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Table 3 Significant data points ordered by gene and by variant, according to the positive signals of association found across studies (not significant data points were omitted). Sample size and effect size were reported as abstracted from the source article. Genes and HLA loci were listed separately

From: Genetic variants of the human host influencing the coronavirus-associated phenotypes (SARS, MERS and COVID-19): rapid systematic review and field synopsis

Author, year Disease Ancestry Outcome Sample N Cases N Controls N Notes on sample Gene/locus Variant Risk allele Effect size, OR 95% CI P value    Notes on statistics Main finding Ref.
Itoyama S, 2004 SARS VIE Hypoxemia 44 44 n/a # ACE I/D (rs4646994) D 3.04 1.12–8.25 0.029    22 severe vs 22 non-severe cases No association with disease [30]
Kuo CL, 2020 COVID-19 EUR COVID-19 positivity status 323570 622 322948 General population as control APOE rs429358 + rs7412 ε4 2.31 1.71–3.35 <0.001   m Statistics from the whole cohort; strata available Association with the ε4 homozygous genotype [57]
Ng MW, 2007 SARS CHI Manifest disease 1073 495 578   CCL5 rs2107538 G 2.8 2.11–3.71 <0001 c m Allele-associated OR reported Association with disease [44]
Ng MW, 2007 SARS CHI Severity (death) 495 495 n/a   CCL5 rs2107538 G 2.1 1.30–3.39 0.002 c m 57 deaths vs438 survivals; allele-associated OR reported Association with death (57 deceased vs 438 survived patients) [44]
Ng MW, 2007 SARS CHI Severity (ICU) 356 356 n/a   CCL5 rs2107538 G 2.78 1.37–5.63 0.005 c m 20 severe cases vs 336; allele-associated OR reported Association with severity [44]
Yuan FF, 2007 SARS CHI Manifest disease 152 152 n/a § CD14 159C/T (rs2569190) C n/r n/r 0.027    26 severe cases vs 136 mild CD14 associated with severity [45]
Chan KYK, 2010 SARS CHI LDH level 681 681 n/a $ CD209 (DC-SIGN) -366AG, promoter region G 0.4 0.19–0.85 0.014    LDH modelled as binary variable; univariate statistics reported Association with lower LDH level [51]
Chan VS, 2006 SARS CHI Manifest disease 1127 285 842 $ CLEC4M (L-SIGN) exon 4 tandem repeat homozigosity 0.691 0.523–0.913 0.009    . Homozigosity associated with resistance to infection [38]
Chan KYK, 2010 SARS CHI LDH level 677 677 n/a $ combined CD209 and ICAM3 -366AG, promoter region + rs2304237 A; A 4.34 1.34–14.12 0.021    LDH level modelled as binary variable; univariate statistics reported Association with higher LDH level [51]
Yuan FF, 2005 SARS CHI Severity (ICU or death) 380 26 200 § FcγRIIA R131H (rs1801274) R 3.2 1.1–9.1 0.03    26 patients vs controls Nominal association with severity [36]
Chen WJ, 2006 SARS CHI Positive NPS 188 94 94 0 FGL2 +158 (rs2075761) A 4 1.39–11.48 0.031    GA genotype; outcome modelled as binary variable Nominal association of NPS with 4 genes (IL1A, IL18, FGL2, RelB) [41]
Chan KYK, 2007 SARS CHI LDH level 677 677 n/a $ ICAM3 rs2304237 C (Gly) 4.31 1.37–13.56 0.0067    LDH modelled as binary variable; P corrected for 2 tests ICAM3 associated with LDH level [43]
Zhang Y, 2020 COVID-19 CHI Disease severity 80 80 n/a 24 severe vs 56 mild IFITM3 rs12252 C 6.37 n/r <0.001    CC vs other genotypes; CI n/r Association with severity [59]
Chong WP, 2006 SARS CHI Manifest disease 925 476 449   IFN-γ rs2430561 A 5.19 2.78–9.68 <0.001   m Recessive model; multivariate LR n/r Association with one SNP [39]
Chen WJ, 2006 SARS CHI Positive NPS 188 94 94   IL18 -607 (rs1946518) T 10.6 2.03–55.0 0.014    Outcome modelled as binary variable Nominal association of NPS with 4 genes (IL1A, IL18, FGL2, RelB) [41]
Chen WJ, 2006 SARS CHI Positive NPS 188 94 94   IL1A −889 (rs1800587) T 10.2 1.82–56.8 0.008    Outcome modelled as binary variable Nominal association of NPS with 4 genes (IL1A, IL18, FGL2, RelB) [41]
Ip WK, 2005 SARS CHI Manifest disease 1541 353 1188   MBL −221X/Y (rs7096206); ex1 54A/B (rs1800450) YB 1.55 1.21–1.99 <0.001   m Statistics n/r Association of YB haplotype with disease [34]
Ip WK, 2005 SARS CHI Serum MBL level 353 353 n/a   MBL −221X/Y (rs7096206); ex1 54A/B (rs1800450) YB n/r n/r n/r   m Statistics n/r Association of YB haplotype with low serum MBL level [34]
Zhang H, 2005 SARS CHI Manifest disease 744 352 392   MBL 230[codon 54]A/B (rs1800450) B 1.73 1.25–2.39 0.00086 c    Association of B allele with disease [37]
Zhang H, 2005 SARS CHI Serum MBL level 744 352 392   MBL 230[codon 54]A/B (rs1800450) B 1.67 1.21–2.29 0.00187 c    Association of B allele with MBL level [37]
Hamano E, 2005 SARS VIE Severity (oxygen therapy) 44 44 n/a   MxA rs2071430 − 88) G 3.75 1.08–10.7 0.0346     Association with severity [33]
He J, 2006 SARS CHI Manifest disease 66 66 64 Cohort assessed for risk factors MxA rs2071430 T 3.22 1.13–9.18 0.029   m   Association with AG genotype, dominant G protective [40]
Ching JCY, 2010 SARS CHI Manifest disease 1210 792 418 $ MxA rs17000900 (−123) A 0.58 0.41–0.82 0.002 c m   Association with resistance to infection [52]
Hamano E, 2005 SARS VIE Severity (oxygen therapy) 44 44 n/a 0 OAS-1 rs3741981 G 2.68 1.17–6.15 0.0178     Association with disease [33]
He J, 2006 SARS CHI Manifest disease 66 66 64 Cohort assessed for risk factors OAS-1 rs2660 G 0.38 0.14–0.98 0.047   m   Association with GT genotype, dominant T [40]
Chen WJ, 2006 SARS CHI Positive NPS 188 94 94   RelB +23692 (rs2288918) T 7.2 1.47–35.3 0.034     Nominal association of NPS with 4 genes (IL1A, IL18, FGL2, RelB) [41]
Wang S, 2008 SARS CHI Manifest disease 54 54 n/a   TNF-α −1031 C 6 1.60–22.55 0.04    24 severe cases vs 30 mild Nominal association with femoral head necrosis [47]
Wang S, 2008 SARS CHI Manifest disease 54 54 n/a   TNF-α −863 A 8.4 1.76–40.02 0.01    24 severe cases vs 30 mild Nominal association with femoral head necrosis [47]
Chen YM, 2006 SARS CHI Seropositivity 100 20 80   HLA-Cw,   Cw0801 3.4 1.50–7.58 0.003 c   Number of tests not shown Association found in recessive model [42]
Lin M, 2003 SARS n/r Manifest disease 134 33 101   HLA-B   B*4601 10.62 2.80–40.26 0.0279 c   6 severe cases vs 101 health care workers Association with both infection and severity [28]
Ng MHL, 2004 SARS CHI Manifest disease 18864 90 18774   HLA-B   B*0301 0.06 0.01–0.47 0.0042 c   . Association with resistance to infection [31]
Ng MHL, 2004 SARS CHI Manifest disease 18864 90 18774   HLA-B   B*0703 4.08 2.03–8.18 0.0022 c   . Association with infection [31]
Wang W, 2020 COVID-19 CHI Manifest disease 3630 82 3548   HLA-B   B*15:27 3.59 1.72–7.50 0.03 c    Association with infection [58]
Wang W, 2020 COVID-19 CHI Manifest disease 3630 82 3548   HLA-C   C*07:29 130.2 5.28–3211 0.025 c    Association with infection [58]
Wang SF, 2011 SARS n/r Manifest disease 97 56 41   HLA-Cw   Cw 1502 0.17 0.04–0.81 0.01    . Association with resistance to infection [54]
Hajeer AH, 2016 MERS SAU Manifest disease 184 23 161   HLA-DRB1   DRB1*11:01 6.11 1.36–24.76 0.022 c   . Association with the disease [56]
  1. Notes and legend: gene and polymorphism names were reported as described in articles; the dbSNP nomenclature was added in brackets.
  2. CHI Chinese, EUR European, SAU Saudi Arabia, VIE Vietnamese, ICU intensive care unit, LDH lactate dehydrogenase, WBC white blood counts, NPS nasopharyngeal shedding
  3. #: Same cohort used by Itoyama S 2004, 2005, Keicho N 2009; § Same cohort used by Yuan FF 2005, 2007; $: Same cohort used by Chan VS 2006, Chan KYK 2007, 2010, Ching JCY 2010; LR logistic regression, ns: not significant, n/r not reported, n/a not applicable, c corrected for multiple testing, m multivariate analysis
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Human Genomics

ISSN: 1479-7364

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