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      Pharmacogenomics of COVID-19 therapies

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          Abstract

          A new global pandemic of coronavirus disease 2019 (COVID-19) has resulted in high mortality and morbidity. Currently numerous drugs are under expedited investigations without well-established safety or efficacy data. Pharmacogenomics may allow individualization of these drugs thereby improving efficacy and safety. In this review, we summarized the pharmacogenomic literature available for COVID-19 drug therapies including hydroxychloroquine, chloroquine, azithromycin, remdesivir, favipiravir, ribavirin, lopinavir/ritonavir, darunavir/cobicistat, interferon beta-1b, tocilizumab, ruxolitinib, baricitinib, and corticosteroids. We searched PubMed, reviewed the Pharmacogenomics Knowledgebase (PharmGKB ®) website, Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines, the U.S. Food and Drug Administration (FDA) pharmacogenomics information in the product labeling, and the FDA pharmacogenomics association table. We found several drug-gene variant pairs that may alter the pharmacokinetics of hydroxychloroquine/chloroquine (CYP2C8, CYP2D6, SLCO1A2, and SLCO1B1); azithromycin (ABCB1); ribavirin (SLC29A1, SLC28A2, and SLC28A3); and lopinavir/ritonavir (SLCO1B1, ABCC2, CYP3A). We also identified other variants, that are associated with adverse effects, most notable in hydroxychloroquine/chloroquine (G6PD; hemolysis), ribavirin (ITPA; hemolysis), and interferon β -1b (IRF6; liver toxicity). We also describe the complexity of the risk for QT prolongation in this setting because of additive effects of combining more than one QT-prolonging drug (i.e., hydroxychloroquine/chloroquine and azithromycin), increased concentrations of the drugs due to genetic variants, along with the risk of also combining therapy with potent inhibitors. In conclusion, although direct evidence in COVID-19 patients is lacking, we identified potential actionable genetic markers in COVID-19 therapies. Clinical studies in COVID-19 patients are deemed warranted to assess potential roles of these markers.

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          Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

          Summary Background A recent cluster of pneumonia cases in Wuhan, China, was caused by a novel betacoronavirus, the 2019 novel coronavirus (2019-nCoV). We report the epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of these patients. Methods All patients with suspected 2019-nCoV were admitted to a designated hospital in Wuhan. We prospectively collected and analysed data on patients with laboratory-confirmed 2019-nCoV infection by real-time RT-PCR and next-generation sequencing. Data were obtained with standardised data collection forms shared by WHO and the International Severe Acute Respiratory and Emerging Infection Consortium from electronic medical records. Researchers also directly communicated with patients or their families to ascertain epidemiological and symptom data. Outcomes were also compared between patients who had been admitted to the intensive care unit (ICU) and those who had not. Findings By Jan 2, 2020, 41 admitted hospital patients had been identified as having laboratory-confirmed 2019-nCoV infection. Most of the infected patients were men (30 [73%] of 41); less than half had underlying diseases (13 [32%]), including diabetes (eight [20%]), hypertension (six [15%]), and cardiovascular disease (six [15%]). Median age was 49·0 years (IQR 41·0–58·0). 27 (66%) of 41 patients had been exposed to Huanan seafood market. One family cluster was found. Common symptoms at onset of illness were fever (40 [98%] of 41 patients), cough (31 [76%]), and myalgia or fatigue (18 [44%]); less common symptoms were sputum production (11 [28%] of 39), headache (three [8%] of 38), haemoptysis (two [5%] of 39), and diarrhoea (one [3%] of 38). Dyspnoea developed in 22 (55%) of 40 patients (median time from illness onset to dyspnoea 8·0 days [IQR 5·0–13·0]). 26 (63%) of 41 patients had lymphopenia. All 41 patients had pneumonia with abnormal findings on chest CT. Complications included acute respiratory distress syndrome (12 [29%]), RNAaemia (six [15%]), acute cardiac injury (five [12%]) and secondary infection (four [10%]). 13 (32%) patients were admitted to an ICU and six (15%) died. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNFα. Interpretation The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Major gaps in our knowledge of the origin, epidemiology, duration of human transmission, and clinical spectrum of disease need fulfilment by future studies. Funding Ministry of Science and Technology, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, and Beijing Municipal Science and Technology Commission.
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            Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study

            Summary Background An ongoing outbreak of pneumonia associated with the severe acute respiratory coronavirus 2 (SARS-CoV-2) started in December, 2019, in Wuhan, China. Information about critically ill patients with SARS-CoV-2 infection is scarce. We aimed to describe the clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia. Methods In this single-centered, retrospective, observational study, we enrolled 52 critically ill adult patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) of Wuhan Jin Yin-tan hospital (Wuhan, China) between late December, 2019, and Jan 26, 2020. Demographic data, symptoms, laboratory values, comorbidities, treatments, and clinical outcomes were all collected. Data were compared between survivors and non-survivors. The primary outcome was 28-day mortality, as of Feb 9, 2020. Secondary outcomes included incidence of SARS-CoV-2-related acute respiratory distress syndrome (ARDS) and the proportion of patients requiring mechanical ventilation. Findings Of 710 patients with SARS-CoV-2 pneumonia, 52 critically ill adult patients were included. The mean age of the 52 patients was 59·7 (SD 13·3) years, 35 (67%) were men, 21 (40%) had chronic illness, 51 (98%) had fever. 32 (61·5%) patients had died at 28 days, and the median duration from admission to the intensive care unit (ICU) to death was 7 (IQR 3–11) days for non-survivors. Compared with survivors, non-survivors were older (64·6 years [11·2] vs 51·9 years [12·9]), more likely to develop ARDS (26 [81%] patients vs 9 [45%] patients), and more likely to receive mechanical ventilation (30 [94%] patients vs 7 [35%] patients), either invasively or non-invasively. Most patients had organ function damage, including 35 (67%) with ARDS, 15 (29%) with acute kidney injury, 12 (23%) with cardiac injury, 15 (29%) with liver dysfunction, and one (2%) with pneumothorax. 37 (71%) patients required mechanical ventilation. Hospital-acquired infection occurred in seven (13·5%) patients. Interpretation The mortality of critically ill patients with SARS-CoV-2 pneumonia is considerable. The survival time of the non-survivors is likely to be within 1–2 weeks after ICU admission. Older patients (>65 years) with comorbidities and ARDS are at increased risk of death. The severity of SARS-CoV-2 pneumonia poses great strain on critical care resources in hospitals, especially if they are not adequately staffed or resourced. Funding None.
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              Liver injury in COVID-19: management and challenges

              In December, 2019, an outbreak of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], previously 2019-nCoV) started in Wuhan, China, and has since become a global threat to human health. The number of confirmed cases of 2019 coronavirus disease (COVID-19) has reached 87 137 worldwide as of March 1, 2020, according to WHO COVID-19 situation report 41; most of these patients are in Wuhan, China. Many cases of COVID-19 are acute and resolve quickly, but the disease can also be fatal, with a mortality rate of around 3%. 1 Onset of severe disease can result in death due to massive alveolar damage and progressive respiratory failure. 2 SARS-CoV-2 shares 82% genome sequence similarity to SARS-CoV and 50% genome sequence homology to Middle East respiratory syndrome coronavirus (MERS-CoV)—all three coronaviruses are known to cause severe respiratory symptoms. Liver impairment has been reported in up to 60% of patients with SARS 3 and has also been reported in patients infected with MERS-CoV. 4 At least seven relatively large-scale case studies have reported the clinical features of patients with COVID-19.1, 5, 6, 7, 8, 9, 10 In this Comment, we assess how the liver is affected using the available case studies and data from The Fifth Medical Center of PLS General Hospital, Beijing, China. These data indicate that 2–11% of patients with COVID-19 had liver comorbidities and 14–53% cases reported abnormal levels of alanine aminotransferase and aspartate aminotransferase (AST) during disease progression (table ). Patients with severe COVID-19 seem to have higher rates of liver dysfunction. In a study in The Lancet by Huang and colleagues, 5 elevation of AST was observed in eight (62%) of 13 patients in the intensive care unit (ICU) compared with seven (25%) of 28 patients who did not require care in the ICU. Moreover, in a large cohort including 1099 patients from 552 hospitals in 31 provinces or provincial municipalities, more severe patients with disease had abnormal liver aminotransferase levels than did non-severe patients with disease. 1 Furthermore, in another study, 8 patients who had a diagnosis of COVID-19 confirmed by CT scan while in the subclinical phase (ie, before symptom onset) had significantly lower incidence of AST abnormality than did patients diagnosed after the onset of symptoms. Therefore, liver injury is more prevalent in severe cases than in mild cases of COVID-19. Table Comorbidity with liver disease and liver dysfunction in patients with SARS-CoV-2 infection Patients with SARS-CoV-2 infection Patients with pre-existing liver conditions Patients with abnormal liver function Notes Guan et al 1 1099 23 (2·3%) AST abnormal (22·2%), ALT abnormal (21·3%) Elevated levels of AST were observed in 112 (18·2%) of 615 patients with non-severe disease and 56 (39·4%) of 142 patients with severe disease. Elevated levels of ALT were observed in 120 (19·8%) of patients with non-severe disease and 38 (28·1%) of 135 patients with severe disease. Huang et al 5 41 1 (2·0%) 15 (31·0%) Patients with severe disease had increased incidence of abnormal liver function. Elevation of AST level was observed in eight (62%) of 13 patients in the ICU compared with seven (25%) 25 patients who did not require care in the ICU. Chen et al 6 99 NA 43 (43·0%) One patient with severe liver function damage. Wang et al 7 138 4 (2·9%) NA .. Shi et al 8 81 7 (8·6%) 43 (53·1%) Patients who had a diagnosis of COVID-19 confirmed by CT scan while in the subclinical phase had significantly lower incidence of AST abnormality than did patients diagnosed after the onset of symptoms. Xu et al 9 62 7 (11·0%) 10 (16·1%) .. Yang et al 10 52 NA 15 (29·0%) No difference for the incidences of abnormal liver function between survivors (30%) and non-survivors (28%). Our data (unpublished) 56 2 (3·6%) 16 (28·6%) One fatal case, with evaluated liver injury. 13 AST= aspartate aminotransferase. ALT= alanine aminotransferase. ICU=intensive care unit. Liver damage in patients with coronavirus infections might be directly caused by the viral infection of liver cells. Approximately 2–10% of patients with COVID-19 present with diarrhoea, and SARS-CoV-2 RNA has been detected in stool and blood samples. 11 This evidence implicates the possibility of viral exposure in the liver. Both SARS-CoV-2 and SARS-CoV bind to the angiotensin-converting enzyme 2 (ACE2) receptor to enter the target cell, 7 where the virus replicates and subsequently infects other cells in the upper respiratory tract and lung tissue; patients then begin to have clinical symptoms and manifestations. Pathological studies in patients with SARS confirmed the presence of the virus in liver tissue, although the viral titre was relatively low because viral inclusions were not observed. 3 In patients with MERS, viral particles were not detectable in liver tissue. 4 Gamma-glutamyl transferase (GGT), a diagnostic biomarker for cholangiocyte injury, has not been reported in the existing COVID-19 case studies; we found that it was elevated in 30 (54%) of 56 patients with COVID-19 during hospitalisation in our centre (unpublished). We also found that elevated alkaline phosphatase levels were observed in one (1·8%) of 56 patients with COVID-19 during hospitalisation. A preliminary study (albeit not peer-reviewed) suggested that ACE2 receptor expression is enriched in cholangiocytes, 12 indicating that SARS-CoV-2 might directly bind to ACE2-positive cholangiocytes to dysregulate liver function. Nevertheless, pathological analysis of liver tissue from a patient who died from COVID-19 showed that viral inclusions were not observed in the liver. 13 It is also possible that the liver impairment is due to drug hepatotoxicity, which might explain the large variation observed across the different cohorts. In addition, immune-mediated inflammation, such as cytokine storm and pneumonia-associated hypoxia, might also contribute to liver injury or even develop into liver failure in patients with COVID-19 who are critically ill. Liver damage in mild cases of COVID-19 is often transient and can return to normal without any special treatment. However, when severe liver damage occurs, liver protective drugs have usually been given to such patients in our unit. Chronic liver disease represents a major disease burden globally. Liver diseases including chronic viral hepatitis, non-alcoholic fatty liver disease, and alcohol-related liver disease affect approximately 300 million people in China. Given this high burden, how different underlying liver conditions influence liver injury in patients with COVID-19 needs to be meticulously evaluated. However, the exact cause of pre-existing liver conditions has not been outlined in the case studies of COVID-19 and the interaction between existing liver disease and COVID-19 has not been studied. Immune dysfunction—including lymphopenia, decreases of CD4+ T-cell levels, and abnormal cytokine levels (including cytokine storm)—is a common feature in cases of COVID-19 and might be a critical factor associated with disease severity and mortality. For patients with chronic hepatitis B in immunotolerant phases or with viral suppression under long-term treatment with nucleos(t)ide analogues, evidence of persistent liver injury and active viral replication after co-infection with SARS-CoV-2 need to be further investigated. In patients with COVID-19 with autoimmune hepatitis, the effects of administration of glucocorticoids on disease prognosis is unclear. Given the expression of the ACE2 receptor in cholangiocytes, whether infection with SARS-CoV-2 aggravates cholestasis in patients with primary biliary cholangitis, or leads to an increase in alkaline phosphatase and GGT, also needs to be monitored. Moreover, patients with COVID-19 with liver cirrhosis or liver cancer might be more susceptible to SARS-CoV-2 infection because of their systemic immunocompromised status. The severity, mortality, and incidence of complications in these patients, including secondary infection, hepatic encephalopathy, upper gastrointestinal bleeding, and liver failure, need to be examined in large-cohort clinical studies. Considering their immunocompromised status, more intensive surveillance or individually tailored therapeutic approaches is needed for severe patients with COVID-19 with pre-existing conditions such as advanced liver disease, especially in older patients with other comorbidities. Further research should focus on the causes of liver injury in COVID-19 and the effect of existing liver-related comorbidities on treatment and outcome of COVID-19.
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                Author and article information

                Contributors
                jacob117@umn.edu
                Journal
                NPJ Genom Med
                NPJ Genom Med
                NPJ Genomic Medicine
                Nature Publishing Group UK (London )
                2056-7944
                18 August 2020
                18 August 2020
                2020
                : 5
                : 35
                Affiliations
                [1 ]GRID grid.17635.36, ISNI 0000000419368657, Department of Experimental and Clinical Pharmacology, , College of Pharmacy University of Minnesota, ; Minneapolis, MN USA
                [2 ]GRID grid.17635.36, ISNI 0000000419368657, Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, , University of Minnesota, ; Minneapolis, MN USA
                [3 ]GRID grid.214458.e, ISNI 0000000086837370, Department of Clinical Pharmacy, , University of Michigan College of Pharmacy, ; Ann Arbor, MI USA
                Author information
                http://orcid.org/0000-0001-8296-6412
                http://orcid.org/0000-0003-3639-717X
                http://orcid.org/0000-0001-5513-5509
                Article
                143
                10.1038/s41525-020-00143-y
                7435176
                32864162
                7437d0c0-b1a6-4565-aae1-0650104c2732
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 29 April 2020
                : 23 July 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000060, U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID);
                Award ID: R01AI140303
                Award ID: K08AI134262
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
                Categories
                Review Article
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                © The Author(s) 2020

                genetic markers,viral infection
                genetic markers, viral infection

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