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

Scripts are off

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 401 to 492, in pages of 100, sorted by symbol for reading. The order carries no ranking. 13 of the rows shown carry an id the identity file does not name, kept as the source wrote it.

Genes Reactome places in this human pathway, page 5 of 5
Gene	Authority id	Mapping file id	Evidence codes
GeneSNRPF	AuthorityHGNC:11162	Mapping file id6636 NCBI file	EvidenceTAS
GeneSNRPG	AuthorityHGNC:11163	Mapping file id6637 NCBI file	EvidenceTAS
GeneSOS1	AuthorityHGNC:11187	Mapping file id6654 NCBI file	EvidenceTAS
GeneSP1	AuthorityHGNC:11205	Mapping file id6667 NCBI file	EvidenceTAS
GeneSRPK1	AuthorityHGNC:11305	Mapping file id6732 NCBI file	EvidenceTAS
GeneSRPK2	AuthorityHGNC:11306	Mapping file id6733 NCBI file	EvidenceTAS
GeneST3GAL1	AuthorityHGNC:10862	Mapping file id6482 NCBI file	EvidenceIEA, TAS
GeneST3GAL2	AuthorityHGNC:10863	Mapping file id6483 NCBI file	EvidenceIEA, TAS
GeneST3GAL3	AuthorityHGNC:10866	Mapping file id6487 NCBI file	EvidenceIEA, TAS
GeneST3GAL4	AuthorityHGNC:10864	Mapping file id6484 NCBI file	EvidenceIEA, TAS
GeneST6GAL1	AuthorityHGNC:10860	Mapping file id6480 NCBI file	EvidenceIEA, TAS
GeneST6GALNAC2	AuthorityHGNC:10867	Mapping file id10610 NCBI file	EvidenceIEA, TAS
GeneST6GALNAC3	AuthorityHGNC:19343	Mapping file id256435 NCBI file	EvidenceIEA, TAS
GeneST6GALNAC4	AuthorityHGNC:17846	Mapping file id27090 NCBI file	EvidenceIEA, TAS
GeneSTAT1	AuthorityHGNC:11362	Mapping file id6772 NCBI file	EvidenceTAS
GeneSTAT2	AuthorityHGNC:11363	Mapping file id6773 NCBI file	EvidenceTAS
GeneSTING1	AuthorityHGNC:27962	Mapping file id340061 NCBI file	EvidenceTAS
GeneSTT3A	AuthorityHGNC:6172	Mapping file id3703 NCBI file	EvidenceTAS
GeneSTT3B	AuthorityHGNC:30611	Mapping file id201595 NCBI file	EvidenceTAS
GeneSUDS3	AuthorityHGNC:29545	Mapping file id64426 NCBI file	EvidenceTAS
GeneSUMO1	AuthorityHGNC:12502	Mapping file id7341 NCBI file	EvidenceIEA, TAS
GeneSYK	AuthorityHGNC:11491	Mapping file id6850 NCBI file	EvidenceTAS
GeneTAB1	AuthorityHGNC:18157	Mapping file id10454 NCBI file	EvidenceTAS
GeneTAB2	AuthorityHGNC:17075	Mapping file id23118 NCBI file	EvidenceTAS
GeneTAB3	AuthorityHGNC:30681	Mapping file id257397 NCBI file	EvidenceTAS
GeneTBK1	AuthorityHGNC:11584	Mapping file id29110 NCBI file	EvidenceTAS
GeneTJP1	AuthorityHGNC:11827	Mapping file id7082 NCBI file	EvidenceIEA, TAS
GeneTKFC	AuthorityHGNC:24552	Mapping file id26007 NCBI file	EvidenceIEA, TAS
GeneTLR1	AuthorityHGNC:11847	Mapping file id7096 NCBI file	EvidenceTAS
GeneTLR2	AuthorityHGNC:11848	Mapping file id7097 NCBI file	EvidenceTAS
GeneTLR7	AuthorityHGNC:15631	Mapping file id51284 NCBI file	EvidenceTAS
GeneTLR8	AuthorityHGNC:15632	Mapping file id51311 NCBI file	EvidenceTAS
GeneTLR9	AuthorityHGNC:15633	Mapping file id54106 NCBI file	EvidenceTAS
GeneTMEM258	AuthorityHGNC:1164	Mapping file id746 NCBI file	EvidenceTAS
GeneTMPRSS2	AuthorityHGNC:11876	Mapping file id7113 NCBI file	EvidenceTAS
GeneTOMM70	AuthorityHGNC:11985	Mapping file id9868 NCBI file	EvidenceTAS
GeneTPR	AuthorityHGNC:12017	Mapping file id7175 NCBI file	EvidenceTAS
GeneTRAF3	AuthorityHGNC:12033	Mapping file id7187 NCBI file	EvidenceTAS
GeneTRAF6	AuthorityHGNC:12036	Mapping file id7189 NCBI file	EvidenceTAS
GeneTRIM25	AuthorityHGNC:12932	Mapping file id7706 NCBI file	EvidenceTAS
GeneTRIM4	AuthorityHGNC:16275	Mapping file id89122 NCBI file	EvidenceTAS
GeneTUBB	AuthorityHGNC:20778	Mapping file id203068 NCBI file	EvidenceTAS
GeneTUFM	AuthorityHGNC:12420	Mapping file id7284 NCBI file	EvidenceTAS
GeneTUSC3	AuthorityHGNC:30242	Mapping file id7991 NCBI file	EvidenceTAS
GeneTYK2	AuthorityHGNC:12440	Mapping file id7297 NCBI file	EvidenceTAS
GeneUBA52	AuthorityHGNC:12458	Mapping file id7311 NCBI file	EvidenceIEA, TAS
GeneUBB	AuthorityHGNC:12463	Mapping file id7314 NCBI file	EvidenceIEA, TAS
GeneUBC	AuthorityHGNC:12468	Mapping file id7316 NCBI file	EvidenceIEA, TAS
GeneUBE2I	AuthorityHGNC:12485	Mapping file id7329 NCBI file	EvidenceIEA, TAS
GeneUBE2N	AuthorityHGNC:12492	Mapping file id7334 NCBI file	EvidenceTAS
GeneUBE2V1	AuthorityHGNC:12494	Mapping file id7335 NCBI file	EvidenceTAS
GeneUVRAG	AuthorityHGNC:12640	Mapping file id7405 NCBI file	EvidenceIEA, TAS
GeneVAV1	AuthorityHGNC:12657	Mapping file id7409 NCBI file	EvidenceTAS
GeneVCP	AuthorityHGNC:12666	Mapping file id7415 NCBI file	EvidenceIEA, TAS
GeneVEGFA	AuthorityHGNC:12680	Mapping file id7422 NCBI file	EvidenceTAS
GeneVHL	AuthorityHGNC:12687	Mapping file id7428 NCBI file	EvidenceIEA, TAS
GeneVPS11	AuthorityHGNC:14583	Mapping file id55823 NCBI file	EvidenceTAS
GeneVPS16	AuthorityHGNC:14584	Mapping file id64601 NCBI file	EvidenceTAS
GeneVPS18	AuthorityHGNC:15972	Mapping file id57617 NCBI file	EvidenceTAS
GeneVPS33A	AuthorityHGNC:18179	Mapping file id65082 NCBI file	EvidenceTAS
GeneVPS33B	AuthorityHGNC:12712	Mapping file id26276 NCBI file	EvidenceTAS
GeneVPS39	AuthorityHGNC:20593	Mapping file id23339 NCBI file	EvidenceTAS
GeneVPS41	AuthorityHGNC:12713	Mapping file id27072 NCBI file	EvidenceTAS
GeneVPS45	AuthorityHGNC:14579	Mapping file id11311 NCBI file	EvidenceTAS
GeneYWHAB	AuthorityHGNC:12849	Mapping file id7529 NCBI file	EvidenceTAS
GeneYWHAE	AuthorityHGNC:12851	Mapping file id7531 NCBI file	EvidenceTAS
GeneYWHAG	AuthorityHGNC:12852	Mapping file id7532 NCBI file	EvidenceTAS
GeneYWHAH	AuthorityHGNC:12853	Mapping file id7533 NCBI file	EvidenceTAS
GeneYWHAQ	AuthorityHGNC:12854	Mapping file id10971 NCBI file	EvidenceTAS
GeneYWHAZ	AuthorityHGNC:12855	Mapping file id7534 NCBI file	EvidenceTAS
GeneZBP1	AuthorityHGNC:16176	Mapping file id81030 NCBI file	EvidenceTAS
GeneZCRB1	AuthorityHGNC:29620	Mapping file id85437 NCBI file	EvidenceIEA, TAS
GeneZDHHC11	AuthorityHGNC:19158	Mapping file id79844 NCBI file	EvidenceTAS
GeneZDHHC2	AuthorityHGNC:18469	Mapping file id51201 NCBI file	EvidenceTAS
GeneZDHHC20	AuthorityHGNC:20749	Mapping file id253832 NCBI file	EvidenceTAS
GeneZDHHC3	AuthorityHGNC:18470	Mapping file id51304 NCBI file	EvidenceTAS
GeneZDHHC5	AuthorityHGNC:18472	Mapping file id25921 NCBI file	EvidenceTAS
GeneZDHHC8	AuthorityHGNC:18474	Mapping file id29801 NCBI file	EvidenceTAS
GeneZDHHC9	AuthorityHGNC:18475	Mapping file id51114 NCBI file	EvidenceTAS
Geneno symbol in the identity file	Authoritynone	Mapping file id1489680 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740568 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740569 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740570 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740571 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740572 NCBI file	EvidenceTAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740573 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740575 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740577 NCBI file	EvidenceTAS
Geneno symbol in the identity file	Authoritynone	Mapping file id43740578 NCBI file	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file idM12294.2 as written	EvidenceTAS
Geneno symbol in the identity file	Authoritynone	Mapping file idMN908947.3 as written	EvidenceIEA, TAS
Geneno symbol in the identity file	Authoritynone	Mapping file idNC_004718.3 as written	EvidenceIEA, TAS

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.