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 201 to 300, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 3 of 5
Gene	Authority id	Mapping file id	Evidence codes
GeneIKBKE	AuthorityHGNC:14552	Mapping file id9641 NCBI file	EvidenceTAS
GeneIKBKG	AuthorityHGNC:5961	Mapping file id8517 NCBI file	EvidenceTAS
GeneIL17A	AuthorityHGNC:5981	Mapping file id3605 NCBI file	EvidenceTAS
GeneIL17F	AuthorityHGNC:16404	Mapping file id112744 NCBI file	EvidenceTAS
GeneIL17RA	AuthorityHGNC:5985	Mapping file id23765 NCBI file	EvidenceTAS
GeneIL17RC	AuthorityHGNC:18358	Mapping file id84818 NCBI file	EvidenceTAS
GeneIL1R1	AuthorityHGNC:5993	Mapping file id3554 NCBI file	EvidenceTAS
GeneIL6R	AuthorityHGNC:6019	Mapping file id3570 NCBI file	EvidenceTAS
GeneIMPDH1	AuthorityHGNC:6052	Mapping file id3614 NCBI file	EvidenceTAS
GeneIMPDH2	AuthorityHGNC:6053	Mapping file id3615 NCBI file	EvidenceTAS
GeneIRAK1	AuthorityHGNC:6112	Mapping file id3654 NCBI file	EvidenceTAS
GeneIRAK2	AuthorityHGNC:6113	Mapping file id3656 NCBI file	EvidenceTAS
GeneIRF3	AuthorityHGNC:6118	Mapping file id3661 NCBI file	EvidenceTAS
GeneIRF7	AuthorityHGNC:6122	Mapping file id3665 NCBI file	EvidenceTAS
GeneISCU	AuthorityHGNC:29882	Mapping file id23479 NCBI file	EvidenceTAS
GeneISG15	AuthorityHGNC:4053	Mapping file id9636 NCBI file	EvidenceTAS
GeneITCH	AuthorityHGNC:13890	Mapping file id83737 NCBI file	EvidenceTAS
GeneITGA4	AuthorityHGNC:6140	Mapping file id3676 NCBI file	EvidenceTAS
GeneITGB1	AuthorityHGNC:6153	Mapping file id3688 NCBI file	EvidenceTAS
GeneJAK1	AuthorityHGNC:6190	Mapping file id3716 NCBI file	EvidenceTAS
GeneJAK2	AuthorityHGNC:6192	Mapping file id3717 NCBI file	EvidenceTAS
GeneJAK3	AuthorityHGNC:6193	Mapping file id3718 NCBI file	EvidenceTAS
GeneKDM1A	AuthorityHGNC:29079	Mapping file id23028 NCBI file	EvidenceTAS
GeneKEAP1	AuthorityHGNC:23177	Mapping file id9817 NCBI file	EvidenceTAS
GeneKPNA2	AuthorityHGNC:6395	Mapping file id3838 NCBI file	EvidenceTAS
GeneKPNB1	AuthorityHGNC:6400	Mapping file id3837 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
GeneMBD3	AuthorityHGNC:6918	Mapping file id53615 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
GeneMTA1	AuthorityHGNC:7410	Mapping file id9112 NCBI file	EvidenceTAS
GeneMTA2	AuthorityHGNC:7411	Mapping file id9219 NCBI file	EvidenceTAS
GeneMTA3	AuthorityHGNC:23784	Mapping file id57504 NCBI file	EvidenceTAS
GeneNCK1	AuthorityHGNC:7664	Mapping file id4690 NCBI file	EvidenceTAS
GeneNDC1	AuthorityHGNC:25525	Mapping file id55706 NCBI file	EvidenceTAS
GeneNFE2L2	AuthorityHGNC:7782	Mapping file id4780 NCBI file	EvidenceTAS
GeneNFKB1	AuthorityHGNC:7794	Mapping file id4790 NCBI file	EvidenceTAS
GeneNFKBIA	AuthorityHGNC:7797	Mapping file id4792 NCBI file	EvidenceTAS
GeneNLRP12	AuthorityHGNC:22938	Mapping file id91662 NCBI file	EvidenceTAS
GeneNLRP3	AuthorityHGNC:16400	Mapping file id114548 NCBI file	EvidenceTAS
GeneNMI	AuthorityHGNC:7854	Mapping file id9111 NCBI file	EvidenceTAS
GeneNOD1	AuthorityHGNC:16390	Mapping file id10392 NCBI file	EvidenceTAS
GeneNOD2	AuthorityHGNC:5331	Mapping file id64127 NCBI file	EvidenceTAS
GeneNPIPB3	AuthorityHGNC:28989	Mapping file idENSG00000169246 Ensembl file	EvidenceTAS
GeneNPM1	AuthorityHGNC:7910	Mapping file id4869 NCBI file	EvidenceTAS
GeneNR3C1	AuthorityHGNC:7978	Mapping file id2908 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, TAS
GenePARP14	AuthorityHGNC:29232	Mapping file id54625 NCBI file	EvidenceIEA, TAS
GenePARP16	AuthorityHGNC:26040	Mapping file id54956 NCBI file	EvidenceIEA, TAS
GenePARP4	AuthorityHGNC:271	Mapping file id143 NCBI file	EvidenceIEA, TAS
GenePARP6	AuthorityHGNC:26921	Mapping file id56965 NCBI file	EvidenceIEA, TAS
GenePARP8	AuthorityHGNC:26124	Mapping file id79668 NCBI file	EvidenceIEA, TAS
GenePARP9	AuthorityHGNC:24118	Mapping file id83666 NCBI file	EvidenceIEA, TAS
GenePATJ	AuthorityHGNC:28881	Mapping file id10207 NCBI file	EvidenceTAS
GenePCBP2	AuthorityHGNC:8648	Mapping file id5094 NCBI file	EvidenceTAS
GenePDCD1	AuthorityHGNC:8760	Mapping file id5133 NCBI file	EvidenceTAS
GenePDPK1	AuthorityHGNC:8816	Mapping file id5170 NCBI file	EvidenceTAS
GenePHF21A	AuthorityHGNC:24156	Mapping file id51317 NCBI file	EvidenceTAS
GenePIK3C3	AuthorityHGNC:8974	Mapping file id5289 NCBI file	EvidenceIEA, TAS
GenePIK3R4	AuthorityHGNC:8982	Mapping file id30849 NCBI file	EvidenceIEA, TAS
GenePKLR	AuthorityHGNC:9020	Mapping file id5313 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.