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        "status": "ok",
        "total_count": 813,
        "returned": 100,
        "incomplete_results": false,
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        "name_collisions_skipped": 0
      },
      {
        "query": "topic:binary-analysis is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T10:47:14.703120Z",
        "run_id": "2026-10-16T10:44:37.221963Z",
        "status": "ok",
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        "incomplete_results": false,
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        "name_collisions_skipped": 0
      },
      {
        "query": "topic:javascript topic:reverse-engineering is:public fork:false archived:false",
        "page": 2,
        "per_page": 100,
        "observed_at": "2026-10-16T10:47:18.678576Z",
        "run_id": "2026-10-16T10:44:37.221963Z",
        "status": "ok",
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        "returned": 100,
        "incomplete_results": false,
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        "name_collisions_skipped": 0
      },
      {
        "query": "topic:unity topic:reverse-engineering is:public fork:false archived:false",
        "page": 2,
        "per_page": 100,
        "observed_at": "2026-10-16T10:47:23.007365Z",
        "run_id": "2026-10-16T10:44:37.221963Z",
        "status": "ok",
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        "returned": 41,
        "incomplete_results": false,
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        "name_collisions_skipped": 0
      },
      {
        "query": "topic:ios topic:reverse-engineering is:public fork:false archived:false",
        "page": 2,
        "per_page": 100,
        "observed_at": "2026-10-16T10:47:25.246942Z",
        "run_id": "2026-10-16T10:44:37.221963Z",
        "status": "ok",
        "total_count": 263,
        "returned": 100,
        "incomplete_results": false,
        "retained_attempts_skipped": 10,
        "name_collisions_skipped": 0
      },
      {
        "query": "topic:firmware-analysis is:public fork:false archived:false",
        "page": 2,
        "per_page": 100,
        "observed_at": "2026-10-16T10:47:29.321518Z",
        "run_id": "2026-10-16T10:44:37.221963Z",
        "status": "ok",
        "total_count": 183,
        "returned": 83,
        "incomplete_results": false,
        "retained_attempts_skipped": 2,
        "name_collisions_skipped": 0
      },
      {
        "query": "\"web\" \"reconstruction\" in:description is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:53:42.002137Z",
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        "status": "ok",
        "total_count": 280,
        "returned": 100,
        "incomplete_results": false,
        "retained_attempts_skipped": 0,
        "name_collisions_skipped": 0
      },
      {
        "query": "topic:source-maps topic:reverse-engineering is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:53:47.009224Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 10,
        "returned": 10,
        "incomplete_results": false,
        "retained_attempts_skipped": 7,
        "name_collisions_skipped": 0
      },
      {
        "query": "\"JavaScript\" \"bundle\" \"recover\" in:description is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:53:48.060462Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 1,
        "returned": 1,
        "incomplete_results": false,
        "retained_attempts_skipped": 0,
        "name_collisions_skipped": 0
      },
      {
        "query": "topic:react-native topic:reverse-engineering is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:53:49.907832Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 26,
        "returned": 26,
        "incomplete_results": false,
        "retained_attempts_skipped": 5,
        "name_collisions_skipped": 0
      },
      {
        "query": "topic:dotnet topic:decompiler is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:53:52.939512Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 39,
        "returned": 39,
        "incomplete_results": false,
        "retained_attempts_skipped": 9,
        "name_collisions_skipped": 0
      },
      {
        "query": "\"Flutter\" \"snapshot\" in:description is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:53:55.522916Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 85,
        "returned": 85,
        "incomplete_results": false,
        "retained_attempts_skipped": 5,
        "name_collisions_skipped": 0
      },
      {
        "query": "topic:static-recompilation is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:53:59.675102Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 316,
        "returned": 100,
        "incomplete_results": false,
        "retained_attempts_skipped": 5,
        "name_collisions_skipped": 0
      },
      {
        "query": "\"matching decompilation\" in:description is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:54:02.696958Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 251,
        "returned": 100,
        "incomplete_results": false,
        "retained_attempts_skipped": 9,
        "name_collisions_skipped": 0
      },
      {
        "query": "topic:game-preservation topic:reverse-engineering is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:54:06.371112Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 318,
        "returned": 100,
        "incomplete_results": false,
        "retained_attempts_skipped": 20,
        "name_collisions_skipped": 0
      },
      {
        "query": "\"game\" \"asset\" \"extractor\" in:description is:public fork:false archived:false",
        "page": 1,
        "per_page": 100,
        "observed_at": "2026-10-16T11:54:09.884892Z",
        "run_id": "2026-10-16T11:51:56.511504Z",
        "status": "ok",
        "total_count": 164,
        "returned": 100,
        "incomplete_results": false,
        "retained_attempts_skipped": 4,
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      }
    ],
    "method": "Public, non-fork, non-archived GitHub repository discovery through search, retained unattempted repository-ID lookups on resume, and optional curated-resource or bibliography-artifact metadata lookups, followed by an actual authenticated GET of each repository README. README bytes are decoded, analyzed for document features, SHA-256 hashed and discarded.",
    "description_policy": "English and Simplified Chinese descriptions are AI-assisted localizations of retained upstream repository text. description_original preserves retained text; oversized new descriptions are omitted with length and SHA-256 evidence in description_omission. Translation does not imply verification.",
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      "per_page": 100
    },
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      "Automated README scanning is distinct from the curated source-reviewed catalog.",
      "No repository code, binaries, installers, tests or linked commands are executed.",
      "Search membership and README availability do not establish quality, safety, licensing permission, REA compatibility, or successful operation.",
      "Stars, topics, license identifiers and timestamps come from GitHub repository metadata and are snapshots.",
      "Upstream repository descriptions are attributed source text, not original editorial summaries. README text is not retained.",
      "Repositories without a readable nonempty README, oversized README files and failed requests do not count as successful sources.",
      "Search results are relevance-limited by queries, sorted by stars within each query, and capped by GitHub pagination; this is not an exhaustive census.",
      "README URLs can change after collection; content hashes and Git blob identifiers record the observed bytes."
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    "unattempted_candidates": 252,
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        "method": "Public, non-fork, non-archived GitHub repository search followed by an actual authenticated GET of each repository README. README bytes are decoded, analyzed for document features, SHA-256 hashed and discarded.",
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        "successful_readme_scans": 2000,
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        "unattempted_candidates": 164,
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          "max_readme_bytes": 8388608,
          "max_pages_per_query": 5,
          "per_page": 100
        },
        "method": "Public, non-fork, non-archived GitHub repository discovery through search and optional curated-reference metadata lookups, followed by an actual authenticated GET of each repository README. README bytes are decoded, analyzed for document features, SHA-256 hashed and discarded.",
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        "query_count": 39,
        "candidate_ids_retained": true,
        "known_repository_ids": 2180,
        "run": {
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          "started_at": "2026-10-16T07:14:06.240200Z",
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          "mode": "resume",
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          "requested_new_successful_scans": 400,
          "readme_queue_candidates": 569,
          "seed_curated": true,
          "query_plan": [
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            "topic:javascript topic:reverse-engineering is:public fork:false archived:false",
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            "topic:webassembly topic:reverse-engineering is:public fork:false archived:false",
            "topic:unity topic:reverse-engineering is:public fork:false archived:false",
            "topic:unreal-engine topic:reverse-engineering is:public fork:false archived:false",
            "topic:gamemaker topic:decompiler is:public fork:false archived:false",
            "topic:decompilation topic:gameboy-advance is:public fork:false archived:false",
            "topic:decompilation topic:nintendo-ds is:public fork:false archived:false",
            "topic:ios topic:reverse-engineering is:public fork:false archived:false",
            "topic:flutter topic:reverse-engineering is:public fork:false archived:false",
            "topic:android topic:frida-script is:public fork:false archived:false",
            "topic:decompiler is:public fork:false archived:false",
            "topic:game-decompilation is:public fork:false archived:false",
            "topic:android-reverse-engineering is:public fork:false archived:false",
            "topic:firmware-analysis is:public fork:false archived:false",
            "topic:binary-analysis is:public fork:false archived:false"
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      },
      {
        "started_at": "2026-10-16T01:34:02.145710Z",
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        "last_checkpoint_at": "2026-10-16T10:48:15.816658Z",
        "status": "complete",
        "requested_successful_scans": 2500,
        "unique_repos": 2716,
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        "failed": 25,
        "unattempted_candidates": 191,
        "limits": {
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          "max_readme_bytes": 8388608,
          "max_pages_per_query": 5,
          "per_page": 100
        },
        "method": "Public, non-fork, non-archived GitHub repository discovery through search, retained unattempted repository-ID lookups on resume, and optional curated-resource or bibliography-artifact metadata lookups, followed by an actual authenticated GET of each repository README. README bytes are decoded, analyzed for document features, SHA-256 hashed and discarded.",
        "source_sha256": "80a1fc371a2672220b4c6525ff99c92b20585c9131d7ab70b662108644b27c13",
        "query_count": 62,
        "candidate_ids_retained": true,
        "known_repository_ids": 2716,
        "run": {
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          "started_at": "2026-10-16T10:44:37.221963Z",
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          "mode": "resume",
          "query_start_index": 39,
          "retained_successful_readme_scans": 2000,
          "retained_failed_readme_scans": 16,
          "requested_new_successful_scans": 500,
          "readme_queue_candidates": 700,
          "seed_curated": true,
          "seed_papers": true,
          "retained_unattempted_repository_ids": 164,
          "query_plan": [
            "topic:javascript topic:deobfuscation is:public fork:false archived:false",
            "topic:javascript topic:reverse-engineering is:public fork:false archived:false",
            "topic:electron topic:reverse-engineering is:public fork:false archived:false",
            "topic:webassembly topic:reverse-engineering is:public fork:false archived:false",
            "topic:unity topic:reverse-engineering is:public fork:false archived:false",
            "topic:unreal-engine topic:reverse-engineering is:public fork:false archived:false",
            "topic:gamemaker topic:decompiler is:public fork:false archived:false",
            "topic:decompilation topic:gameboy-advance is:public fork:false archived:false",
            "topic:decompilation topic:nintendo-ds is:public fork:false archived:false",
            "topic:ios topic:reverse-engineering is:public fork:false archived:false",
            "topic:firmware-analysis is:public fork:false archived:false",
            "topic:protocol-analysis is:public fork:false archived:false",
            "\"firmware\" \"analysis\" in:description is:public fork:false archived:false",
            "\"protocol\" \"reverse engineering\" in:description is:public fork:false archived:false",
            "topic:flutter topic:reverse-engineering is:public fork:false archived:false",
            "topic:android topic:frida-script is:public fork:false archived:false",
            "topic:decompiler is:public fork:false archived:false",
            "topic:decompilation is:public fork:false archived:false",
            "topic:binary-analysis is:public fork:false archived:false"
          ],
          "seed_observation_start_index": 33,
          "resume_observation_start_index": 0,
          "status": "complete",
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          "seed_observation_count": 17,
          "resume_observation_count": 164,
          "new_successful_readme_scans": 500,
          "new_failed_readme_scans": 9
        }
      }
    ],
    "unique_repos_policy": "Distinct persisted repository IDs from retained attempts and discovery observations. Historical count-only unattempted candidates are not added to this union unless rediscovered; their original counts remain in resume_history.",
    "current_run": {
      "run_id": "2026-10-16T11:51:56.511504Z",
      "started_at": "2026-10-16T11:51:56.511504Z",
      "completed_at": "2026-10-16T11:55:19.172701Z",
      "mode": "resume",
      "query_start_index": 62,
      "retained_successful_readme_scans": 2500,
      "retained_failed_readme_scans": 25,
      "requested_new_successful_scans": 500,
      "readme_queue_candidates": 771,
      "seed_curated": true,
      "seed_papers": true,
      "retained_unattempted_repository_ids": 191,
      "query_plan": [
        "\"web\" \"reconstruction\" in:description is:public fork:false archived:false",
        "topic:source-maps topic:reverse-engineering is:public fork:false archived:false",
        "\"JavaScript\" \"bundle\" \"recover\" in:description is:public fork:false archived:false",
        "topic:react-native topic:reverse-engineering is:public fork:false archived:false",
        "topic:dotnet topic:decompiler is:public fork:false archived:false",
        "\"Flutter\" \"snapshot\" in:description is:public fork:false archived:false",
        "topic:static-recompilation is:public fork:false archived:false",
        "\"matching decompilation\" in:description is:public fork:false archived:false",
        "topic:game-preservation topic:reverse-engineering is:public fork:false archived:false",
        "\"game\" \"asset\" \"extractor\" in:description is:public fork:false archived:false",
        "\"Electron\" \"unpack\" in:description is:public fork:false archived:false",
        "\"browser\" \"reimplementation\" in:description is:public fork:false archived:false",
        "\"API\" \"reverse engineering\" \"client\" in:description is:public fork:false archived:false",
        "\"software\" \"reconstruction\" in:description is:public fork:false archived:false"
      ],
      "seed_observation_start_index": 50,
      "resume_observation_start_index": 164,
      "status": "complete",
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      "resume_observation_count": 191,
      "new_successful_readme_scans": 500,
      "new_failed_readme_scans": 19
    },
    "seed_observations": [
      {
        "full_name": "angr/angr",
        "observed_at": "2026-10-16T07:14:06.273823Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
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        "status": "candidate",
        "repository_id": "scan-40328394"
      },
      {
        "full_name": "assetripper/assetripper",
        "observed_at": "2026-10-16T07:14:06.631645Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
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        ],
        "status": "candidate",
        "repository_id": "scan-385118073"
      },
      {
        "full_name": "baldurk/renderdoc",
        "observed_at": "2026-10-16T07:14:06.987079Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
          "renderdoc"
        ],
        "status": "candidate",
        "repository_id": "scan-17253131"
      },
      {
        "full_name": "bigtower17/picoprint",
        "observed_at": "2026-10-16T07:14:07.257230Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
          "picoprint-rea-investigation"
        ],
        "status": "candidate",
        "repository_id": "scan-1420877270"
      },
      {
        "full_name": "bytecodealliance/wasm-tools",
        "observed_at": "2026-10-16T07:14:07.562888Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
          "wasm-tools"
        ],
        "status": "candidate",
        "repository_id": "scan-265302687"
      },
      {
        "full_name": "chromedevtools/chrome-devtools-mcp",
        "observed_at": "2026-10-16T07:14:07.942622Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
          "chrome-devtools-mcp"
        ],
        "status": "candidate",
        "repository_id": "scan-1054793726"
      },
      {
        "full_name": "crissyfield/super-trouper",
        "observed_at": "2026-10-16T07:14:08.293221Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
          "super-trouper"
        ],
        "status": "candidate",
        "repository_id": "scan-1353687754"
      },
      {
        "full_name": "dnspyex/dnspy",
        "observed_at": "2026-10-16T07:14:08.627833Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
          "dnspyex"
        ],
        "status": "ineligible"
      },
      {
        "full_name": "electron/asar",
        "observed_at": "2026-10-16T07:14:09.055556Z",
        "run_id": "2026-10-16T07:14:06.240200Z",
        "method": "curated-repository-reference",
        "reference_ids": [
          "electron-asar"
        ],
        "status": "candidate",
        "repository_id": "scan-24328822"
      },
      {
        "full_name": "ersith/dsh-mcp-rea",
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      "description_zh": "RNA 疫苗已成为应对当前疫情及众多其他公共卫生和医学挑战的重要工具。随着 COVID-19 疫苗推广，这些合成 mRNA 已成为广泛分布于众多人群中的 RNA 类型。尽管它们十分普遍，其序列却并非总是可得；标准方法可以完成此类测序。本文提供初版 Moderna（https://pubmed.ncbi.nlm.nih.gov/32756549/）和 Pfizer/BioNTech（https://pubmed.ncbi.nlm.nih.gov/33301246/）COVID-19 疫苗 RNA 成分的实验序列信息，从而组装前者的可用序列，并确认后者此前报道的 RNA 序列。共享广泛使用的治疗制剂的序列信息，有助于采用测序方法的研究人员或临床医生迅速判断这些序列来自治疗制剂，而非宿主或感染源。本研究的 RNA 来自接种后疫苗瓶中剩余少量剂量的废弃部分；这些部分原本必须丢弃，并在 FDA 授权的研究用途下接受分析。为获得表征所需的少量 RNA，我们使用 TRIzol Reagent（Invitrogen）对疫苗残留物进行酚-氯仿提取，并在提取前后用 Agilent 2100 Bioanalyzer 评估其完整性。虽然分析主要针对废弃后尽快获取的 RNA，我们也分析了添加或未添加 EDTA、在约 4 ℃ 冷藏最长 42 天的样本。有意思的是，这些制备物中相当一部分 RNA 仍保持完整。需要说明的是，疫苗配方包含多种关键化学成分，它们在这些条件下很可能不稳定，因此这些数据绝不意味着疫苗作为生物制剂仍然稳定。不过，RNA 本身的化学稳定性并不足以排除未来开发出冷链储运要求低得多的疫苗，这一点值得关注。进一步分析时，先将 RNA 加热至 94℃ 使其片段化，用带随机六聚体尾部接头的引物引发，再采用模板切换方案（Takara SMARTerer Stranded RNA-seq kit）扩增，并使用 MiSeq 仪器（Illumina）进行双端测序，每端 78 个碱基。在特定测定中，我们纳入已知浓度和序列的 RNA（来自 MS2 噬菌体）作为参考材料。从这些数据中获得了部分链向信息，以及一组可用于组装的片段。这对 Moderna 疫苗尤为有用，因为研究进行时其原始疫苗 RNA 序列尚未公开。我们从 Moderna 和 Pfizer 数据集中组装出编码全长刺突蛋白的重叠群。Pfizer/BioNTech 数据［图 1］验证了此前报道的该疫苗序列（https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/），而 Moderna 序列［图 2］则无法与已发表的参考序列核对。疫苗配方宜使用不含 dsRNA 的 RNA 制备物，以尽量降低脊椎动物对 RNA 双链特征产生的强烈且非特异性的生物反应（https://www.nature.com/articles/nrd.2017.243）。在我们分析的序列数据中，绝大多数读段来自预期的正义链。此外，少数反义链读段似乎与正义链读段不同，缺少模板切换方案预期产生的特征性延伸。仅检查具有明显模板切换的读段（将其作为来源链的指示）时，两种疫苗产生的读段均以正义链为绝大多数（>99.99%）。独立测序及其他实验测量仍在进行，需借助这些实验判断 SmarterSeq 方案中经过模板切换的正义链读段比例，是否确实反映原始材料中的实际 dsRNA 含量。本研究对两种现已成为人类生态系统组成部分的 RNA 作出初步评估；在部分受试者可能已接种疫苗的其他高通量 RNA-seq 研究中，它们也很可能出现。初步致谢：感谢同事们的帮助与建议（Nimit Jain、Emily Greenwald、Lamia Wahba、William Wang、Amisha Kumar、Sameer Sundrani、David Lipman、Bijoyita Roy）。图 1：由 BioNTech/Pfizer BNT-162b2 疫苗组装的刺突蛋白编码重叠群。尽管包含完整编码区，所用测序与组装方法的性质决定了组装结果可能缺少 RNA 两端的部分序列。在已组装范围内，该推定序列与网上公开文档中的对应序列完全匹配，这些文档来源于制造商与世界卫生组织的通信［见 https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/ 的报道］。组装序列的 5’ 端与这些文档所述起始位点一致，但基于读段的组装结果缺少预期存在于 mRNA 中的间断 polyA 尾（A30(GCATATGACT)A70）。",
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