave genome sequences of Ebola virus in under 24 hours from the receipt of a positive sample, with the sequencing itself taking as little as 15 to 60 minutes; 142 samples collected between March and October 2015 were sequenced.[15] For poliovirus in stool and environmental samples, the cell-culture routine takes 2 to 3 weeks on average from receipt of a sample to sequence; a protocol built on nested PCR and nanopore sequencing took under 3 days. Against culture its sensitivity was 90.9% and its specificity 99.2% for wild-type poliovirus 1 in 155 stool samples from Pakistan.[16]

At Molecular Reality

The company's statement of purpose of 2022, "Our North Star", lists the sites for its hardware as "air handling systems, toilets, and drains", and the work of preparing the sample as everyday life: "washing vegetables in the sink, brushing your teeth, washing your hands, taking a shower, using the toilet, breathing in and out, etc."[17] The company calls the defensive use the Planetary Bioshield. The same document discusses the Nucleic Acid Observatory, a proposal to detect new pandemics by sequencing, which it calls "a damn good start", and argues that organisms with "chemically novel genomes" could escape sequencing methods that depend on DNA polymerases, while "Solid-state nanopore sequencing will not have this vulnerability".[17] In the company's quiz dungeon the Planetary Bioshield is "a network of molecular sentinels that could detect pathogens before pandemics spread, identify toxins before they contaminate, and monitor the molecular health of Earth itself."[18]

In January 2020 the company tried to build its Molecular Aquarium quickly because of COVID-19, a project that survives as a badge named CoronaPore.[19] In August 2026 its guide said: "Today we have one instrument in one lab."[20] The long-range goal is called Utility-scale molecular sensing. The guide adds that "nothing on the stream is a medical claim".[20]

See also

References

  1. ^ "Homeland Security Presidential Directive 21: Public Health and Medical Preparedness". The White House. October 18, 2007.
  2. ^ Madoff, L. C.; Woodall, J. P. (2005). "The Internet and the global monitoring of emerging diseases: lessons from the first 10 years of ProMED-mail". Archives of Medical Research 36 (6): 724-730. doi:10.1016/j.arcmed.2005.06.005.
  3. ^ Mykhalovskiy, E.; Weir, L. (2006). "The Global Public Health Intelligence Network and early warning outbreak detection: a Canadian contribution to global public health". Canadian Journal of Public Health 97 (1): 42-44. doi:10.1007/BF03405213.
  4. ^ Heymann, D. L.; Rodier, G. (2004). "Global surveillance, national surveillance, and SARS". Emerging Infectious Diseases 10 (2): 173-175. doi:10.3201/eid1002.031038.
  5. ^ Paul, J. R.; Trask, J. D.; Culotta, C. S. (1939). "Poliomyelitic virus in sewage". Science 90 (2333): 258-259. doi:10.1126/science.90.2333.258.
  6. ^ Paul, J. R.; Trask, J. D.; Gard, S. (1940). "II. Poliomyelitic virus in urban sewage". Journal of Experimental Medicine 71 (6): 765-777. doi:10.1084/jem.71.6.765.
  7. ^ "Enhancing BioWatch Capabilities Through Technology and Collaboration: Proceedings of a Workshop". National Academies Press. 2017.
  8. ^ Biosurveillance: Observations on the Cancellation of BioWatch Gen-3 and Future Considerations for the Program. U.S. Government Accountability Office. June 10, 2014.
  9. ^ a b Peccia, J.; et al. (2020). "Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics". Nature Biotechnology 38 (10): 1164-1167. doi:10.1038/s41587-020-0684-z.
  10. ^ a b Medema, G.; et al. (2020). "Presence of SARS-Coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands". Environmental Science & Technology Letters 7 (7): 511-516. doi:10.1021/acs.estlett.0c00357.
  11. ^ a b Link-Gelles, R.; et al. (2022). "Public health response to a case of paralytic poliomyelitis in an unvaccinated person and detection of poliovirus in wastewater: New York, June to August 2022". MMWR Morbidity and Mortality Weekly Report 71 (33): 1065-1068. doi:10.15585/mmwr.mm7133e2.
  12. ^ Karthikeyan, S.; et al. (2022). "Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission". Nature 609 (7925): 101-108. doi:10.1038/s41586-022-05049-6.
  13. ^ Larremore, D. B.; et al. (2021). "Test sensitivity is secondary to frequency and turnaround time for COVID-19 screening". Science Advances 7 (1): eabd5393. doi:10.1126/sciadv.abd5393.
  14. ^ Sheehan, P. E.; Whitman, L. J. (2005). "Detection limits for nanoscale biosensors". Nano Letters 5 (4): 803-807. doi:10.1021/nl050298x.
  15. ^ Quick, J.; et al. (2016). "Real-time, portable genome sequencing for Ebola surveillance". Nature 530 (7589): 228-232. doi:10.1038/nature16996.
  16. ^ Shaw, A. G.; et al. (2020). "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples by use of nanopore sequencing". Journal of Clinical Microbiology 58 (9): e00920-20. doi:10.1128/JCM.00920-20.
  17. ^ a b "Our North Star: Utility-Scale Molecular Sensing". Molecular Reality Corporation. 2022.
  18. ^ "Dungeons & Diligence: The Disclosure Crawl, Level 6: Oracle's Chamber". Molecular Reality Corporation. April 2026.
  19. ^ "Company records". Molecular Reality Corporation. October 2026.
  20. ^ a b "Keltar's Field Guide to Molecular Reality". Molecular Reality Corporation. August 2026.
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