BACKGROUND & AIMS: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gastrointestinal tissues, little is known about the roles of gut commensal microbes in susceptibility to and severity of infection. We investigated changes in fecal microbiomes of patients with SARS-CoV-2 infection during hospitalization and associations with severity and fecal shedding of virus. METHODS: We performed shotgun metagenomic sequencing analyses of fecal samples from 15 patients with Coronavirus Disease 2019 (COVID-19) in Hong Kong, from February 5 through March 17, 2020. Fecal samples were collected 2 or 3 times per week from time of hospitalization until discharge; disease was categorized as mild (no radiographic evidence of pneumonia), moderate (pneumonia was present), severe (respiratory rate !30/min, or oxygen saturation 93% when breathing ambient air), or critical (respiratory failure requiring mechanical ventilation, shock, or organ failure requiring intensive care). We compared microbiome data with those from 6 subjects with communityacquired pneumonia and 15 healthy individuals (controls). We assessed gut microbiome profiles in association with disease severity and changes in fecal shedding of SARS-CoV-2. RESULTS: Patients with COVID-19 had significant alterations in fecal microbiomes compared with controls, characterized by enrichment of opportunistic pathogens and depletion of beneficial commensals, at time of hospitalization and at all timepoints during hospitalization. Depleted symbionts and gut dysbiosis persisted even after clearance of SARS-CoV-2 (determined from throat swabs) and resolution of respiratory Gastroenterology 2020;159:944-955 BASIC AND TRANSLATIONAL AT symptoms. The baseline abundance of Coprobacillus, Clostridium ramosum, and Clostridium hathewayi correlated with COVID-19 severity; there was an inverse correlation between abundance of Faecalibacterium prausnitzii (an antiinflammatory bacterium) and disease severity. Over the course of hospitalization, Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, and Bacteroides ovatus, which downregulate expression of angiotensin-converting enzyme 2 (ACE2) in murine gut, correlated inversely with SARS-CoV-2 load in fecal samples from patients. CONCLUSIONS: In a pilot study of 15 patients with COVID-19, we found persistent alterations in the fecal microbiome during the time of hospitalization, compared with controls. Fecal microbiota alterations were associated with fecal levels of SARS-CoV-2 and COVID-19 severity. Strategies to alter the intestinal microbiota might reduce disease severity.

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Rapid and accurate laboratory diagnosis of active COVID-19 infection is one of the cornerstones of pandemic control. With the myriad of tests available in the market, the use of correct specimen type and laboratory-testing technique in the right clinical scenario could be challenging for non-specialists. In this mini-review, we will discuss the difference in diagnostic performance for different upper and lower respiratory tract specimens, and the role of blood and fecal specimens. We will analyze the performance characteristics of laboratory testing techniques of nucleic acid amplification tests, antigen detection tests, antibody detection tests, and point-of-care tests. Finally, the dynamics of viral replication and antibody production, and laboratory results interpretation in conjunction with clinical scenarios will be discussed.

Baricitinib therapy in COVID-19: A pilot study on safety and clinical impactDear Editor , 38.1 (37.7-38.7) 0.356 Breath rate N/min, median (IQR), 23 (19.5-24.2) 22 (19.7-24) 0.665 SpO2 (%),median (IQR) 91 (90-92.5) 92 (91.2-93) 0.157 PaO2/FiO2, median (IQR) 290 (199.2-292.2) 268.6 (264.4-295) 0.603 Pulse rate, median (IQR) 82 (73-88.3) 90 (87.2-94.5) 0.069 SBP mm/Hg, median (IQR) 120 (110-131.2) 105 (100-111.25) 0.003 DBP mm/Hg, median (IQR) 70 (60-80) 62.5 (60-66.25) 0.094 WBC (x10 9 /L), median (IQR) 7.8 (5.8-10.8) 8.2 (7.3-8.8) 0.908 Neutrophils (x10 9 /L), median (IQR) 6,5 (4.5-7.7) 6.9 (6.4-7.6) 0.707 Lymphocytes (x10 9 /L), median (IQR) 0.7 (0.7-1.2) 0.89 (0.7-0.9) 1.0 0 0 Hemoglobin (g/L), median (IQR) 118 (102-134.2) 125 (108-134) 0.568 Platelets (x10 9 /L), median (IQR) 203 (174-227) 366 (340-407) 0.0 0 0 ALT (U/L), median (IQR) 28.5 (23.5-52) 44 (37-50) 0.157 AST (U/L), median (IQR) 34 (26.2-48) 44 (34.7-47) 0.525 Creatinine (mg/dl), median (IQR)1.0 (0.9-1.1) 1.00 (0.9-1) 0.583 CRP (mg/dl), median (IQR) 8.2 (5.8-14.5) 3 (1.5-3.2) 0.002 Procalcitonin ng/ml, median (IQR) 0.7 (0.4-1.1) 1.2 (0.8-2.1) 0.902 MEWS, median (IQR) 3 ( 2-3.25) 3 (3-4) 0.544 Abbreviations and symbols: N = number;% = percentage; °C: grade Celsius; min = minute; SpO2 = peripheral capillary oxygen saturation; PaO2/FiO2 = ratio of arterial oxygen partial pressure to fractional inspired oxygen; SBP = systolic blood pressure; DBP = diastolic blood pressure; WBC = white blood cells; AST = serum glutamic oxaloacetic transaminase; ALT = serum alanine aminotransferase; MEWS = Modified Early Warning Score; IQR: Interquartile range.

Introduction: Recent studies showed that SARS-CoV-2 RNA may be found in fecal specimens of COVID-19 patients, but the sample size is limited. This systematic review and meta-analysis examined the detection rate of SARS-CoV-2 RNA in fecal specimens of these patients according to their clinical characteristics. Methods: MEDLINE, Embase, Scopus, and three Chinese biomedical databases were searched up to 25 March 2020 with no language restriction. We included original observational studies that reported the detection rate of SARS-CoV-2 RNA in fecal specimens of COVID-19 patients. Two separate reviewers conducted the review. Metaprop was adopted to conduct a meta-analysis of prevalence with variances stabilized by Freeman-Tukey Double Arcsine Transformation. A random-effects model was used. Heterogeneity across different studies was computed using Cochran's Q test and chi square statistics. Results: From 17 studies, the pooled detection rate of fecal SARS-CoV-2 RNA was 43.7% (95% CI 32.6%-55.0%) and 33.7% (95% C.I. 33.7%, 95% C.I. 20.1%-48.8%) by patient and number of specimens as a unit count, respectively. Female individuals (59.6% vs. 53.5%), those who presented with gastrointestinal symptoms (77.1% vs. 57.7%), and patients with more severe disease (68.3% vs. 34.6%) tended to have a higher detection rate. Discussion: A significant proportion of COVID-19 patients carry SARS-CoV-2 in their intestinal tract. Feces being a self-collected specimen bears a potential to improve case identification in community, especially for young children where proper respiratory sampling at home is difficult. Specific infection control strategies focusing on spread via fecal contamination and faulty toilet drainage are urgently needed.

Background Self-collected specimens has been advocated to avoid infectious exposure to healthcare workers. Self-induced sputum in those with a productive cough, and saliva in those without a productive cough have been proposed, but sensitivity remains uncertain. Methods We performed a prospective study in two regional hospitals in Hong Kong Results We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep-throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. DTS had the lowest overall RT-PCR positive rate (68.7% vs. 89.4% [sputum] and 80.9% [pooled NP and throat swabs]), and the lowest viral RNA concentration (mean log copy/mL 3.54 vs. 5.03 [sputum] and 4.63 [pooled NP and throat swabs]). Analyses with respect to time from symptom onset and severity also revealed similar results. Virus yield of DTS correlated with that of sputum (Pearson correlation index [95% CI]: 0.76 [0.62 – 0.86]). We estimated the overall false-negative rate of DTS could be 31.3%, and increased 2.7 times among patients without sputum. Conclusion DTS produced the lowest viral RNA concentration and RT-PCR positive rate compared to conventional respiratory specimens in all phases of illness. Self-collect sputum should be the choice for patients with sputum.

"Engyodontium album" is an environmental saprobic mould and an emerging opportunistic pathogen able to cause both superficial and systemic infections. In this study, we isolated a mould from the skin lesion biopsy specimen of the right shin in a patient who received renal transplantation for end-stage renal failure with prednisolone, tacrolimus, and azathioprine immunosuppressant therapy. Histology of the skin biopsy showed mild squamous hyperplasia and neutrophilic infiltrate in the epidermis, active chronic inflammation in the dermis, and fat necrosis in the subcutis, with numerous fungal elements within the serum crusts. On Sabouraud glucose agar, the fungus grew as white, cobweb-like, floccose colonies. Microscopically, conidiogenous cells were arranged in whorls of one to seven at wide angles, with zigzag-shaped terminal fertile regions and smooth, hyaline, oval, apiculate conidia. DNA sequencing showed the mould isolate belonged to "E. album" but matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate. Phylogenetic analyses based on the internal transcribed spacer region, 28S nuclear ribosomal DNA, and β-tubulin gene and MALDI-TOF MS coupled with hierarchical cluster analysis showed that "E. album" is distantly related to other Engyodontium species and should be transferred to a novel genus within the family Cordycipitaceae, for which the name Parengyodontium album gen. et comb. nov. is proposed. Three potential cryptic species within this species complex were also revealed. Antifungal susceptibility testing showed posaconazole and voriconazole had high activities against all clinical P. album isolates and may be better drug options for treating P. album infections.

Background: Vaccine hesitancy represents one of the major global health issues around the world. We examined the perception, attitude, perceived barriers and facilitation measures of receiving the COVID-19 vaccine in a Chinese population with free vaccine choices (Sinovac [Coronavac] vs. BioNTech/Fosun [Comirnaty]) and adequate doses. Method: We conducted a random telephone survey of the general population in 1195 subjects aged 18 years or above from 23 April 2021 to 8 May 2021 after two months of vaccine rollout. A descriptive analysis of the levels of enabling factors, obstacles and perception of COVID-19 vaccination was conducted using ANOVA and Chi-square tests for trend. Results: Only 10.1% and 13.5% had received one and two COVID-19 vaccine doses, respectively. Among those who had not received any COVID-19 vaccine (75.4%), only 25.1% expressed their intention to receive in the coming 6 months. The barriers with the highest scores included “having heard of cases with serious adverse events or death after vaccination” (score: 8.17 out 10, 95% C.I. 7.99, 8.35), “lack of confidence on governmental recommendations” (7.69, 95% C.I. 7.47, 7.91), and “waiting for a better vaccine” (7.29, 95% C.I. 7.07, 7.52). The highest score for the impact of various incentives for vaccination was for “vaccine passports for overseas travel” (4.44, 95% C.I. 4.18, 4.71). Conclusions: Vaccine hesitancy is commonly observed in this Chinese population despite adequate provision of vaccine doses and choices. No single incentive is strong enough to promote vaccination, and multiple facilitation measures for different groups of population are needed to encourage vaccine uptake. Active clarification and promotion by medical professionals together with a variety of incentives are needed to drive vaccine uptake.