Activity

Filter

Cancel
Date Panel Item Activity
124 actions
Viral resistance v0.63 DDX58 Eleanor Williams commented on gene: DDX58
Viral resistance v0.63 DDX58 Eleanor Williams Tag new-gene-name tag was added to gene: DDX58.
Viral resistance v0.62 IFNG Sarah Leigh Publications for gene: IFNG were set to 12854077; 17981204; 17215375; 26458193
Viral resistance v0.61 IFNG Sarah Leigh Mode of inheritance for gene: IFNG was changed from to Unknown
Viral resistance v0.60 IFNG Sarah Leigh Publications for gene: IFNG were set to 12854077
Viral resistance v0.59 CLEC4M Rebecca Foulger changed review comment from: Comment on list classification: Although a 2006 study (PMID:16369534) finds an association between CLEC4M variable number tandem repeat polymoprhisms, and protection against SARS viral infection, subsequent studies do not support this association (PMIDs 17534354, 17534355, 18697825). Therefore rated as Red awaiting further evidence.; to: Comment on list classification: Although a 2006 study (PMID:16369534) finds an association between CLEC4M variable number tandem repeat polymorphisms, and protection against SARS viral infection, subsequent studies do not support this association (PMIDs 17534354, 17534355, 18697825). Therefore rated as Red awaiting further evidence.
Viral resistance v0.59 CLEC4M Rebecca Foulger changed review comment from: Added to panel based on OMIM search. CLEC4M has considerable polymorphism in the tandem repeat domain of exon 4 (3 to 9 repeats of a 69-basepair segment, with 7 repeats being predominant in the general population). Chan et al. (2006, PMID:16369534) performed a genetic risk association study and found that individuals homozygous for CLEC4M tandem repeats are less susceptible to SARS infection. CLEC4M was expressed in both non-SARS and SARS-CoV-infected lung. Compared with cells heterozygous for CLEC4M, cells homozygous for CLEC4M showed higher binding capacity for SARS-CoV, higher proteasome-dependent viral degradation, and a lower capacity for trans infection. Thus, homozygosity for CLEC4M plays a protective role during SARS infection.
Sources: Other; to: Added to panel based on OMIM search. CLEC4M has considerable polymorphism in the tandem repeat domain of exon 4 (3 to 9 repeats of a 69-basepair segment, with 7 repeats being predominant in the general population). Chan et al. (2006, PMID:16369534) performed a genetic risk association study and found that individuals homozygous for CLEC4M tandem repeats are less susceptible to SARS infection. Compared with cells heterozygous for CLEC4M, cells homozygous for CLEC4M showed higher binding capacity for SARS-CoV, higher proteasome-dependent viral degradation, and a lower capacity for trans infection. Thus, homozygosity for CLEC4M tandem repeats plays a protective role during SARS infection.
Sources: Other
Viral resistance v0.59 CLEC4M Rebecca Foulger changed review comment from: Comment on list classification: Although a 2006 study (PMID:16369534) finds an association between tandem repeats within CLEC4M, and protection against SARS viral infection, subsequent studies do not support this association (PMIDs 17534354, 17534355, 18697825). Therefore rated as Red awaiting further evidence.; to: Comment on list classification: Although a 2006 study (PMID:16369534) finds an association between CLEC4M variable number tandem repeat polymoprhisms, and protection against SARS viral infection, subsequent studies do not support this association (PMIDs 17534354, 17534355, 18697825). Therefore rated as Red awaiting further evidence.
Viral resistance v0.59 CLEC4M Rebecca Foulger changed review comment from: Comment on list classification: Although a 2006 study finds an association between tandem repeats within CLEC4M , and protection against SARS viral infection, subsequent studies do not support this association. Therefore rated as Red awaiting further evidence.; to: Comment on list classification: Although a 2006 study (PMID:16369534) finds an association between tandem repeats within CLEC4M, and protection against SARS viral infection, subsequent studies do not support this association (PMIDs 17534354, 17534355, 18697825). Therefore rated as Red awaiting further evidence.
Viral resistance v0.59 CLEC4M Rebecca Foulger changed review comment from: PMID:18697825 (Li et al., 2008) suggested that the previously reported association with polymorphisms in the CLEC4M neck region may be due to population stratification.; to: PMID:18697825 (Li et al., 2008) suggested that the previously reported association with polymorphisms in the CLEC4M gene may be due to population stratification.
Viral resistance v0.59 CLEC4M Rebecca Foulger changed review comment from: In contrast to Chan et al., 2006 (PMID:16369534), Tang et al. (2007, PMID:17534354) found no support for an association between CLEC4M homozygosity and protection against SARS. Zhi et al. (2007, PMID:17534355]) also found that the protective effect of CLEC4M homozygosity could not be replicated. The authors from the original study (PMID:16369534) suggested that controls were not matched in these subsequent studies.; to: In contrast to Chan et al., 2006 (PMID:16369534), Tang et al. (2007, PMID:17534354) found no support for an association between CLEC4M homozygosity and protection against SARS. Zhi et al. (2007, PMID:17534355) also found that the protective effect of CLEC4M homozygosity could not be replicated. The authors from the original study (PMID:16369534) suggested that controls were not matched in these subsequent studies.
Viral resistance v0.59 CLEC4M Rebecca Foulger Classified gene: CLEC4M as Red List (low evidence)
Viral resistance v0.59 CLEC4M Rebecca Foulger Added comment: Comment on list classification: Although a 2006 study finds an association between tandem repeats within CLEC4M , and protection against SARS viral infection, subsequent studies do not support this association. Therefore rated as Red awaiting further evidence.
Viral resistance v0.59 CLEC4M Rebecca Foulger Gene: clec4m has been classified as Red List (Low Evidence).
Viral resistance v0.58 CLEC4M Rebecca Foulger Publications for gene: CLEC4M were set to 16369534
Viral resistance v0.57 CLEC4M Rebecca Foulger commented on gene: CLEC4M: PMID:18697825 (Li et al., 2008) suggested that the previously reported association with polymorphisms in the CLEC4M neck region may be due to population stratification.
Viral resistance v0.57 CLEC4M Rebecca Foulger commented on gene: CLEC4M: In contrast to Chan et al., 2006 (PMID:16369534), Tang et al. (2007, PMID:17534354) found no support for an association between CLEC4M homozygosity and protection against SARS. Zhi et al. (2007, PMID:17534355]) also found that the protective effect of CLEC4M homozygosity could not be replicated. The authors from the original study (PMID:16369534) suggested that controls were not matched in these subsequent studies.
Viral resistance v0.57 CLEC4M Rebecca Foulger gene: CLEC4M was added
gene: CLEC4M was added to Viral resistance. Sources: Other
Mode of inheritance for gene: CLEC4M was set to Unknown
Publications for gene: CLEC4M were set to 16369534
Phenotypes for gene: CLEC4M were set to SARS infection, protection against, 605872
Added comment: Added to panel based on OMIM search. CLEC4M has considerable polymorphism in the tandem repeat domain of exon 4 (3 to 9 repeats of a 69-basepair segment, with 7 repeats being predominant in the general population). Chan et al. (2006, PMID:16369534) performed a genetic risk association study and found that individuals homozygous for CLEC4M tandem repeats are less susceptible to SARS infection. CLEC4M was expressed in both non-SARS and SARS-CoV-infected lung. Compared with cells heterozygous for CLEC4M, cells homozygous for CLEC4M showed higher binding capacity for SARS-CoV, higher proteasome-dependent viral degradation, and a lower capacity for trans infection. Thus, homozygosity for CLEC4M plays a protective role during SARS infection.
Sources: Other
Viral resistance v0.56 CD209 Ivone Leong commented on gene: CD209
Viral resistance v0.56 CD209 Ivone Leong Publications for gene: CD209 were set to 16189667
Viral resistance v0.55 CXCL12 Ivone Leong Classified gene: CXCL12 as Amber List (moderate evidence)
Viral resistance v0.55 CXCL12 Ivone Leong Gene: cxcl12 has been classified as Amber List (Moderate Evidence).
Viral resistance v0.54 CXCL12 Ivone Leong Added comment: Comment on publications: PMID: 26168882 showed that rs17540465 of SDF1 conferred resistance to HIV-1 infection in intravenous drug users when not sharing syringes but not in those who share syringes.
Viral resistance v0.54 CXCL12 Ivone Leong Publications for gene: CXCL12 were set to 8752280; 8752281
Viral resistance v0.53 DDX58 Ivone Leong Classified gene: DDX58 as Amber List (moderate evidence)
Viral resistance v0.53 DDX58 Ivone Leong Gene: ddx58 has been classified as Amber List (Moderate Evidence).
Viral resistance v0.52 IFNG Ivone Leong Phenotypes for gene: IFNG were changed from {AIDS, rapid progression to} 609423 to {AIDS, rapid progression to} 609423; {Hepatitis C virus, response to therapy of}, 609532
Viral resistance v0.50 IL4R Ivone Leong Mode of inheritance for gene: IL4R was changed from to BIALLELIC, autosomal or pseudoautosomal
Viral resistance v0.49 MX1 Ivone Leong Publications for gene: MX1 were set to 3162334; 14872030; 21935451; https://doi.org/10.1101/2020.05.04.07591
Viral resistance v0.48 MX1 Ivone Leong Classified gene: MX1 as Amber List (moderate evidence)
Viral resistance v0.48 MX1 Ivone Leong Added comment: Comment on list classification: PMID: 30696001 fused a cell penetrating peptide to the C-terminus of the Mx1 protein and found that it inhibited viral replication and viral RNA expression in infected cells. Administration of this fused protein improved the survival of mice infected with PR8 influenza viral strain. The paper suggests that this fused protein could be used as a therapeutic agent.
Viral resistance v0.48 MX1 Ivone Leong Gene: mx1 has been classified as Amber List (Moderate Evidence).
Viral resistance v0.47 TNF Ivone Leong Classified gene: TNF as Green List (high evidence)
Viral resistance v0.47 TNF Ivone Leong Added comment: Comment on list classification: Based on the following evidece there is enough evidence to make this gene Green.
Viral resistance v0.47 TNF Ivone Leong Gene: tnf has been classified as Green List (High Evidence).
Viral resistance v0.46 TNF Ivone Leong Added comment: Comment on publications: PMID: 25047809, 25661729 are two papers describing mouse models where blocking TNFa impairs HBV clearance.

PMID: 24077913, 19447932, 25447852 describe how anti-TNFa treatments increase the risk of HBV reactivation in patients who have chronic HBV infection.
Viral resistance v0.46 TNF Ivone Leong Publications for gene: TNF were set to 12915457
Viral resistance v0.45 TNF Ivone Leong Mode of inheritance for gene: TNF was changed from to Unknown
Viral resistance v0.44 CXCR1 Ivone Leong Classified gene: CXCR1 as Green List (high evidence)
Viral resistance v0.44 CXCR1 Ivone Leong Gene: cxcr1 has been classified as Green List (High Evidence).
Viral resistance v0.43 CXCR1 Ivone Leong Mode of inheritance for gene: CXCR1 was changed from to Unknown
Viral resistance v0.42 DPP4 Eleanor Williams gene: DPP4 was added
gene: DPP4 was added to Viral resistance. Sources: Literature
Mode of inheritance for gene: DPP4 was set to Unknown
Publications for gene: DPP4 were set to 31964246
Review for gene: DPP4 was set to RED
Added comment: PMID: 31964246 - Kleine-Weber et al 2020- looked at naturally-occurring polymorphisms in DPP4 from public databases, that alter amino acid residues required for MERS-CoV S binding to see if they influence cellular entry of MERS-CoV. Four polymorphisms (K267E, K267N, A291P and Δ346-348) strongly reduced binding of MERS-CoV S to DPP4 and S protein-driven host cell entry, as determined using soluble S protein and S protein bearing rhabdoviral vectors, respectively. Two polymorphisms (K267E and A291P) were analyzed in the context of authentic MERS-CoV and were found to attenuate viral replication.
Sources: Literature
Viral resistance v0.41 DDX58 Sarah Leigh gene: DDX58 was added
gene: DDX58 was added to Viral resistance. Sources: Literature
Mode of inheritance for gene: DDX58 was set to Unknown
Publications for gene: DDX58 were set to 21939710; 16625202; 15737993; 25749629
Review for gene: DDX58 was set to AMBER
Added comment: PMID 21939710 found DDX5 (formerly known as RIGI) was essential for virus-induced expression of IRF3 and concluded that DDX5 is essential for detection and eradication of replicating viral genomes. PMID 16625202 reported that DDX58 is essential for the production of interferons in response to certain RNA viruses including paramyxoviruses, influenza virus, and Japanese encephalitis virus.
Numerous reports of wild type DDX5 activity in anti-viral responses.
Sources: Literature
Viral resistance v0.40 MX1 Sarah Leigh gene: MX1 was added
gene: MX1 was added to Viral resistance. Sources: Literature
Mode of inheritance for gene: MX1 was set to Unknown
Publications for gene: MX1 were set to 3162334; 14872030; 21935451; https://doi.org/10.1101/2020.05.04.07591
Review for gene: MX1 was set to AMBER
Added comment: MX1 is an interferon-induced protein with antiviral activity (PMID 3162334).
PMID 14872030 c.-88G>T was more frequent in 40 unrelated Japanese patients with subacute sclerosing panencephalitisis (associated with CNS infection with measles virus), than in 90 controls (0.42 in patients vs 0.29 in controls). Variant c.-88G>T results increased MX1 expression, the authors suggest that MX1 may paradoxically enable persistence of the virus in the CNS by attenuating viral gene expression and preventing complete immunologic clearance.
PMID 21935451 concluded that genetic variation in the interferon response pathway is associated with risk for symptomatic West Nile viru infection and disease progression.
Preprint https://doi.org/10.1101/2020.05.04.075911 Reports that rs35074065 of TMPRSS2 results in increased expression of the nearby gene MX1.
Sources: Literature
Viral resistance v0.39 SELPLG Sarah Leigh gene: SELPLG was added
gene: SELPLG was added to Viral resistance. Sources: Literature
Mode of inheritance for gene: SELPLG was set to Unknown
Publications for gene: SELPLG were set to 19543284; 30833724; doi.org/10.1101/2020.05.01.073387
Review for gene: SELPLG was set to RED
Added comment: PMID: 30833724 identifies SELPLG (refered to as PSGL1 in the literature) as an HIV restriction factor, SELPLG is induced by interferon-γ in activated CD4+ T cells to inhibit HIV-1 reverse transcription and potently block viral infectivity by incorporating in progeny virions.
Preprint https://doi.org/10.1101/2020.05.01.073387 report that virion incorporation of SELPLG on SARS-CoV and SARS-CoV-2 pseudovirions blocks S protein-mediated virus attachment and infection of target cells, Suggesting that SELPLG-imprinted non-infectious viral particles could serve as a live attenuated vaccine for SARS-CoV-2 infection.

In PMID 19543284 SELPLG (refered to as PSGL1 in the literature) is a receptor for 5 of 8 the Enterovirus-71 (EV71) strains. EV71 interaction and viral replication could be inhibited by monoclonal antibodies to SELPLG. The authors concluded that SELPLG-positive leukocytes are involved in the cell tropism and pathogenesis of hand, foot and mouth disease and other EV71-mediated diseases.
Sources: Literature
Viral resistance v0.38 LDLR Ivone Leong Classified gene: LDLR as Green List (high evidence)
Viral resistance v0.38 LDLR Ivone Leong Added comment: Comment on list classification: Promoted to Green based on review from Sarah Leigh (Genomics England Curator).
Viral resistance v0.38 LDLR Ivone Leong Gene: ldlr has been classified as Green List (High Evidence).
Viral resistance v0.37 CCL3 Ivone Leong Publications for gene: CCL3 were set to 16773571
Viral resistance v0.36 CCL2 Ivone Leong changed review comment from: Comment on list classification: PMID: 14571188 found that three SNPs (-2136T CCL2 promoter region, 767G intron 1 of CCL2 and -1385A of Eotaxin promoter) were nearly always found together on a 31kb haplotype (H7), which contains all three regoins. The frequencies for these three variants and H7 haplotype were significantly increased in uninfected European-Americans who were repeatedly exposed to HIV-1. The study suggests that this region influences HIV susceptibility/resistance.

There is currently not enough evidence so this gene will remain Red.; to: Comment on list classification: PMID: 14571188 found that three SNPs (-2136T CCL2 promoter region, 767G intron 1 of CCL2 and -1385A of Eotaxin promoter) were nearly always found together on a 31kb haplotype (H7), which contains all three regoins. The frequencies for these three variants and H7 haplotype were significantly increased in uninfected European-Americans who were repeatedly exposed to HIV-1. The study suggests that this region influences HIV susceptibility/resistance.
Viral resistance v0.36 CCL2 Ivone Leong Classified gene: CCL2 as Red List (low evidence)
Viral resistance v0.36 CCL2 Ivone Leong Added comment: Comment on list classification: PMID: 14571188 found that three SNPs (-2136T CCL2 promoter region, 767G intron 1 of CCL2 and -1385A of Eotaxin promoter) were nearly always found together on a 31kb haplotype (H7), which contains all three regoins. The frequencies for these three variants and H7 haplotype were significantly increased in uninfected European-Americans who were repeatedly exposed to HIV-1. The study suggests that this region influences HIV susceptibility/resistance.

There is currently not enough evidence so this gene will remain Red.
Viral resistance v0.36 CCL2 Ivone Leong Gene: ccl2 has been classified as Red List (Low Evidence).
Viral resistance v0.35 LDLR Sarah Leigh gene: LDLR was added
gene: LDLR was added to Viral resistance. Sources: Literature
Mode of inheritance for gene: LDLR was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: LDLR were set to 10535997; 32268133; 31386864; 31358055
Phenotypes for gene: LDLR were set to Hypercholesterolemia, familial, 1 143890; LDL cholesterol level QTL2 143890
Review for gene: LDLR was set to GREEN
Added comment: Hepatitis C virus (HCV) and other viruses can enter cells via LDLR mediated endocytosis (PMID 32268133). PMID 10535997 demonstrates that lack of detectable LDL receptor on cells results in resistance to infection by bovine viral diarrheal virus. Dengue virus genome replication and protein synthesis was significantly inhibited by the serine protease inhibitor AEBSF [4-(2-aminoethyl) benzene sulfonyl fluoride] that inhibits the expression of genes HMGCS, HMGCR & LDLR (PMID 31386864). A recent LDLR-null FH cell model has been developed, which is permisive to HCV infection, but virus production was significantly decreased compared with cells in which the LDLR activity had been corrected to normal levels (PMID 31358055).
Sources: Literature
Viral resistance v0.34 TNF Sarah Leigh commented on gene: TNF
Viral resistance v0.34 IFNG Sarah Leigh commented on gene: IFNG
Viral resistance v0.34 HLA-DQB1 Sarah Leigh commented on gene: HLA-DQB1
Viral resistance v0.34 HLA-C Sarah Leigh commented on gene: HLA-C
Viral resistance v0.34 CD209 Sarah Leigh commented on gene: CD209
Viral resistance v0.34 IL4R Sarah Leigh edited their review of gene: IL4R: Added comment: Homozygous rs1805010 p.Ile75Val (referred to as I50V using obsolete numbering), is associated with slow progression to AIDS after HIV infection (PMID 16189667) ; Changed publications: 16189667; Changed phenotypes: ACQUIRED IMMUNODEFICIENCY SYNDROME, SLOW PROGRESSION TO
Viral resistance v0.33 TNF Sarah Leigh gene: TNF was added
gene: TNF was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: TNF was set to
Publications for gene: TNF were set to 12915457
Viral resistance v0.33 IFNG Sarah Leigh gene: IFNG was added
gene: IFNG was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: IFNG was set to
Publications for gene: IFNG were set to 12854077
Phenotypes for gene: IFNG were set to {AIDS, rapid progression to} 609423
Viral resistance v0.33 HLA-DQB1 Sarah Leigh gene: HLA-DQB1 was added
gene: HLA-DQB1 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: HLA-DQB1 was set to
Publications for gene: HLA-DQB1 were set to 10609818
Viral resistance v0.33 HLA-C Sarah Leigh gene: HLA-C was added
gene: HLA-C was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: HLA-C was set to
Publications for gene: HLA-C were set to 21051598; 19935663
Phenotypes for gene: HLA-C were set to {HIV-1 viremia, susceptibility to} 609423
Viral resistance v0.33 CD209 Sarah Leigh gene: CD209 was added
gene: CD209 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: CD209 was set to
Publications for gene: CD209 were set to 16189667
Phenotypes for gene: CD209 were set to {Dengue fever, protection against} 614371
Viral resistance v0.32 CXCR1 Ivone Leong Classified gene: CXCR1 as Amber List (moderate evidence)
Viral resistance v0.32 CXCR1 Ivone Leong Added comment: Comment on list classification: PMID: 17360650 found a CXCR1 haplotype made up of 2 SNPs (rs16858811) that caused M31R change in the N-terminal extracellular domain, and rs1658808 caused R335C in the C-terminal intracellular domain. The frequency of this haplotype was significantly lower in 84 French HIV-1-infected patients who progressed rapidly to AIDS compared with 253 French HIV-1-infected patients who progressed slowly to AIDS. The authors concluded that the CXCR1 haplotype protects against rapid progression of HIV-1 infected patients to AIDS.

PMID: 25121556 showed the mechanism of how the CXCR1 haplotype affects AIDS progression.
Viral resistance v0.32 CXCR1 Ivone Leong Gene: cxcr1 has been classified as Amber List (Moderate Evidence).
Viral resistance v0.31 CXCR1 Ivone Leong Publications for gene: CXCR1 were set to 17360650
Viral resistance v0.30 IL4R Ivone Leong Added comment: Comment on publications: PMID: 16189667 showed that individuals with homozygous V50 variant is associated with slow progression of HIV to AIDS.
Viral resistance v0.30 IL4R Ivone Leong Publications for gene: IL4R were set to 16189667
Viral resistance v0.29 KIR3DL1 Ivone Leong Mode of inheritance for gene: KIR3DL1 was changed from to Unknown
Viral resistance v0.28 KIR3DL1 Ivone Leong Classified gene: KIR3DL1 as Green List (high evidence)
Viral resistance v0.28 KIR3DL1 Ivone Leong Added comment: Comment on list classification: KIR3DL1 and KIR3DS1 are highly homologous (both exon and intron) and are considered to be alleles of the same gene

PMID: 12134147 found that activation of KIR3DS1 in combination of HLA-B (HLA-B Bw4-80Ile), is associated with delayed progression of AIDS in people infected with HIV-1. If KIR3DS1 is missing then HLA-B Bw4-80Ile is not associated with any AIDS outcomes; however, if HLA-B Bw4-80Ile is missing then KIR3DS1 is associated with more rapid AIDS progression.

PMID: 18317000 found that there is an increased proportion of KIR3DS1 in HIV-exposed uninfected individuals compared with individuals who have primary HIV infections. This suggest that KIR3DS1 may contribute to more active natural killer cell function seen in HIV-exposed uninfected individuals.

PMID: 16933987 showed that KIR3DS1 in combination with HLA-B Bw4-80Ile confers early direct containment of HIV viral load and protection against development of AIDS defining opportunistic infections (such as pneumocystis carinii pneumonia, CMV retinitis and mycobacterium avium complex).

PMID: 31288555 is a meta-analysis based on 25 studies that looked at KIR genes in HIV-1 control or susceptibility. This study found that KIR3DS1 may be associated to protection against HIV-1 infection. KIR3DS1/S1 individuals were significantly slower in getting HIV infection than KIR3DL1/S1 individuals.

Therefore, there is enough evidence to promote this gene to Green status.
Viral resistance v0.28 KIR3DL1 Ivone Leong Gene: kir3dl1 has been classified as Green List (High Evidence).
Viral resistance v0.27 KIR3DL1 Ivone Leong Publications for gene: KIR3DL1 were set to 12134147
Viral resistance v0.26 TLR3 Ivone Leong Publications for gene: TLR3 were set to 20636339
Viral resistance v0.25 TLR3 Ivone Leong Mode of inheritance for gene: TLR3 was changed from to Unknown
Viral resistance v0.24 TLR3 Ivone Leong Classified gene: TLR3 as Green List (high evidence)
Viral resistance v0.24 TLR3 Ivone Leong Added comment: Comment on list classification: PMID: 22174453 and 23962581 found that rs3775291 (Leu412Phe) confers resistance to HIV-1 infection in Spanish and Estonian HIV-1 exposed seronegative i.v. drug users.

PMID: 20636339 found that activating TLR3 inhibits HIV replication and that TLR3-mediated induction of multiple anti-HIV factors (i.e. type I interferon inducible antiviral factors - APOBEC3G and tetherin) should be beneficial for HIV treatment.

Therefore, there is enough evidence to promote this gene to Green status.
Viral resistance v0.24 TLR3 Ivone Leong Gene: tlr3 has been classified as Green List (High Evidence).
Viral resistance v0.23 IL4R Sarah Leigh reviewed gene: IL4R: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Viral resistance v0.23 ACKR1 Ivone Leong Classified gene: ACKR1 as Red List (low evidence)
Viral resistance v0.23 ACKR1 Ivone Leong Added comment: Comment on list classification: Demoted to Red as this gene is associated to confering resistance to malaria infections.
Viral resistance v0.23 ACKR1 Ivone Leong Gene: ackr1 has been classified as Red List (Low Evidence).
Viral resistance v0.22 CCR5 Ivone Leong Classified gene: CCR5 as Green List (high evidence)
Viral resistance v0.22 CCR5 Ivone Leong Added comment: Comment on list classification: CCR5 is the primary HIV co-receptor (PMID: 29932942). PMID: 8751444, 8756719 and 8791590 found that individuals with homozygous 32 bp del in CCR5 (caused frameshift and premature termination) were protected from HIV-1 infection. This variant has AF of ~1% in Caucasian populations but absent in western and central Africa and Japan. Those with a heterozygous variant have a moderate but consistent decrease in the rate of disease progression. PMID: 19213682 describes a case ("Berline patient") where an HIV-1 infected patient received a hematopoietic stem cell transplantation where the donor was homozygous for CCR5 32del. The patient has remained HIV free for >10 years.

It has also been suggested that CCR5 32del confers resistance to hepatitis C virus (HVC) infections; however, more data is still needed for this (PMID: 29415549).

Therefore, there is sufficient evidence for this gene to be rated Green on this panel.
Viral resistance v0.22 CCR5 Ivone Leong Gene: ccr5 has been classified as Green List (High Evidence).
Viral resistance v0.21 CCR5 Ivone Leong Publications for gene: CCR5 were set to
Viral resistance v0.20 TLR3 Sarah Leigh gene: TLR3 was added
gene: TLR3 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: TLR3 was set to
Publications for gene: TLR3 were set to 20636339
Phenotypes for gene: TLR3 were set to {HIV1 infection, resistance to} 609423
Viral resistance v0.20 KIR3DL1 Sarah Leigh gene: KIR3DL1 was added
gene: KIR3DL1 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: KIR3DL1 was set to
Publications for gene: KIR3DL1 were set to 12134147
Phenotypes for gene: KIR3DL1 were set to {AIDS, delayed/rapid progression to} 609423
Viral resistance v0.20 IL4R Sarah Leigh gene: IL4R was added
gene: IL4R was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: IL4R was set to
Publications for gene: IL4R were set to 16189667
Phenotypes for gene: IL4R were set to {AIDS, slow progression to} 609423
Viral resistance v0.20 CXCR1 Sarah Leigh gene: CXCR1 was added
gene: CXCR1 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: CXCR1 was set to
Publications for gene: CXCR1 were set to 17360650
Phenotypes for gene: CXCR1 were set to {AIDS, slow progression to} 609423
Viral resistance v0.20 CXCL12 Sarah Leigh gene: CXCL12 was added
gene: CXCL12 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: CXCL12 was set to
Publications for gene: CXCL12 were set to 8752280; 8752281
Phenotypes for gene: CXCL12 were set to {AIDS, resistance to} 609423
Viral resistance v0.20 CCL3 Sarah Leigh gene: CCL3 was added
gene: CCL3 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: CCL3 was set to
Publications for gene: CCL3 were set to 16773571
Phenotypes for gene: CCL3 were set to {HIV infection, resistance to} 609423
Viral resistance v0.20 CCL2 Sarah Leigh gene: CCL2 was added
gene: CCL2 was added to Viral resistance. Sources: OMIM
Mode of inheritance for gene: CCL2 was set to
Publications for gene: CCL2 were set to 14571188
Phenotypes for gene: CCL2 were set to {HIV-1, resistance to} 609423
Viral resistance v0.19 CCR5 Ivone Leong Added comment: Comment on mode of inheritance: In reference to HIV resistance, Biallelic mutations confer stronger resistance against infection than Monoallelic mutations.
Viral resistance v0.19 CCR5 Ivone Leong Mode of inheritance for gene: CCR5 was changed from Unknown to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Viral resistance v0.18 Ivone Leong Panel status changed from internal to public
Viral resistance v0.17 CCR5 Ivone Leong Phenotypes for gene: CCR5 were changed from to {Hepatitis C virus, resistance to}, 609532; {HIV infection, susceptibility/resistance to}
Viral resistance v0.16 FUT2 Ivone Leong Classified gene: FUT2 as Green List (high evidence)
Viral resistance v0.16 FUT2 Ivone Leong Added comment: Comment on list classification: There are >3 published papers describing homozygous variant (G428A), which inactivates the FUT2 protein causing it to not make H type-1 ligand that is required for virus binding, conferring virus resistance. This variant is present in ~20% of European population.

Therefore there is enough evidence to promote this gene to Green status.
Viral resistance v0.16 FUT2 Ivone Leong Gene: fut2 has been classified as Green List (High Evidence).
Viral resistance v0.15 FUT2 Ivone Leong Publications for gene: FUT2 were set to
Viral resistance v0.14 FUT2 Ivone Leong Mode of inheritance for gene: FUT2 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Viral resistance v0.13 FUT2 Ivone Leong Phenotypes for gene: FUT2 were changed from to {Norwalk virus infection, resistance to}
Viral resistance v0.12 ACKR1 Ivone Leong Phenotypes for gene: ACKR1 were changed from to {Malaria, vivax, protection against}, 611162
Viral resistance v0.11 CCL11 Sarah Leigh Publications for gene: CCL11 were set to 14571188
Viral resistance v0.10 CCL11 Sarah Leigh Classified gene: CCL11 as Red List (low evidence)
Viral resistance v0.10 CCL11 Sarah Leigh Added comment: Comment on list classification: A cytokine (inflammatory biomarker), that is released in response to viral infections. Increased levels of CCL11 amongst other cytokines, is associated with immunity to West Nile virus (PMID 30915442). A haplotype that included c.-1385G>A was associated with resistance to HIV-1 infection (PMID 14571188).
Viral resistance v0.10 CCL11 Sarah Leigh Gene: ccl11 has been classified as Red List (Low Evidence).
Viral resistance v0.9 IL22 Rebecca Foulger gene: IL22 was added
gene: IL22 was added to Viral resistance. Sources: Literature
Mode of inheritance for gene: IL22 was set to Unknown
Publications for gene: IL22 were set to 22952908
Phenotypes for gene: IL22 were set to resistance to lethal West Nile virus
Added comment: Mouse model in PMID:22952908: Il22(-/-) mice were more resistant to lethal West Nile virus (WNV) encephalitis.
Sources: Literature
Viral resistance v0.8 HLA-B Rebecca Foulger gene: HLA-B was added
gene: HLA-B was added to Viral resistance. Sources: Literature
Mode of inheritance for gene: HLA-B was set to Unknown
Publications for gene: HLA-B were set to 32303592
Phenotypes for gene: HLA-B were set to immunity to COVID-19
Added comment: PMID:32303592 (Nguyen et al., 2020) performed in-silico analysis of viral-binding affinity across HLA genotypes for SARS-CoV-2 peptides. Based on in-silico results, they suggest that individuals with HLA-B*46:01 may be vulnerable to COVID-19. Conversely, HLA-B*15:03 may enable greater immunity.
Sources: Literature
Viral resistance v0.7 CCL11 Sarah Leigh gene: CCL11 was added
gene: CCL11 was added to Viral resistance. Sources: Other
Mode of inheritance for gene: CCL11 was set to Unknown
Publications for gene: CCL11 were set to 14571188
Phenotypes for gene: CCL11 were set to {HIV1, resistance to} 609423
Review for gene: CCL11 was set to RED
Added comment: Sources: Other
Viral resistance v0.6 ACKR1 Ivone Leong Classified gene: ACKR1 as Amber List (moderate evidence)
Viral resistance v0.6 ACKR1 Ivone Leong Gene: ackr1 has been classified as Amber List (Moderate Evidence).
Viral resistance v0.5 ACKR1 Ivone Leong gene: ACKR1 was added
gene: ACKR1 was added to Viral resistance. Sources: Expert list,Literature
Mode of inheritance for gene: ACKR1 was set to Unknown
Review for gene: ACKR1 was set to AMBER
Added comment: This gene has been added from https://www.covidhge.com/ and will require further curation, therefore it is currently rated as Amber.
Sources: Expert list, Literature
Viral resistance v0.4 FUT2 Ivone Leong Classified gene: FUT2 as Amber List (moderate evidence)
Viral resistance v0.4 FUT2 Ivone Leong Gene: fut2 has been classified as Amber List (Moderate Evidence).
Viral resistance v0.3 FUT2 Ivone Leong gene: FUT2 was added
gene: FUT2 was added to Viral resistance. Sources: Expert list,Literature
Mode of inheritance for gene: FUT2 was set to Unknown
Review for gene: FUT2 was set to AMBER
Added comment: This gene has been added from https://www.covidhge.com/ and will require further curation, therefore it is currently rated as Amber.
Sources: Expert list, Literature
Viral resistance v0.2 CCR5 Ivone Leong Classified gene: CCR5 as Amber List (moderate evidence)
Viral resistance v0.2 CCR5 Ivone Leong Gene: ccr5 has been classified as Amber List (Moderate Evidence).
Viral resistance v0.1 CCR5 Ivone Leong gene: CCR5 was added
gene: CCR5 was added to Viral resistance. Sources: Literature,Expert list
Mode of inheritance for gene: CCR5 was set to Unknown
Review for gene: CCR5 was set to AMBER
Added comment: This gene has been added from https://www.covidhge.com/ and will require further curation, therefore it is currently rated as Amber.
Sources: Literature, Expert list
Viral resistance v0.0 Ivone Leong Added Panel Viral resistance
Set panel types to: Research