TUT4/7-mediated uridylation of a coronavirus subgenomic RNAs delays viral replication.

Coronaviruses are positive-strand RNA viruses with 3' polyadenylated genomes and subgenomic transcripts. The lengths of the viral poly(A) tails change during infection by mechanisms that remain poorly understood. Here, we use a splint-ligation method to measure the poly(A) tail length and poly(A) terminal uridylation and guanylation of the mouse hepatitis virus (MHV) RNAs. Upon infection of 17-CL1 cells with MHV, a member of the Betacoronavirus genus, we observe two populations of terminally uridylated viral transcripts, one with poly(A) tails ~44 nucleotides long and the other with poly(A) tails shorter than ~22 nucleotides. The mammalian terminal uridylyl-transferase 4 (TUT4) and terminal uridylyl-transferase 7 (TUT7), referred to as TUT4/7, add non-templated uracils to the 3'-end of endogenous transcripts with poly(A) tails shorter than ~30 nucleotides to trigger transcript decay. Here we find that depletion of the host TUT4/7 results in an increased replication capacity of the MHV virus. At late stages of infection, the population of uridylated subgenomic RNAs with tails shorter than ~22 nucleotides is reduced in the absence of TUT4/7 while the viral RNA load increases. Our findings indicate that TUT4/7 uridylation marks the MHV subgenomic RNAs for decay and delays viral replication.

NMR study of human macroPARPs domains: 1H, 15N and 13C resonance assignment of hPARP14 macro domain 2 in the free and the ADPr bound state.

hPARP14 is a human ADP-ribosyl-transferase (ART) that belongs to the macroPARPs family, together with hPARP9 and hPARP15. It contains a tandem of three macro domains (MD) while each of them has different properties. The first one, namely MD1, has not been reported to exhibit a high binding affinity for ADP-ribose (ADPr) in contrast to the following two (MD2 and MD3). All three MDs exhibit an α/ß/α sandwich-like fold as reported by the deposited crystallographic structures. MD2 and MD3 recognize mono-ADP-ribosylated (MARylated) but not poly-ADP-ribosylated (PARylated) substrates and thus they allow hPARP14 to bind its targets, which can be potentially MARylated by its catalytic domain (CD). hPARP14 participates in DNA damage repair process and immune response against viruses like SARS-CoV-2, which also harbors an MD fold. Furthermore, hPARP14 like the other two macroPARPs (hPARP9 and hPARP15), is implicated in numerous types of cancer, such as B-aggressive lymphoma and sarcoma, rendering its MDs as potential important drug targets. Herein, we report the complete NMR backbone and side chain assignment (1H, 13C, 15N) of hPARP14 MD2 in the free and ADPr bound states and the NMR chemical shift-based prediction of its secondary structure elements. This is the first reported NMR study of a hPARP macro domain, paving the way to screen by NMR chemical compounds which may alter the ability of hPARP14 to interact with its substrates affecting its function.

High Levels of Serum Bile Acids in COVID-19 Patients on Hospital Admission.

INTRODUCTION: Bile acids are signaling molecules with immune, metabolic and intestinal microbiota control actions. In high serum concentrations they increase inflammatory response from the liver-gut axis, until causing multiorgan failure and death; therefore, they may be associated with COVID-19's clinical progression, as a consequence of tissue and metabolic damage caused by SARS-CoV-2. While this topic is of considerable clinical interest, to our knowledge, it has not been studied in Cuba. OBJECTIVE: Study and preliminarily characterize patients admitted with a diagnosis of COVID-19 and high levels of serum bile acids. METHODS: A preliminary exploratory study was carried out with descriptive statistical techniques in 28 COVID-19 patients (17 women, 11 men; aged 19-92 years) who exhibited high levels of serum bile acids (≥10.1 µmol/L) on admission to the Dr. Luis Díaz Soto Central Military Hospital in Havana, Cuba, from September through November 2021. RESULTS: On admission patients presented hypocholesterolemia (13/28; 46.4%), hyperglycemia (12/28; 43.0%) and hyper gamma-glutamyl transpeptidase (23/28; 84.2%). Median blood glucose (5.8 mmol/L) and cholesterol (4.1 mmol/L) were within normal ranges (3.2‒6.2 mmol/L and 3.9‒5.2 mmol/L, respectively). Severe or critical stage was the most frequent (13/28) and median serum bile acids (31.6 µmol/L) and gamma-glutamyl transferase (108.6 U/L) averaged well above their respective normal ranges (serum bile acids: 0‒10 µmol/L; GGT: 9‒36 U/L). Arterial hypertension was the most frequent comorbidity (19/28; 67.9%). CONCLUSIONS: Severe or critical stage predominated, with serum bile acids and gamma-glutamyl transferase blood levels above normal ranges. The study suggests that serum bile acid is toxic at levels ≥10.1 µmol/L, and at such levels is involved in the inflammatory process and in progression to severe and critical clinical stages of the disease. In turn, this indicates the importance of monitoring bile acid homeostasis in hospitalized COVID-19 patients and including control of its toxicity in treatment protocols.

Aspartate transferase-to-platelet ratio index-plus: A new simplified model for predicting the risk of mortality among patients with COVID-19.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has a spectrum of clinical syndromes with serious involvement of the lung and frequent effection of the liver and hemostatic system. Blood biomarkers are affordable, rapid, objective, and useful in the evaluation and prognostication of COVID-19 patients. AIM: To investigate the association between aspartate transferase-to-platelet ratio index (APRI) and in-hospital mortality to develop a COVID-19 mortality prediction model. METHODS: A multicenter cohort study with a retrospective design was conducted. Medical records of all consecutive adult patients admitted to Al-Azhar University Hospital (Assiut, Egypt) and Chest Hospital (Assiut, Egypt) with confirmed COVID-19 from July 1, 2020 to October 1, 2020, were retrieved and analyzed. The patient cohort was classified into the following two categories based on the APRI: (1) COVID-19 presenting with APRI ≤ 0.5; and (2) COVID-19 presenting with APRI (> 0.5 and ≤ 1.5). The association between APRI and all-cause in-hospital mortality was analyzed, and the new model was developed through logistic regression analyses. RESULTS: Of the 353 patients who satisfied the inclusion criteria, 10% were admitted to the intensive care unit (n = 36) and 7% died during the hospital stay (n = 25). The median age was 40 years and 50.7% were male. On admission, 49% had aspartate transferase-dominant liver injury. On admission, APRI (> 0.5 and ≤ 1.5) was independently associated with all-cause in-hospital mortality in unadjusted regression analysis and after adjustment for age and sex; after stepwise adjustment for several clinically relevant confounders, APRI was still significantly associated with all-cause in-hospital mortality. On admission, APRI (> 0.5 and ≤ 1.5) increased the odds of mortality by five-times (P < 0.006). From these results, we developed a new predictive model, the APRI-plus, which includes the four predictors of age, aspartate transferase, platelets, and serum ferritin. Performance for mortality was very good, with an area under the receiver operating curve of 0.90. CONCLUSION: APRI-plus is an accurate and simplified prediction model for mortality among patients with COVID-19 and is associated with in-hospital mortality, independent of other relevant predictors.

Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19.

OBJECTIVE: Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus. METHODS: In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma. RESULTS: Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase. CONCLUSION: Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.

Elevated liver enzimes induced by COVID-19 in pregnancy / Elevación de enzimas hepáticas inducida por COVID-19 en embarazada

INTRODUCCIÓN: Las alteraciones del perfil hepático durante el embarazo ocurren en 3-5% de las gestantes. Una nueva etiología que se ha presentado en el contexto de pandemia actual es el síndrome respiratorio agudo severo relacionado con el nuevo coronavirus (SARS-CoV-2). Éste es responsable de alteraciones hepáticas en 2 a 11% de la población general infectada por este virus, y de hasta un 30% en las embarazadas que se infectan con SARS-CoV-2. Con el objetivo de mostrar una presentación poco frecuente del SARS-CoV-2 se expone un caso clínico de elevación de transaminasas en embarazada inducida por este nuevo virus. CASO CLÍNICO: Paciente de 36 años, cursando embarazo de 20+6 semanas, consulta por dolor abdominal asociado a ictericia y coluria. Se solicita estudio donde destaca elevación de transaminasas. Ecografía abdominal con vía biliar fina. Se descartan diferentes etiologías de hepatitis aguda y crónica (dada la falta de antecedentes). Finalmente se solicita PCR para COVID-19 que resulta positiva. CONCLUSIÓN: Luego de un estudio exhaustivo de diferentes etiologías de elevación de transaminasas, se atribuye esta alteración enzimática a SARS-CoV-2. Se decide seguimiento ambulatorio estricto con pruebas hepáticas cada dos semanas. La paciente evoluciona estable con exámenes normales luego de un mes desde que se indica el alta hospitalaria. Después de descartar etiologías frecuentes de elevación de transaminasas durante el embarazo, sugerimos solicitar el estudio de este virus con PCR para COVID-19, ya que podría ser una presentación poco frecuente de SARS-CoV-2.

INTRODUCTION: Approximately 3-5% of women present alterations of hepatic enzymes during pregnancy. Under the new circumstances that the world is facing with the SARS-COV2 pandemic, a new etiology for hepatic enzyme alterations has risen. The severe acute respiratory syndrome that the novel coronavirus causes is responsible for hepatic enzyme alterations in 2 to 11% of the sick population that did not have a previous underlying hepatic condition. Furthermore, hepatic enzyme alterations in pregnant women infected with SARS-COV2 presents in up to 30% of the cases. An infrequent presentation of SARS-COV2 is presented as our clinical case. CLINICAL CASE: A 36-year-old patient with a 20+6 week pregnancy presents abdominal pain, jaundice and choluria. General blood workup shows elevated transaminases. The abdominal ultrasound revealed a thin bile duct. Acute and chronic hepatitis etiologies were discarded. Finally, a PCR of COVID-19 was solicited, which turned out to be positive. CONCLUSIÓN: After an exhaustive study to determine the etiology of the elevated transaminases, the hepatic alterations were attributed to SARS-COV2 infection. A conservative management was adopted, with outpatient follow-up with liver testing every two weeks. The patient progresses with a stable steady decline in hepatic enzyme levels, and one-month post hospital discharge, her transaminases had reached normal values. Based on this clinical case, after ruling out frequent etiologies for elevated transaminases during pregnancy, it seems reasonable to request a PCR for COVID-19, since it could be a rare presentation of SARS-CoV-2.