Pathway Human Homo sapiens

SARS-CoV Infections

R-HSA-9679506 in Reactome release 97: under Viral Infection Pathways, with 492 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-9679506.7
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: yes, as Reactome flags it
Released: 2020-06-10
Last updated: 2023-03-29
Events inside: 3, counted from the record

Coronaviruses (CoVs) are large, enveloped, positive strand RNA viruses that can be classified into four genera: alpha, beta, delta, and gamma. Coronaviruses are ecologically diverse, infecting animals including camels, cattle, cats, and bats, with the greatest variety seen in bats, suggesting that bats are the reservoirs for many of these viruses. Rarely, A and B lineage beta coronaviruses of non-human origin can infect people and then spread directly between people. Four human coronaviruses (HCoVs), HCoV 229E, NL63, OC43, and HKU1, are endemic globally and account for 10% to 30% of upper respiratory tract infections in adults, typically presenting as common colds (van der Hoek 2007). However, in the 21st century, three highly pathogenic HCoVs - severe acute respiratory syndrome coronavirus (SARS-CoV-1) in 2003, Middle East Respiratory Syndrome coronavirus (MERS CoV) in 2012, and SARS-CoV-2 in 2019 - emerged from animal reservoirs to cause global epidemics with alarming morbidity and mortality (De Wit et al. 2016; Fung & Liu 2019; Marra et al. 2003; Paules et al. 2020).

During the 2003 outbreak of SARS-CoV-1, 8,098 people worldwide became sick. Of these, 774 died. In the United States, only eight people had laboratory evidence of SARS-CoV-1 infection. All of these people had traveled to other parts of the world where the disease was spreading. Community spread was not observed in the United States (De Wit et al. 2016; WHO - SARS). A second human coronavirus, MERS-CoV, first observed in 2012, has been identified in 2,494 patients with respiratory distress of whom 858 have died. Human-to-human transmission of the virus appears to be limited (De Wit et al. 2016; WHO – MERS).

In December 2019, yet another pathogenic HCoV, 2019 novel coronavirus (2019 nCoV), was recognized, initially in Wuhan, China. The World Health Organization has named the disease caused by the 2019 novel coronavirus COronaVIrus Disease 2019, or COVID-19. The disease has also been referred to as 2019 novel coronavirus or 2019 nCoV.

SARS-CoV-1 and SARS-CoV-2 viral infection pathways are annotated in this section, as are drugs that potentially modulate the infection processes. Many of the steps of SARS-CoV-1 infection have been characterized experimentally in the past 15 years (Fung & Liu 2019; Masters 2006), and this experimental work has allowed the annotation here of the infection process and interactions with host proteins in molecular detail. Less comparable data is yet available for SARS-CoV-2 infection, but the similarity in the genomes and predicted proteomes of the two viruses allows the inference of a detailed infection pathway for SARS-CoV-2 that has been manually annotated as well with experimental results published in the first half of 2020.

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 492 genes in this human pathway; showing 301 to 400, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 4 of 5
Gene	Authority id	Mapping file id	Evidence codes
GenePLCG2	AuthorityHGNC:9066	Mapping file id5336 NCBI file	EvidenceTAS
GenePOM121	AuthorityHGNC:19702	Mapping file id9883 NCBI file	EvidenceTAS
GenePOM121C	AuthorityHGNC:34005	Mapping file idENSG00000272391 Ensembl file	EvidenceTAS
GenePPIA	AuthorityHGNC:9253	Mapping file id5478 NCBI file	EvidenceTAS
GenePPIB	AuthorityHGNC:9255	Mapping file id5479 NCBI file	EvidenceTAS
GenePPIG	AuthorityHGNC:14650	Mapping file id9360 NCBI file	EvidenceTAS
GenePPIH	AuthorityHGNC:14651	Mapping file id10465 NCBI file	EvidenceTAS
GenePRKCSH	AuthorityHGNC:9411	Mapping file id5589 NCBI file	EvidenceTAS
GenePRMT1	AuthorityHGNC:5187	Mapping file id3276 NCBI file	EvidenceTAS
GenePSMC6	AuthorityHGNC:9553	Mapping file id5706 NCBI file	EvidenceTAS
GenePTGES3	AuthorityHGNC:16049	Mapping file id10728 NCBI file	EvidenceTAS
GenePTPN11	AuthorityHGNC:9644	Mapping file id5781 NCBI file	EvidenceTAS
GenePTPN6	AuthorityHGNC:9658	Mapping file id5777 NCBI file	EvidenceTAS
GenePYCARD	AuthorityHGNC:16608	Mapping file id29108 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, TAS
GeneRBBP4	AuthorityHGNC:9887	Mapping file id5928 NCBI file	EvidenceTAS
GeneRBBP7	AuthorityHGNC:9890	Mapping file id5931 NCBI file	EvidenceTAS
GeneRBX1	AuthorityHGNC:9928	Mapping file id9978 NCBI file	EvidenceTAS
GeneRCAN3	AuthorityHGNC:3042	Mapping file id11123 NCBI file	EvidenceTAS
GeneRCOR1	AuthorityHGNC:17441	Mapping file id23186 NCBI file	EvidenceTAS
GeneRELA	AuthorityHGNC:9955	Mapping file id5970 NCBI file	EvidenceTAS
GeneREST	AuthorityHGNC:9966	Mapping file id5978 NCBI file	EvidenceTAS
GeneRIGI	AuthorityHGNC:19102	Mapping file id23586 NCBI file	EvidenceTAS
GeneRIPK1	AuthorityHGNC:10019	Mapping file id8737 NCBI file	EvidenceTAS
GeneRIPK2	AuthorityHGNC:10020	Mapping file id8767 NCBI file	EvidenceTAS
GeneRIPK3	AuthorityHGNC:10021	Mapping file id11035 NCBI file	EvidenceTAS
GeneRNF103-CHMP3	AuthorityHGNC:38847	Mapping file id100526767 NCBI file	EvidenceIEA, TAS
GeneRNF135	AuthorityHGNC:21158	Mapping file id84282 NCBI file	EvidenceTAS
GeneROCK1	AuthorityHGNC:10251	Mapping file id6093 NCBI file	EvidenceTAS
GeneROCK2	AuthorityHGNC:10252	Mapping file id9475 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
GeneRPS3	AuthorityHGNC:10420	Mapping file id6188 NCBI file	EvidenceTAS
GeneRPS3A	AuthorityHGNC:10421	Mapping file id6189 NCBI file	EvidenceTAS
GeneRPS4X	AuthorityHGNC:10424	Mapping file id6191 NCBI file	EvidenceTAS
GeneRPS4Y1	AuthorityHGNC:10425	Mapping file id6192 NCBI file	EvidenceTAS
GeneRPS4Y2	AuthorityHGNC:18501	Mapping file id140032 NCBI file	EvidenceTAS
GeneRPS5	AuthorityHGNC:10426	Mapping file id6193 NCBI file	EvidenceTAS
GeneRPS6	AuthorityHGNC:10429	Mapping file id6194 NCBI file	EvidenceTAS
GeneRPS7	AuthorityHGNC:10440	Mapping file id6201 NCBI file	EvidenceTAS
GeneRPS8	AuthorityHGNC:10441	Mapping file id6202 NCBI file	EvidenceTAS
GeneRPS9	AuthorityHGNC:10442	Mapping file id6203 NCBI file	EvidenceTAS
GeneRPSA	AuthorityHGNC:6502	Mapping file id3921 NCBI file	EvidenceTAS
GeneRUNX1	AuthorityHGNC:10471	Mapping file id861 NCBI file	EvidenceTAS
GeneS1PR1	AuthorityHGNC:3165	Mapping file id1901 NCBI file	EvidenceTAS
GeneSAP18	AuthorityHGNC:10530	Mapping file id10284 NCBI file	EvidenceTAS
GeneSAP30	AuthorityHGNC:10532	Mapping file id8819 NCBI file	EvidenceTAS
GeneSAP30L	AuthorityHGNC:25663	Mapping file id79685 NCBI file	EvidenceTAS
GeneSAR1B	AuthorityHGNC:10535	Mapping file id51128 NCBI file	EvidenceTAS
GeneSDC1	AuthorityHGNC:10658	Mapping file id6382 NCBI file	EvidenceIEA, TAS
GeneSDC2	AuthorityHGNC:10659	Mapping file id6383 NCBI file	EvidenceIEA, TAS
GeneSDC3	AuthorityHGNC:10660	Mapping file id9672 NCBI file	EvidenceIEA, TAS
GeneSDC4	AuthorityHGNC:10661	Mapping file id6385 NCBI file	EvidenceIEA, TAS
GeneSEC13	AuthorityHGNC:10697	Mapping file id6396 NCBI file	EvidenceTAS
GeneSEC23A	AuthorityHGNC:10701	Mapping file id10484 NCBI file	EvidenceTAS
GeneSEC24A	AuthorityHGNC:10703	Mapping file id10802 NCBI file	EvidenceTAS
GeneSEC24B	AuthorityHGNC:10704	Mapping file id10427 NCBI file	EvidenceTAS
GeneSEC24C	AuthorityHGNC:10705	Mapping file id9632 NCBI file	EvidenceTAS
GeneSEC24D	AuthorityHGNC:10706	Mapping file id9871 NCBI file	EvidenceTAS
GeneSEH1L	AuthorityHGNC:30379	Mapping file id81929 NCBI file	EvidenceTAS
GeneSERPINE1	AuthorityHGNC:8583	Mapping file idENSG00000106366 Ensembl file	EvidenceTAS
GeneSFN	AuthorityHGNC:10773	Mapping file id2810 NCBI file	EvidenceTAS
GeneSFTPD	AuthorityHGNC:10803	Mapping file id6441 NCBI file	EvidenceTAS
GeneSH3KBP1	AuthorityHGNC:13867	Mapping file id30011 NCBI file	EvidenceTAS
GeneSIGMAR1	AuthorityHGNC:8157	Mapping file id10280 NCBI file	EvidenceTAS
GeneSIKE1	AuthorityHGNC:26119	Mapping file id80143 NCBI file	EvidenceTAS
GeneSMAD3	AuthorityHGNC:6769	Mapping file id4088 NCBI file	EvidenceTAS
GeneSMAD4	AuthorityHGNC:6770	Mapping file id4089 NCBI file	EvidenceTAS
GeneSMN1	AuthorityHGNC:11117	Mapping file id6606 NCBI file	EvidenceTAS
GeneSMN2	AuthorityHGNC:11118	Mapping file id6607 NCBI file	EvidenceTAS
GeneSNRPB	AuthorityHGNC:11153	Mapping file id6628 NCBI file	EvidenceTAS
GeneSNRPD1	AuthorityHGNC:11158	Mapping file id6632 NCBI file	EvidenceTAS
GeneSNRPD2	AuthorityHGNC:11159	Mapping file id6633 NCBI file	EvidenceTAS
GeneSNRPD3	AuthorityHGNC:11160	Mapping file id6634 NCBI file	EvidenceTAS
GeneSNRPE	AuthorityHGNC:11161	Mapping file id6635 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

Viral Infection PathwaysR-HSA-98244461,279 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.