Pathway Human Homo sapiens

SARS-CoV-2 Infection

R-HSA-9694516 in Reactome release 97: under SARS-CoV Infections, with 313 genes placed in it by the mapping files and 3 child pathways in the hierarchy.

The same number in the other species

Reactome writes the mouse and rat events it infers from a human pathway under the human number with the species token. A door opens only where that species' own list in this release holds the id; neither of the other two lists holds it. Whether the event was inferred from this one is what the record says.

The record
The genes
Parents and children

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This page reads the pathway's record from its source while you read the rest; with scripts off the card stays at its loading line. Reload with scripts on to see it, or open the source's own page from the link in the card.

01The record

Reactome's own record of this pathway

What this tells you

The pathway list, the hierarchy and the genes on this page are read from the files Reactome publishes for Reactome release 97, built into this site on 2026-09-09: the pathway list, the hierarchy relationship file and the two gene mapping files. The record card is the one live read, Reactome's own record of this pathway.

Reactome's download page describes the mapping files: Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway, all levels of the pathway hierarchy or database identifier to all reactions. [R13] The gene list here is the all-levels mapping of NCBI Gene ids, filled from the all-levels mapping of Ensembl ids where the NCBI file has no row for a gene; each row names which file it came from by the shape of its source id. Each row carries the evidence codes the file writes for it, as written and unranked, and both where the file writes both; no page of Reactome's documentation the survey read defines the codes, so this page does not expand them. A gene id the identity files do not name is kept as the source's own id with no door rather than turned into a symbol.

On citing what a search finds, Reactome says: It should be remembered that while we strive to contain the most current and accurate data, Reactome should not be used in citations where other primary sources of information are available. [R12] The record card prints the literature Reactome attaches to a curated pathway for that reason. The data are public domain: All data in the Reactome database and files derived from that data are licensed under the Creative Commons Public Domain Dedication (CC0). User may copy, modify, and distribute these data, even for commercial purposes, without asking for permission. Attribution is encouraged but not required. [R10] The pathway illustrations are licensed apart, under CC BY 4.0, and none is shown here.

A gene on this list is one Reactome places in this pathway in this release, and that is all the row says: it does not say the gene is expressed in a tissue or associated with a disease, which are the other two explorers' questions, read from other sources. Reactome's papers of record are [R01] [R02].

[R01] Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, et al. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Research 54:D673-D681. PMID 41251150, doi 10.1093/nar/gkaf1223.
[R02] Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, et al. (2024). The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research 52:D672-D678. PMID 37941124, doi 10.1093/nar/gkad1025.
[R10] Reactome, reactome.org. License Agreement. https://reactome.org/license, read 2026-09-09.
[R12] Reactome, reactome.org. Citing us. https://reactome.org/cite, read 2026-09-09.
[R13] Reactome, reactome.org. Download. https://reactome.org/download-data, read 2026-09-09.

Stable id: R-HSA-9694516.9
Class: Pathway
Species: Homo sapiens (human)
Inferred: yes
Disease pathway: yes, as Reactome flags it
Released: 2020-09-15
Last updated: 2022-09-14
Events inside: 3, counted from the record

Reactome's caveat

The electronically inferred reactions presented in Reactome are thus not data, but hypotheses useful to direct the design of confirmatory experiments.
Reactome, on its computationally inferred events.

This pathway, SARS-CoV-2 infection of human cells (COVID-19), was initially generated via electronic inference from the manually curated and reviewed Reactome SARS-CoV-1 (Human SARS coronavirus) infection pathway. The inference process created SARS-CoV-2 events corresponding to each event in the SARS-CoV-1 pathway and populated those events with SARS-CoV-2 protein-containing physical entities based on orthology to SARS-CoV-1 proteins (https://reactome.org/documentation/inferred-events). All of these computationally created events and entities have been reviewed by Reactome curators and modified as appropriate where recently published experimental data indicate the existences of differences between the molecular details of the SARS-CoV-1 and SARS-CoV-2 infection pathways.

SARS‑CoV‑2 infection begins with the binding of viral S (spike) protein to cell surface angiotensin converting enzyme 2 (ACE2) and endocytosis of the bound virion. Within the endocytic vesicle, host proteases mediate cleavage of S protein into S1 and S2 fragments, leading to S2‑mediated fusion of the viral and host endosome membranes and release of the viral capsid into the host cell cytosol. The capsid is uncoated to free the viral genomic RNA, whose cap‑dependent translation produces polyprotein pp1a and, by means of a 1‑base frameshift, polyprotein pp1ab. Autoproteolytic cleavage of pp1a and pp1ab generates 15 or 16 nonstructural proteins (nsps) with various functions. Importantly, the RNA dependent RNA polymerase (RdRP) activity is encoded in nsp12. Nsp3, 4, and 6 induce rearrangement of the cellular endoplasmic reticulum membrane to form cytosolic double membrane vesicles (DMVs) where the viral replication transcription complex is assembled and anchored. With viral genomic RNA as a template, viral replicase‑transcriptase synthesizes a full length negative sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA. The replicase‑transcriptase can also switch template during discontinuous transcription of the genome at transcription regulated sequences to produce a nested set of negative‑sense subgenomic (sg) RNAs, which are used as templates for the synthesis of positive‑sense sgRNAs that are translated to generate viral proteins. Finally, viral particle assembly occurs in the ER Golgi intermediate compartment (ERGIC). Viral M protein provides the scaffold for virion morphogenesis (Hartenian et al. 2020; Fung & Liu 2019; Masters 2006).

This Reactome module also describes molecular mechanisms by which SARS-CoV-2 modulates innate and adaptive immune responses, autophagy, host translation, intracellular signaling and regulatory pathways, and PDZ-mediated cell-cell junctions, mostly annotated from studies of cells infected with SARS-CoV-2.

Literature Reactome attaches

The Genome sequence of the SARS-associated coronavirusScience, 2003, vol. 300, p. 1399-404PubMed 12730501
Human Coronavirus: Host-Pathogen InteractionAnnu. Rev. Microbiol., 2019, vol. 73, p. 529-557PubMed 31226023

Reactome ContentService, this pathway's record · Reactome v97 · read 2026-10-06 ET · Reactome pathway browser"SARS-CoV-2 Infection". Reactome, release 97, https://reactome.org/PathwayBrowser/#/R-HSA-9694516 with StableID: R-HSA-9694516.9 (accessed 2026-10-06 ET). Reactome version 97 (CC0).

Reading this pathway's record from Reactome (the pathway record).Still reading. A first read of a pathway can take a while; this page waits up to 35 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.

02The genes

Genes Reactome places in this human pathway

The mapping files place 313 genes in this human pathway; showing 101 to 200, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 2 of 4
Gene	Authority id	Mapping file id	Evidence codes
GeneISCU	AuthorityHGNC:29882	Mapping file id23479 NCBI file	EvidenceTAS
GeneISG15	AuthorityHGNC:4053	Mapping file id9636 NCBI file	EvidenceTAS
GeneJAK1	AuthorityHGNC:6190	Mapping file id3716 NCBI file	EvidenceTAS
GeneKPNA2	AuthorityHGNC:6395	Mapping file id3838 NCBI file	EvidenceTAS
GeneLARP1	AuthorityHGNC:29531	Mapping file id23367 NCBI file	EvidenceTAS
GeneMAGT1	AuthorityHGNC:28880	Mapping file id84061 NCBI file	EvidenceTAS
GeneMAN1B1	AuthorityHGNC:6823	Mapping file id11253 NCBI file	EvidenceTAS
GeneMAN2A1	AuthorityHGNC:6824	Mapping file id4124 NCBI file	EvidenceTAS
GeneMAP1LC3B	AuthorityHGNC:13352	Mapping file id81631 NCBI file	EvidenceIEA, TAS
GeneMAP3K7	AuthorityHGNC:6859	Mapping file id6885 NCBI file	EvidenceTAS
GeneMASP1	AuthorityHGNC:6901	Mapping file id5648 NCBI file	EvidenceTAS
GeneMASP2	AuthorityHGNC:6902	Mapping file id10747 NCBI file	EvidenceTAS
GeneMAVS	AuthorityHGNC:29233	Mapping file id57506 NCBI file	EvidenceTAS
GeneMBL2	AuthorityHGNC:6922	Mapping file id4153 NCBI file	EvidenceTAS
GeneMGAT1	AuthorityHGNC:7044	Mapping file id4245 NCBI file	EvidenceTAS
GeneMGAT2	AuthorityHGNC:7045	Mapping file id4247 NCBI file	EvidenceTAS
GeneMGAT4A	AuthorityHGNC:7047	Mapping file id11320 NCBI file	EvidenceTAS
GeneMGAT4B	AuthorityHGNC:7048	Mapping file id11282 NCBI file	EvidenceTAS
GeneMGAT4C	AuthorityHGNC:30871	Mapping file id25834 NCBI file	EvidenceTAS
GeneMGAT5	AuthorityHGNC:7049	Mapping file id4249 NCBI file	EvidenceTAS
GeneMOGS	AuthorityHGNC:24862	Mapping file id7841 NCBI file	EvidenceTAS
GeneNDC1	AuthorityHGNC:25525	Mapping file id55706 NCBI file	EvidenceTAS
GeneNLRP12	AuthorityHGNC:22938	Mapping file id91662 NCBI file	EvidenceTAS
GeneNLRP3	AuthorityHGNC:16400	Mapping file id114548 NCBI file	EvidenceTAS
GeneNOD1	AuthorityHGNC:16390	Mapping file id10392 NCBI file	EvidenceTAS
GeneNOD2	AuthorityHGNC:5331	Mapping file id64127 NCBI file	EvidenceTAS
GeneNRP1	AuthorityHGNC:8004	Mapping file id8829 NCBI file	EvidenceTAS
GeneNUP107	AuthorityHGNC:29914	Mapping file id57122 NCBI file	EvidenceTAS
GeneNUP133	AuthorityHGNC:18016	Mapping file id55746 NCBI file	EvidenceTAS
GeneNUP153	AuthorityHGNC:8062	Mapping file id9972 NCBI file	EvidenceTAS
GeneNUP155	AuthorityHGNC:8063	Mapping file id9631 NCBI file	EvidenceTAS
GeneNUP160	AuthorityHGNC:18017	Mapping file id23279 NCBI file	EvidenceTAS
GeneNUP188	AuthorityHGNC:17859	Mapping file id23511 NCBI file	EvidenceTAS
GeneNUP205	AuthorityHGNC:18658	Mapping file id23165 NCBI file	EvidenceTAS
GeneNUP210	AuthorityHGNC:30052	Mapping file id23225 NCBI file	EvidenceTAS
GeneNUP214	AuthorityHGNC:8064	Mapping file id8021 NCBI file	EvidenceTAS
GeneNUP35	AuthorityHGNC:29797	Mapping file id129401 NCBI file	EvidenceTAS
GeneNUP37	AuthorityHGNC:29929	Mapping file id79023 NCBI file	EvidenceTAS
GeneNUP42	AuthorityHGNC:17010	Mapping file id11097 NCBI file	EvidenceTAS
GeneNUP43	AuthorityHGNC:21182	Mapping file id348995 NCBI file	EvidenceTAS
GeneNUP50	AuthorityHGNC:8065	Mapping file id10762 NCBI file	EvidenceTAS
GeneNUP54	AuthorityHGNC:17359	Mapping file id53371 NCBI file	EvidenceTAS
GeneNUP58	AuthorityHGNC:20261	Mapping file id9818 NCBI file	EvidenceTAS
GeneNUP62	AuthorityHGNC:8066	Mapping file id23636 NCBI file	EvidenceTAS
GeneNUP85	AuthorityHGNC:8734	Mapping file id79902 NCBI file	EvidenceTAS
GeneNUP88	AuthorityHGNC:8067	Mapping file id4927 NCBI file	EvidenceTAS
GeneNUP93	AuthorityHGNC:28958	Mapping file id9688 NCBI file	EvidenceTAS
GeneNUP98	AuthorityHGNC:8068	Mapping file id4928 NCBI file	EvidenceTAS
GeneOST4	AuthorityHGNC:32483	Mapping file id100128731 NCBI file	EvidenceTAS
GeneOSTC	AuthorityHGNC:24448	Mapping file id58505 NCBI file	EvidenceTAS
GenePALS1	AuthorityHGNC:18669	Mapping file id64398 NCBI file	EvidenceIEA, TAS
GenePARP10	AuthorityHGNC:25895	Mapping file id84875 NCBI file	EvidenceIEA
GenePARP14	AuthorityHGNC:29232	Mapping file id54625 NCBI file	EvidenceIEA
GenePARP16	AuthorityHGNC:26040	Mapping file id54956 NCBI file	EvidenceIEA
GenePARP4	AuthorityHGNC:271	Mapping file id143 NCBI file	EvidenceIEA
GenePARP6	AuthorityHGNC:26921	Mapping file id56965 NCBI file	EvidenceIEA
GenePARP8	AuthorityHGNC:26124	Mapping file id79668 NCBI file	EvidenceIEA
GenePARP9	AuthorityHGNC:24118	Mapping file id83666 NCBI file	EvidenceIEA
GenePATJ	AuthorityHGNC:28881	Mapping file id10207 NCBI file	EvidenceTAS
GenePDPK1	AuthorityHGNC:8816	Mapping file id5170 NCBI file	EvidenceTAS
GenePIK3C3	AuthorityHGNC:8974	Mapping file id5289 NCBI file	EvidenceIEA, TAS
GenePIK3R4	AuthorityHGNC:8982	Mapping file id30849 NCBI file	EvidenceIEA, TAS
GenePOM121	AuthorityHGNC:19702	Mapping file id9883 NCBI file	EvidenceTAS
GenePOM121C	AuthorityHGNC:34005	Mapping file idENSG00000272391 Ensembl file	EvidenceTAS
GenePRKCSH	AuthorityHGNC:9411	Mapping file id5589 NCBI file	EvidenceTAS
GenePRMT1	AuthorityHGNC:5187	Mapping file id3276 NCBI file	EvidenceTAS
GenePTPN11	AuthorityHGNC:9644	Mapping file id5781 NCBI file	EvidenceTAS
GenePTPN6	AuthorityHGNC:9658	Mapping file id5777 NCBI file	EvidenceTAS
GeneRAE1	AuthorityHGNC:9828	Mapping file id8480 NCBI file	EvidenceTAS
GeneRANBP2	AuthorityHGNC:9848	Mapping file id5903 NCBI file	EvidenceTAS
GeneRB1	AuthorityHGNC:9884	Mapping file id5925 NCBI file	EvidenceIEA
GeneRIGI	AuthorityHGNC:19102	Mapping file id23586 NCBI file	EvidenceTAS
GeneRIPK2	AuthorityHGNC:10020	Mapping file id8767 NCBI file	EvidenceTAS
GeneRNF103-CHMP3	AuthorityHGNC:38847	Mapping file id100526767 NCBI file	EvidenceIEA
GeneRNF135	AuthorityHGNC:21158	Mapping file id84282 NCBI file	EvidenceTAS
GeneRPN1	AuthorityHGNC:10381	Mapping file id6184 NCBI file	EvidenceTAS
GeneRPN2	AuthorityHGNC:10382	Mapping file id6185 NCBI file	EvidenceTAS
GeneRPS10	AuthorityHGNC:10383	Mapping file id6204 NCBI file	EvidenceTAS
GeneRPS11	AuthorityHGNC:10384	Mapping file id6205 NCBI file	EvidenceTAS
GeneRPS12	AuthorityHGNC:10385	Mapping file id6206 NCBI file	EvidenceTAS
GeneRPS13	AuthorityHGNC:10386	Mapping file id6207 NCBI file	EvidenceTAS
GeneRPS14	AuthorityHGNC:10387	Mapping file id6208 NCBI file	EvidenceTAS
GeneRPS15	AuthorityHGNC:10388	Mapping file id6209 NCBI file	EvidenceTAS
GeneRPS15A	AuthorityHGNC:10389	Mapping file id6210 NCBI file	EvidenceTAS
GeneRPS16	AuthorityHGNC:10396	Mapping file id6217 NCBI file	EvidenceTAS
GeneRPS17	AuthorityHGNC:10397	Mapping file id6218 NCBI file	EvidenceTAS
GeneRPS18	AuthorityHGNC:10401	Mapping file id6222 NCBI file	EvidenceTAS
GeneRPS19	AuthorityHGNC:10402	Mapping file id6223 NCBI file	EvidenceTAS
GeneRPS2	AuthorityHGNC:10404	Mapping file id6187 NCBI file	EvidenceTAS
GeneRPS20	AuthorityHGNC:10405	Mapping file id6224 NCBI file	EvidenceTAS
GeneRPS21	AuthorityHGNC:10409	Mapping file id6227 NCBI file	EvidenceTAS
GeneRPS23	AuthorityHGNC:10410	Mapping file id6228 NCBI file	EvidenceTAS
GeneRPS24	AuthorityHGNC:10411	Mapping file id6229 NCBI file	EvidenceTAS
GeneRPS25	AuthorityHGNC:10413	Mapping file id6230 NCBI file	EvidenceTAS
GeneRPS26	AuthorityHGNC:10414	Mapping file id6231 NCBI file	EvidenceTAS
GeneRPS27	AuthorityHGNC:10416	Mapping file id6232 NCBI file	EvidenceTAS
GeneRPS27A	AuthorityHGNC:10417	Mapping file id6233 NCBI file	EvidenceIEA, TAS
GeneRPS27L	AuthorityHGNC:18476	Mapping file id51065 NCBI file	EvidenceTAS
GeneRPS28	AuthorityHGNC:10418	Mapping file id6234 NCBI file	EvidenceTAS
GeneRPS29	AuthorityHGNC:10419	Mapping file id6235 NCBI file	EvidenceTAS

Evidence codes on this page: IEA, TAS, as the mapping file writes them; a row carrying two was written twice by the file, once under each. The mapping file id says which file placed the gene: an NCBI Gene id from NCBI2Reactome_All_Levels.txt, an Ensembl gene id from Ensembl2Reactome_All_Levels.txt. The two files can disagree about a code, so a row's codes are the one file's view. Measured by this site's build over this release on 2026-09-09: of the 138,908 human pathway-gene pairs both files place, 207 (0.149 per cent, over 47 genes) carry TAS in the Ensembl file where the NCBI rows carry IEA alone.

Reactome mapping files, the human rows for this pathway · Reactome release 97 · read 2026-09-09 · Reactome downloads"NCBI2Reactome_All_Levels.txt" and "Ensembl2Reactome_All_Levels.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.

03The hierarchy

Parents and children in this release's hierarchy

Parents

SARS-CoV InfectionsR-HSA-9679506492 genes

Children

Reactome's hierarchy is a graph rather than a tree: a pathway can sit under more than one parent, and the gene counts are each pathway's own placements at every level under it, so a parent's count is not the sum of its children's.

Reactome, the human pathway list and hierarchy relationship file · Reactome release 97 · read 2026-09-09 · Reactome downloads"ReactomePathways.txt" and "ReactomePathwaysRelation.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.