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EpiStack v1 — FLF competition
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analyses
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covid
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observations and facts
Folder: v1/analyses/covid/observations-and-facts
61 items under this folder.
Jul 23, 2026
orphan
Jul 23, 2026
O-1 - Recomputed Monte Carlo p-values for the market as case center are marginal and weaken toward non-significance as the case sample shrinks
Jul 23, 2026
O-17 - None of 457 animal-source samples from the Huanan market tested positive for SARS-CoV-2
Jul 23, 2026
O-18 - SARS-CoV-2-positive environmental samples were concentrated in the market's western (wildlife) wing
Jul 23, 2026
O-19 - Both early lineages A and B recovered from environmental swabs in the market's west wing
Jul 23, 2026
O-2 - Bootstrap places the market at the edge of the case-centroid cloud with Wanda Plaza an equally admissible center
Jul 23, 2026
O-20 - Positive environmental samples contained abundant genetic material from wildlife species
Jul 23, 2026
O-21 - Pekar 2022 reported two-introduction Bayes factor fell from ~60 to ~4.3 after the 2024 coding-error erratum
Jul 23, 2026
O-22 - Pekar 2022 computed the two-introduction likelihood by squaring only the polytomy criterion, omitting the size-ratio and sequence-difference conditions imposed on one introduction
Jul 23, 2026
O-23 - Individual infectiousness is highly overdispersed across eight directly-transmitted diseases; SARS dispersion k approx 0.16
Jul 23, 2026
O-25 - Almost all Yambuku Ebola cases traced to reused hospital needles or contact with a case, and the outbreak collapsed when the hospital closed
Jul 23, 2026
O-26 - The natural reservoir and the index case exposure route were not identified by the 1976 Ebola investigation
Jul 23, 2026
O-27 - Nationwide survey of -80,000 wildlife, livestock and poultry samples across 31 Chinese provinces found zero SARS-CoV-2 positives
Jul 23, 2026
O-28 - All 457 animal-related market samples (188 individuals, 18 species) were SARS-CoV-2 negative, but were leftover frozen goods and vermin sampled after market closure
Jul 23, 2026
O-29 - 923 Huanan-market environmental samples yielded 73 SARS-CoV-2 positives (3 isolates), with positives clustering at aquatic-cold-chain-meat vendor stalls
Jul 23, 2026
O-30 - December-2019 Wuhan cases were significantly closer to the Huanan market than a population-weighted null
Jul 23, 2026
O-31 - Both lineage A and lineage B early cases cluster near the Huanan market
Jul 23, 2026
O-32 - Market-unlinked December cases lived even closer to the market than market-linked cases
Jul 23, 2026
O-33 - Positive market environmental samples concentrated at a single live-mammal vendor stall
Jul 23, 2026
O-35 - DEFUSE was a consortium of EcoHealth, UNC (Baric), the Wuhan Institute of Virology (Shi), Duke-NUS, USGS and PARC, with WIV assigned viral testing and humanized-mouse work
Jul 23, 2026
O-36 - DEFUSE proposed inserting field-sampled bat spike proteins into WIV1-SHC014 backbones and infecting humanized (hACE2) mice to assess SARS-like disease capacity
Jul 23, 2026
O-37 - DEFUSE proposed introducing human-specific (furin) cleavage sites into SARS-related coronavirus spikes
Jul 23, 2026
O-38 - DEFUSE asserted its chimeric-spike work used bat-SARSr-CoV backbones and was 'exempt from dual use and gain of function concerns'
Jul 23, 2026
O-39 - Market-associated SARS-CoV-2 genomes' tMRCA matches the global pandemic tMRCA and both lineages A and B are present in market environmental samples
Jul 23, 2026
O-4 - Early SARS-CoV-2 split into two lineages A and B differing by two linked substitutions
Jul 23, 2026
O-40 - SARS-CoV-2 positivity concentrated at wildlife stall A, whose five positive samples all contained susceptible-mammal (incl. raccoon dog) mtDNA
Jul 23, 2026
O-41 - In the balanced n=70 wildlife-stall set human mtDNA was uncorrelated with viral RNA while Malayan porcupine and Himalayan marmot mtDNA were significantly positively correlated
Jul 23, 2026
O-42 - Host-specific wildlife viruses (raccoon-dog amdoparvovirus, bamboo-rat betacoronavirus, civet kobuvirus) were recovered from the market, phylogenetically traceable to southern-China farms
Jul 23, 2026
O-43 - 47,381 wild animals of 38 species were sold at four Wuhan markets in 2017-2019, including 7 wild-animal shops at Huanan
Jul 23, 2026
O-44 - SARS-CoV-2-susceptible mammals (raccoon dogs, civets, mink) were sold live in volume at Wuhan markets
Jul 23, 2026
O-47 - In Feb 2023 the DOE shifted to assessing with 'low confidence' that COVID-19 most likely came from a Wuhan lab leak
Jul 23, 2026
O-48 - The FBI has assessed with 'moderate confidence' that COVID-19 most likely came from a lab incident in Wuhan
Jul 23, 2026
O-49 - The 2021 US IC origins investigation was a split verdict- FBI lab (moderate), four agencies natural (low confidence), DOE then agnostic
Jul 23, 2026
O-5 - The 20 apparent A-B intermediate genomes are low-coverage and lab-clustered
Jul 23, 2026
O-50 - Across market samples SARS-CoV-2 abundance correlates most with fish and livestock mtDNA (bass, catfish, cow, carp, snakehead) and negatively with raccoon dog and bamboo rat
Jul 23, 2026
O-51 - Of 14 samples dominated by raccoon-dog mtDNA only one contained any SARS-CoV-2 read (1 of ~2.1x10^8); all six bamboo-rat-dominated samples had zero
Jul 23, 2026
O-52 - FBI Director Wray stated on-record (28 Feb 2023) that the FBI assesses COVID-19's origin as 'most likely a potential lab incident in Wuhan'
Jul 23, 2026
O-53 - The FBI-DOE lab-leaning assessments are classified and self-rated low-moderate confidence; DOE reportedly reached its view via reasoning distinct from the FBI's
Jul 23, 2026
O-54 - All market palm civets and raccoon dogs at Xinyuan market tested positive for SARS-CoV-like virus
Jul 23, 2026
O-57 - Graded SNV series in the civet spike gene from a zero-mutation prototype to human epidemic strains
Jul 23, 2026
O-58 - SARS-CoV-2 RBD has six ACE2-contact residues, five differing from SARS-CoV
Jul 23, 2026
O-59 - Computational analysis predicts the SARS-CoV-2 RBD-ACE2 interaction is not ideal - non-optimal
Jul 23, 2026
O-6 - Molecular-clock dating places tMRCA in mid-December 2019 and lineage B primary infection around 18 Nov 2019
Jul 23, 2026
O-60 - Polybasic furin cleavage site (PRRA insertion) at the S1-S2 junction, absent in related lineage B betacoronaviruses
Jul 23, 2026
O-61 - Three predicted O-linked glycosylation sites flank the SARS-CoV-2 furin cleavage site
Jul 23, 2026
O-62 - SARS-CoV-2 backbone matches no previously described coronavirus reverse-genetics system
Jul 23, 2026
O-64 - Malayan pangolin coronaviruses share all six key RBD residues with SARS-CoV-2
Jul 23, 2026
O-65 - SARS-CoV-2 has five BsaI-BsmBI sites yielding six fragments with unique overhangs
Jul 23, 2026
O-66 - SARS-CoV-2's longest BsaI-BsmBI fragment is 7,578 bp (25% of genome) and it lacks two conserved BsaI sites
Jul 23, 2026
O-67 - All BsaI-BsmBI-site differences from RaTG13-BANAL-52 are silent, at an elevated rate
Jul 23, 2026
O-68 - Three new Lao bat sarbecoviruses; BANAL-52 is 96.8% identical to SARS-CoV-2, exceeding RaTG13
Jul 23, 2026
O-69 - BANAL RBDs match 15-16 of 17 hACE2-contact residues vs only 11-17 for RaTG13
Jul 23, 2026
O-7 - 55% of pre-January-2020 cases were Huanan-market-linked versus 8.6% of later cases
Jul 23, 2026
O-70 - BANAL RBDs bind human ACE2 ~3x more strongly than early SARS-CoV-2; BANAL-236 RBD-hACE2 crystal near-identical
Jul 23, 2026
O-71 - A wild, unmodified BANAL-236 enters and replicates in human cells via hACE2
Jul 23, 2026
O-72 - None of the BANAL viruses has a furin cleavage site
Jul 23, 2026
O-73 - SARS-CoV-2 is a recombinant mosaic of -5 wild bat sarbecoviruses, its RBD fragment nesting in the BANAL clade
Jul 23, 2026
O-74 - SARS-CoV-2 has a RaTG13-like backbone but a pangolin-CoV-like RBD (chimeric structure)
Jul 23, 2026
O-75 - The furin site is a 12-nt PRRA insert with a rare doubled CGG-CGG arginine codon and a FauI site
Jul 23, 2026
O-76 - The PRRA furin-site insertion is out of frame relative to aligned RaTG13-MP789
Jul 23, 2026
O-77 - No close relative has a true S1-S2 insertion; RmYN02's reported insertion is only substitutions
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added after the FLF submission deadline