The genetic and evolutionary determinants of COVID-19 susceptibility

Evolution, genetic diversity, and health

Human genetic diversity in today's world has been shaped by evolutionary history, demographic shifts and environmental exposures, influencing complex traits, disease susceptibility and drug responses. Capturing this diversity is essential for advancing precision medicine and promoting equitable healthcare. Despite the great progress achieved with initiatives such as the human Pangenome and large biobanks that aim for a better representation of human diversity, important challenges remain. In this Perspective, we discuss the importance of diversity in clinical genomics through an evolutionary lens. We highlight progress and challenges and outline key clinical applications of diverse genetic data. We argue that diversifying both datasets and methodologies-integrating ancestral and environmental factors-is crucial for fully understanding the genetic basis of human health and disease.

Aggravating mechanisms from COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces immune-mediated diseases. The pathophysiology of COVID-19 uses the following three mechanisms: (1) inflammasome activation mechanism; (2) cGAS-STING signaling mechanism; and (3) SAMHD1 tetramerization mechanism, which leads to IFN-I production. Interactions between the host and virus govern induction, resulting in multiorgan impacts. The NLRP3 with cGAS-STING constitutes the primary immune response. The expression of SARS-CoV-2 ORF3a, NSP6, NSP7, and NSP8 blocks innate immune activation and facilitates virus replication by targeting the RIG-I/MDA5, TRIF, and cGAS-STING signaling. SAMHD1 has a target motif for CDK1 to protect virion assembly, threonine 592 to modulate a catalytically active tetramer, and antiviral IFN responses to block retroviral infection. Plastic and allosteric nucleic acid binding of SAMHD1 modulates the antiretroviral activity of SAMHD1. Therefore, inflammasome activation, cGAS-STING signaling, and SAMHD1 tetramerization explain acute kidney injury, hepatic, cardiac, neurological, and gastrointestinal injury of COVID-19. It might be necessary to effectively block the pathological courses of diverse diseases.

Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population

Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral and host factors. These findings have highlighted the potential of host genetic markers to identify high-risk individuals and develop target interventions to reduce morbimortality. Despite its importance, genetic host factors remain largely understudied in Latin-American populations. Using a case-control design and a custom next-generation sequencing (NGS) panel encompassing 81 genetic variants and 74 genes previously associated with COVID-19 severity and long-COVID, we analyzed 56 individuals with asymptomatic or mild COVID-19 and 56 severe and critical cases. In agreement with previous studies, our results support the association between several clinical variables, including male sex, obesity and common symptoms like cough and dyspnea, and severe COVID-19. Remarkably, thirteen genetic variants showed an association with COVID-19 severity. Among these variants, rs11385942 (p < 0.01; OR = 10.88; 95% CI = 1.36-86.51) located in the LZTFL1 gene, and rs35775079 (p = 0.02; OR = 8.53; 95% CI = 1.05-69.45) located in CCR3 showed the strongest associations. Various respiratory and systemic symptoms, along with the rs8178521 variant (p < 0.01; OR = 2.51; 95% CI = 1.27-4.94) in the IL10RB gene, were significantly associated with the presence of long-COVID. The results of the predictive model comparison showed that the mixed model, which incorporates genetic and non-genetic variables, outperforms clinical and genetic models. To our knowledge, this is the first study in Colombia and Latin-America proposing a predictive model for COVID-19 severity and long-COVID based on genomic analysis. Our study highlights the usefulness of genomic approaches to studying host genetic risk factors in specific populations. The methodology used allowed us to validate several genetic variants previously associated with COVID-19 severity and long-COVID. Finally, the integrated model illustrates the importance of considering genetic factors in precision medicine of infectious diseases.

Genetic Basis for Mucormycosis Progression in COVID-19 Patients: From Susceptibility to Severity

The dynamics of COVID-19 and mucormycosis reveal a complex interplay of genetic factors that influence the susceptibility, severity, and immune responses. COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibits an increased incidence of mucormycosis, particularly in individuals with comorbidities or corticosteroid therapy. Mucormycosis is a fungal infection that affects the sinuses, orbits, and lungs and demands timely intervention with antifungal medications and surgery because of its life-threatening nature. Research on the genetic underpinnings of this intersection has unveiled key insights into the pathogenicity of Mucorales. Breakthroughs in genetic tools have exposed virulence factors, such as the CotH protein family and high-affinity iron-uptake mechanisms. Genetic susceptibility is a pivotal element in identifying individuals at risk of developing COVID-19, facilitating early detection, and allowing for personalized treatment strategies. DPP9, MIF, and TYK2 are among the genes implicated in COVID-19 severity, emphasizing the intricate relationship between genetic makeup and viral response. The genetic landscape extends to viral entry mechanisms, thereby affecting infection efficiency. Specific polymorphisms in genes such as IFNAR2, OAS3, and TYK2 are associated with COVID-19 severity, indicating shared genetic bases between severe and hospitalized cases. Mucormycosis is genetically predisposed, particularly in immunocompromised individuals. The challenge lies in understanding the genetic factors influencing susceptibility and offering insights into pathogenesis and potential therapeutic avenues. Organ transplantation adds another layer, increasing susceptibility to infections such as COVID-19 and mucormycosis. The impact of immunosuppression on COVID-19 severity remains elusive, necessitating ongoing research on the immunological mechanisms. Despite the challenges posed by emerging SARS-CoV-2 variants, the intricate connection between genetic factors and the interplay of COVID-19 and mucormycosis presents an opportunity for personalized treatment, targeted interventions, and refined public health strategies.

Seroprevalence of Anti-SARS-CoV-2 Antibodies in Cats during Five Waves of COVID-19 Epidemic in Thailand and Correlation with Human Outbreaks

Human-to-animal SARS-CoV-2 transmission was observed, including a veterinarian contracting COVID-19 through close contact with an infected cat, suggesting an atypical zoonotic transmission. This study investigated the prevalence of SARS-CoV-2 antibodies in cats during human outbreaks and elucidated the correlation between cat infections and human epidemics. A total of 1107 cat serum samples were collected and screened for SARS-CoV-2 antibodies using a modified indirect ELISA human SARS-CoV-2 antibody detection kit. The samples were confirmed using a cPass™ neutralization test. The SARS-CoV-2 seropositivity rate was 22.67% (199/878), mirroring the trend observed in concomitant human case numbers. The waves of the epidemic and the provinces did not significantly impact ELISA-positive cats. Notably, Chon Buri exhibited a strong positive correlation (r = 0.99, p = 0.009) between positive cat sera and reported human case numbers. Additionally, the cPass™ neutralization test revealed a 3.99% (35/878) seropositivity rate. There were significant differences in numbers and proportions of positive cat sera between epidemic waves. In Samut Sakhon, a positive correlation (r = 1, p = 0.042) was noted between the proportion of positive cat sera and human prevalence. The findings emphasize the need for ongoing surveillance to comprehend SARS-CoV-2 dynamics in both human and feline populations.

Convalescent Plasma Treatment of Patients Previously Treated with B-Cell-Depleting Monoclonal Antibodies Suffering COVID-19 Is Associated with Reduced Re-Admission Rates

Patients receiving treatment with B-cell-depleting monoclonal antibodies, such as anti-CD20 monoclonal antibodies, such as rituximab and obinutuzumab, either for hematological disease or another diagnosis, such as a rheumatological disease, are at an increased risk for medical complications and mortality from COVID-19. Since inconsistencies persist regarding the use of convalescent plasma (CP), especially in the vulnerable patient population that has received previous treatment with B-cell-depleting monoclonal antibodies, further studies should be performed in thisdirection. The aim of the present study was to describe the characteristics of patients with previous use of B-cell-depleting monoclonal antibodies and describe the potential beneficial effects of CP use in terms of mortality, ICU admission and disease relapse. In this retrospective cohort study, 39 patients with previous use of B-cell-depleting monoclonal antibodies hospitalized in the COVID-19 department of a tertiary hospital in Greece were recorded and evaluated. The mean age was 66.3 years and 51.3% were male. Regarding treatment for COVID-19, remdesivir was used in 89.7%, corticosteroids in 94.9% and CP in 53.8%. In-hospital mortality was 15.4%. Patients who died were more likely to need ICU admission and also had a trend towards a longer hospital stay, even though the last did not reach statistical significance. Patients treated with CP had a lower re-admission rate for COVID-19 after discharge. Further studies should be performed to identify the role of CP in patients with treatment with B-cell-depleting monoclonal antibodies suffering from COVID-19.

Association of COVID-19 with Risk and Progression of Alzheimer's Disease: Non-Overlapping Two-Sample Mendelian Randomization Analysis of 2.6 Million Subjects

BACKGROUND

Epidemiological studies showed that COVID-19 increases risk of Alzheimer's disease (AD). However, it remains unknown if there is a potential genetic predispositional effect.

OBJECTIVE

To examine potential effects of genetic susceptibility of COVID-19 on the risk and progression of AD, we performed a non-overlapping 2-sample Mendelian randomization (MR) study using summary statistics from genome-wide association studies (GWAS).

METHODS

Two-sample Mendelian randomization (MR) analysis of over 2.6 million subjects was used to examine whether genetic susceptibility of COVID-19 is not associated with the risk of AD, cortical amyloid burden, hippocampal volume, or AD progression score. Additionally, a validation analysis was performed on a combined sample size of 536,190 participants.

RESULTS

We show that the AD risk was not associated with genetic susceptibility of COVID-19 risk (OR = 0.98, 95% CI 0.81-1.19) and COVID-19 severity (COVID-19 hospitalization: OR = 0.98, 95% CI 0.9-1.07, and critical COVID-19: OR = 0.98, 95% CI 0.92-1.03). Genetic predisposition to COVID-19 is not associated with AD progression as measured by hippocampal volume, cortical amyloid beta load, and AD progression score. These findings were replicated in a set of 536,190 participants. Consistent results were obtained across models based on different GWAS summary statistics, MR estimators and COVID-19 definitions.

CONCLUSIONS

Our findings indicated that the genetic susceptibility of COVID-19 is not associated with the risk and progression of AD.