An update on the origin of SARS-CoV-2: Despite closest identity, bat (RaTG13) and pangolin derived coronaviruses varied in the critical binding site and O-linked glycan residues.

The initial cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) occurred in Wuhan, China, in December 2019 and swept the world by 23 June 2020 with 8 993 659 active cases, 469 587 deaths across 216 countries, areas or territories. This strongly implies global transmission occurred before the lockdown of China. However, the initial source's transmission routes of SARS-CoV-2 remain obscure and controversial. Research data suggest bat (RaTG13) and pangolin carried CoV were the proximal source of SARS-CoV-2. In this study, we used systematic phylogenetic analysis of Coronavirinae subfamily along with wild type human SARS-CoV, MERS-CoV, and SARS-CoV-2 strains. The key residues of the receptor-binding domain (RBD) and O-linked glycan were compared. SARS-CoV-2 strains were clustered with RaTG13 (97.41% identity), Pangolin-CoV (92.22% identity) and Bat-SL-CoV (80.36% identity), forms a new clade-2 in lineage B of beta-CoV. The alignments of RBD contact residues to ACE2 justified? Those SARS-CoV-2 strains sequences were 100% identical by each other, significantly varied in RaTG13 and pangolin-CoV. SARS-CoV-2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. Only serine (Ser) in pangolin and both threonine (Thr) and serine (Ser) O-linked glycans were seen in RaTG13, suggesting that a detailed study needed in pangolin (Manis javanica) and bat (Rhinolophus affinis) related CoV.

Clinical profile and atypical manifestation of dengue fever cases between 2011 and 2018 in Chennai, India.

INTRODUCTION: Dengue fever is a common mosquito-borne viral disease which has reached alarming size in the past few years. It is endemic in more than 100 countries and significant differences were found in clinical profile and atypical manifestation. AIM OF THE STUDY: A retrospective observational study of clinical profile and atypical manifestations in patients with dengue fever. MATERIALS AND METHODS: Serum samples were collected from clinically suspected cases of dengue fever and it was confirmed by NS1 antigen, IgM, and IgG antibody by ELISA. Clinical details and atypical manifestations were recorded. OBSERVATION: During the study period, a total of 2502 patients were suspected to have dengue infection, of which 464 (18.5%) samples were found to be positive for dengue viral infection. A majority of the cases were males [268 (57%)] when compared with females [196 (42%)]. Fever was the most common clinical presentation seen in all the patients, followed by headache (78.4%), myalgia (61%), body pain (49.3%), vomiting (40%), joint pain (31.5%), dry cough (19%), nausea (14%), abdominal pain (8%), diarrhea (5.6%), retro-orbital pain (04%), burning micturition (2.4%), and rashes (0.6%). Among atypical manifestations, hepatomegaly [32 (7%)] was the most common, followed by splenomegaly [23 (5%)], bradycardia [18 (4%)], meningitis [6 (1.2%)], hemoptysis [5 (1%)], acalculous cholecystitis [4 (0.8%)], and acute pancreatitis [2 (0.4%)]. The study of hematological parameters showed thrombocytopenia was present in 179 (38.5%) patients, followed by leukopenia [77 (17%)] and raised hematocrit [29 (6.2%)]. CONCLUSION: During ongoing epidemics, the clinical profile and atypical manifestations in clinically suspected dengue patients should be investigated early so that severe forms can be treated promptly.

Improved detection of esp, hyl, asa1, gelE, cylA virulence genes among clinical isolates of Enterococci.

OBJECTIVE: Virulence factors (VFs) among the clinical strains of enterococci play a vital role in pathogenesis. This study was aimed to screen for cylA, asa1, gelE, esp and hyl among Enterococcus faecalis (n = 89) and E. faecium (n = 51) by multiplex PCR. The previously reported multiplex PCR was modified to 2 duplex (asa1 and gelE, cylA and esp) PCRs and 1 simplex (hyl) PCR. The idea of the modification of the multiplex PCR proposed here emerged in the course of the research study when majority of the isolates which phenotypically exhibited virulence traits were found to be negative for the respective gene. RESULTS: cylA, gelE and asa1 were significantly predominant in E. faecalis (59.55%, 85.39%, 86.51%) than E. faecium (1.96%, 60.78%, 9.80%) (p < 0.0001, p = 0.001967, p < 0.0001). hyl was detected in E. faecium (5.9%) only. The number of VFs detected in each isolate was recorded as the VF score. E. faecalis isolates had a VF score pattern of score 4 (34.83%), score 3 (26.96%), score 2 (28.08%) and score 1 (8.98%) while E. faecium had score 4 (1.96%), score 3 (7.84%), score 2 (25.49%) and score 1 (41.18%). This modification of the PCR protocol could resolve the problem of decreased detection of virulence determinants in enterococci.

Novel gas producing Vibrio cholerae: a case report of gastroenteritis with acute kidney injury.

BACKGROUND: Bacterial characterization is important in clinical and epidemiological studies. We herein report the first case of gas-producing Vibrio cholera gastroenteritis with acute kidney injury. CASE PRESENTATION: A 30-year-old female presented to the emergency department with complaints of about ten episodes of watery diarrhea, four episodes of vomiting and elevated serum urea/creatinine levels. Although the bacteria were first misidentified as Vibrio furnissii by gas production on carbohydrate fermentation and triple sugar iron agar, it was later confirmed as Vibrio cholerae by 16 S rRNA gene sequencing and specific PCR. The treatment regimen was followed as for Vibrio species with intravenous fluids, ciprofloxacin and doxycycline. The patient recovered without relapse. CONCLUSIONS: Literature survey from the PubMed database shows no gas-producing Vibrio cholerae isolate being reported in the world. Further, genotype studies are warranted to look into the gas production of Vibrio cholerae .

Analysis of Serum Th1/Th2 Cytokine Levels in Patients with Acute Mumps Infection.

BACKGROUND: The mumps virus is frequently the causative agent of parotitis. There has been no study on serum cytokine levels of acute mumps parotitis except for a few which document cytokine levels in cerebrospinal fluid of mumps meningitis. It is with this notion, our study aimed to find Th1/Th2 cytokine levels from patients with acute mumps parotitis. MATERIALS AND METHODS: Concentrations of mumps-specific IgM, mumps, measles, rubella-specific IgG antibody, and Th1/Th2 cytokines, namely interferon-γ (IFN-γ), interleukin-2 (IL-2), IL-4, and IL-10 were measured simultaneously in serum from 74 patients (42 pediatric and 32 adult cases), 40 healthy subjects (20 pediatric and 20 adults) and in the supernatant of peripheral blood mononuclear cells stimulated with mumps virus genotype C which served as the positive control. Statistical significance was analyzed between each group by means of Mann-Whitney U-test, Kruskal-Wallis test, and Spearman's rank correlation coefficient test. RESULTS: IgM positivity confirmed acute infection in all 74 patients and of these 67 were vaccinated cases; however, very few of them (10/67) were positive for mumps IgG. We found that IFN-γ, IL-2, and IL-10 showed a statistically significant increase in both pediatric and adult patients with acute mumps infection when compared to healthy controls and values were comparable to the positive control. CONCLUSION: The Th1 cells play important roles during the acute phase of mumps parotitis.

Low vaccine efficacy of mumps component among MMR vaccine recipients in Chennai, India.

Introduction of MMR vaccine was believed to have resulted in a decline in the incidence of measles, mumps and rubella infections. However, recent reports suggest the re-emergence of mumps infection worldwide in the vaccinated populations. It was proposed that the reason for this re-emergence was poor efficacy of MMR vaccine. The present study was aimed to investigate mumps infection in MMR vaccinated and non-vaccinated populations in Chennai, India. Blood samples were collected from acute mumps cases (n=74, 42<12 yr age, 54% males) and investigated for IgM antibody against mumps, IgG antibody against measles, mumps and rubella viruses by ELISA. Sixty seven (91%) patients had received MMR vaccine. All the 67 vaccinated cases were positive for parotitis, and mumps IgM. However, only 10 (15%) were positive for IgG. All samples (100%) were positive for rubella and measles IgG. These findings showed the occurrence of mumps infection among MMR vaccinated individuals in Chennai, India. The MMR vaccine failed to generate anti-mumps IgG. The reason may be low vaccine efficacy of the mumps component of the MMR vaccine used.