Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs

In consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing (direct RNA seq.) experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily. Here, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retrotranscription. Using an appropriate bioinformatics pipeline, we could identify mutations in the nucleocapsid (N) gene, which have been reported previously in studies conducted in other countries. In conclusion, to the best of our knowledge, the technique used in this study has not been used for SARS-CoV-2 detection previously owing to the difficulties in the extraction of RNA of sufficient quantity and quality from routine oropharyngeal swabs. Despite these limitations, this approach provides the advantages of true native RNA sequencing and does not include amplification steps that could introduce systematic errors. This study can provide novel information relevant to the current strategies adopted in SARS-CoV-2 next-generation sequencing.

Triage Strategies Based on C-Reactive Protein Levels and SARS-CoV-2 Tests among Individuals Referred with Suspected COVID-19: A Prospective Cohort Study

C-reactive protein (CRP) has prognostic value in hospitalized patients with COVID-19; the importance of CRP in pre-hospitalized patients remains to be tested. Methods: Individuals with symptoms of COVID-19 had a SARS-CoV-2 PCR oropharyngeal swab test, and a measurement of CRP was performed at baseline, with an upper reference range of 10 mg/L. After 28 days, information about possible admissions, oxygen treatments, transfers to the ICU, or deaths was obtained from the patient files. Using logistic regression, the prognostic value of the CRP and SARS-CoV-2 test results was evaluated. Results: Among the 1006 patients included, the SARS-CoV-2 PCR test was positive in 59, and the CRP level was elevated (>10 mg/L) in 131. In total, 59 patients were hospitalized, only 3 of whom were SARS-CoV-2 positive, with elevated CRP (n = 2) and normal CRP (n = 1). The probability of being hospitalized with elevated CRP was 4.21 (95%CI 2.38–7.43, p < 0.0001), while the probability of being hospitalized with SARS-CoV-2 positivity alone was 0.85 (95%CI 0.26–2.81, p = 0.79). Conclusions: CRP is not a reliable predictor for the course of SARS-CoV-2 infection in pre-hospitalized patients. CRP, while not a SARS-CoV-2 positive test, had prognostic value in the total population of patients presenting with COVID-19-related symptoms.

First Detection of SARS-CoV-2 Delta (B.1.617.2) Variant of Concern in a Dog with Clinical Signs in Spain

Several cases of naturally infected dogs with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported despite the apparently low susceptibility of this species. Here, we document the first reported case of infection caused by the Delta (B.1.617.2) variant of concern (VOC) in a dog in Spain that lived with several household members suffering from Coronavirus Infectious Disease 2019 (COVID-19). The animal displayed mild digestive and respiratory clinical signs and had a low viral load in the oropharyngeal swab collected at the first sampling. Whole-genome sequencing indicated infection with the Delta variant, coinciding with the predominant variant during the fifth pandemic wave in Spain. The dog seroconverted, as detected 21 days after the first sampling, and developed neutralizing antibodies that cross-neutralized different SARS-CoV-2 variants. This study further emphasizes the importance of studying the susceptibility of animal species to different VOCs and their potential role as reservoirs in the context of COVID-19.

A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection

Infection with the SARS-CoV-2 virus results in manifestation of several clinical observations from asymptomatic to multi-organ failure. Biochemically, the serious effects are due to what is described as cytokine storm. The initial infection region for COVID-19 is the nasopharyngeal/oropharyngeal region which is the site where samples are taken to examine the presence of virus. We have earlier shown that several defensin genes are down regulated in cells from this region in patients who tested positive in the RTPCR test. We have now carried out detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and those tested positive for SARS-CoV-2 by RTPCR, involving high throughput quantitative proteomics analysis. Several proteins like annexins, cytokines and histones were found differentially regulated in the host human cells following SARS-CoV-2 infection. Genes for these proteins were also observed to be differentially regulated when their expression was analyzed. Majority of the cytokine proteins were found to be up regulated in the infected individuals. Cell to Cell signaling interaction, Immune cell trafficking and inflammatory response pathways were found associated with the differentially regulated proteins based on network pathway analysis.

Osteomyelitis in a General Pediatric Ward

INTRODUCTION: Pediatric acute osteomyelitis (AO) is a serious condition and a challenging diagnosis. It mainly affects previously healthy individuals and Staphylococcus aureus is the leading causative agent. The objective of this study was to characterize all pediatric AO cases admitted to a second-level hospital during a six-year period.METHODS: Retrospective single-center study, including all children under 18 years-old with a primary diagnosis of AO. Descriptive statistics analysis was performed.RESULTS: Ten cases were identified, 60% males. The median age was 6.7 years. Previous trauma was referred by five. Affected locations were foot (n=3), tibia (n=3), femur (n=2), sacrum (n=1) and hand (n=1). All presented with local pain and limping or inability to walk (except one case with hand involvement). Four patients had fever and inflammatory signs, namely erythema and edema, were reported by four. At admission, nine had elevated inflammatory markers and six out of eight had normal radiographs. Magnetic resonance imaging confirmed the diagnosis in seven. Blood cultures were positive for Staphylococcus aureus (n=3) and Streptococcus pyogenes (n=1). Salmonella enteritidis was isolated from pus (n=1) and there was one presumed Kingella kingae AO defined as a positive polymerase chain reaction test from an oropharyngeal swab. The average duration of parenteral and oral antibiotherapy was 14.7 days 3.9 weeks, respectively. The antibiotic of choice was flucloxacillin. Two patients developed local complications.DISCUSSION: An unspecific and subacute clinical and radiological presentation together with low positive blood culture rates difficults timely diagnosis and management. An early empirical parenteral antibiotherapy is mandatory, followed by an oral regimen for at least four weeks.

Streptococcus pneumoniae carriage in school children

Purpose. To investigate the serotype distribution, clonal structure and antimicrobial resistance of pneumococci isolated from schoolchildren.Materials and methods. During the period from 2012 to 2018 we examined 498 healthy school children aged 6 to 17 years. Oropharyngeal swab was taken from each child for culture, after that all S. pneumoniae strains were genotyped for serotype and ST-type deduction (PCR and sequencing, respectively). Antimicrobial resistance was also determined.Results. Pneumococcal culture was positive in 10.6 % of children. S. pneumoniae isolates belonged to seven serogroups and seven serotypes. Serogroup 6 and serotype 19F strains (15.1% each), and serogroup 9 strains (13.2%) were the most prevalent. S. pneumoniae33FA/37 and 3 (9.4 and 5.7%), serogroups 15 and 18 (7.6 and 5.7%), and 10A serotype (3.8%) were determined at a lower frequency. 20 detected ST-types belonged to 14 clonal complexes (CCs); CC156, CC447, and CC320 were predominant. 1.9% of isolates were penicillin-resistant; 13.2% – macrolide-, clindamycin-, and tetracycline-resistant. S. pneumoniae antibiotic resistant strains belonged to multidrug-resistant CCs 320, 315, and 156.Conclusion. S. pneumoniae prevalence in school children is not high. Pneumococcal population is characterized by serotype and clonal diversity including ‘invasive’ serotypes and genotypes. Most of strains are susceptible to antimicrobials.

First detection of SARS-CoV-2 B.1.617.2 (Delta) variant of concern in a symptomatic cat in Spain

Natural and experimental SARS-CoV-2 infection in pets has been widely evidenced since the beginning of the COVID-19 pandemic. Among the numerous affected animals, cats are one of the most susceptible species. However, little is known about viral pathogenicity and transmissibility in the case of variants of concern (VOCs) in animal hosts, such as the B.1.617.2 (Delta) variant first detected in India. Here, we have identified the B.1.617.2 (Delta) VOC in a cat living with a COVID-19 positive owner. The animal presented mild symptoms (sneezing) and a high viral load was detected in the oropharyngeal swab, suggesting that an active infection was occurring in the upper respiratory tract of the cat. Transmission from the owner to the cat occurred despite the human being fully vaccinated against SARS-CoV-2. This study documents the first detection of B.1.165.2 VOC in a cat worldwide and emphasizes the importance of performing active surveillance and genomic investigation on infected animals.

Rapidly Fatal COVID-19-associated Acute Necrotizing Encephalopathy in a Previously Healthy 26-year-old Man

No abstract available. Article truncated after 150 words. A 26-year-old man presented to our Emergency Department at 0200 on the day of admission with chief complaints of subjective fever, leg myalgias, and progressive dyspnea of one week duration. An oropharyngeal swab PCR had revealed SARS-CoV-2 RNA three days previously. He had not received a SARS CoV-2 vaccination, but had made an appointment to receive it just a few days prior to the onset of his symptoms. The patient had no significant past medical history, was taking no medications except for ibuprofen and acetaminophen over the past week, and did not take recreational drugs. He specifically denied headache and had no prior history of seizure. On admission, his HR was 150 bpm (sinus), RR 22, BP 105/46 mmHg, temp 40.2° C. and SpO2 92% on room air. He was ill-appearing, but alert and oriented, his neck was supple and lung auscultation revealed bilateral rhonchi, but physical examination was otherwise …

Analysis of SARS-CoV-2 RNA Stability and Infectivity in Oropharyngeal Swab Samples

The reliable detection of SARS-CoV-2 genomic RNA and infectious virus particles from patient samples requires a good sample quality. This is especially critical when the sample has to be transported to the analysing laboratory which can take several days. To determine optimal transport conditions, we simulated oropharyngeal swab samples using defined virus amounts and stored the samples at 4 °C or at room temperature for up to four days. Moreover, we analysed the influence of dry swabs in comparison to swabs stored in transport medium. Our results show that care should be taken when analysing samples for infectious SARS-CoV-2 particles since infectivity is strongly influenced by sample storage.