The First Locally Acquired Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in a Healthcare Worker in the Paris Area

Nosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020

France went through three deadly epidemic waves due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing major public health and socioeconomic issues. We proposed to study the course of the pandemic along 2020 from the outlook of two major Parisian hospitals earliest involved in the fight against COVID-19. Genome sequencing and phylogenetic analysis were performed on samples from patients and health care workers (HCWs) from Bichat (BCB) and Pitié-Salpêtrière (PSL) hospitals. A tree-based phylogenetic clustering method and epidemiological data were used to investigate suspected nosocomial transmission clusters. Clades 20A, 20B and 20C were prevalent during the spring wave and, following summer, clades 20A.EU2 and 20E.EU1 emerged and took over. Phylogenetic clustering identified 57 potential transmission clusters. Epidemiological connections between participants were found for 17 of these, with a higher proportion of HCWs. The joint presence of HCWs and patients suggest viral contaminations between these two groups. We provide an enhanced overview of SARS-CoV-2 phylogenetic changes over 2020 in the Paris area, one of the regions with highest incidence in France. Despite the low genetic diversity displayed by the SARS-CoV-2, we showed that phylogenetic analysis, along with comprehensive epidemiological data, helps to identify and investigate healthcare associated clusters.

Management principles in patients with COVID-19: perspectives from a growing global experience with emphasis on cardiovascular surveillance

The COVID-19, due to SARS-CoV-2, has uncovered many real-world issues when it comes to healthcare management and has led to a widespread mortality. Observations thus far from the reports of COVID-19 have indicated that certain risk groups for example, those with pre-existing cardiovascular (CV) disease, hypertension, diabetes, chronic kidney disease and tobacco use are prone to disease development and specifically development of severe disease and possible fatality. It is increasingly evident that many CV conditions occur frequently. These include myopericarditis, acute coronary syndromes, thrombosis, arrhythmias, hypertension and heart failure. Many professional organisations and societies related to cardiology have produced guidelines or recommendations on most of the above-mentioned aspects. Given these rapid developments, the aims of this review manuscript were to summarise and integrate recent publications with newly developed guidelines and with the first-hand experience of frontline physicians and to yield a pragmatic insight and approach to CV complications of COVID-19. We emphasise on a strategic tier-based approach for initial assessment and management of COVID-19, and then delve into focused areas within CV domains, and additionally highlighting the role of point-of-care ultrasound especially lung ultrasound, echocardiography and electrocardiography, in the management of these patients. We hope this paper will serve as a useful tool in the CV management of COVID-19 for clinicians practicing in both developing and developed countries.

Secretion of severe acute respiratory syndrome coronavirus 2 in urine

PURPOSE OF REVIEW

Despite the plethora of publications discussing the severe respiratory coronavirus 2 (SARS-CoV-2), evidence of viral secretion in urine is sparse.

RECENT FINDINGS

We could identify 34 publications including a total of 2172 patients. Among those, 549 patients were tested for SARS-CoV-2 secretion in urine, which was detected in only 38 patients (6.9%). Within the seven studies displaying positive results, the majority of positive patients (86.8%) was from not yet peer-reviewed studies including weak data and heterogeneous techniques for sample testing. Furthermore, none of the studies available in the literature addressed the virulence of detected viral RNA in urine.

SUMMARY

Overall, only seven studies were able to detect SARS-CoV-2 secretion in urine, all of them with a considerably low rate of positivity. However, these studies were of rather low quality considering their methodology. Despite this, as SARS-CoV-2 has been detected in urine, it is of importance to discuss safety and urinary hygiene protocols. Until further research provides valid data on viral shedding and virulence in urine, potential risk of transmission through urine cannot be ruled out. Therefore, safety and hygiene measures need to be discussed.

Evolution of viral quasispecies during SARS-CoV-2 infection

Objectives

Studies are needed to better understand the genomic evolution of the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe genomic diversity of SARS-CoV-2 by next-generation sequencing (NGS) in a patient with longitudinal follow-up for SARS-CoV-2 infection.

Methods

Sequential samples collected between January 29th and February 4th, 2020, from a patient infected by SARS-CoV-2 were used to perform amplification of two genome fragments—including genes encoding spike, envelope, membrane and nucleocapsid proteins—and NGS was carried out with Illumina® technology. Phylogenetic analysis was performed with PhyML and viral variant identification with VarScan.

Results

Majority consensus sequences were identical in most of the samples (5/7) and differed in one synonymous mutation from the Wuhan reference sequence. We identified 233 variants; each sample harboured in median 38 different minority variants, and only four were shared by different samples. The frequency of mutation was similar between genes and correlated with the length of the gene (r = 0.93, p = 0.0002). Most of mutations were substitution variations (n = 217, 93.1%) and about 50% had moderate or high impact on gene expression. Viral variants also differed between lower and upper respiratory tract samples collected on the same day, suggesting independent sites of replication of SARS-CoV-2.

Conclusions

We report for the first time minority viral populations representing up to 1% during the course of SARS-CoV-2 infection. Quasispecies were different from one day to the next, as well as between anatomical sites, suggesting that in vivo this new coronavirus appears as a complex and dynamic distributions of variants.