Correction: Telford et al. Expanding the Geographic Characterisation of Epstein–Barr Virus Variation through Gene-Based Approaches. Microorganisms 2020, 8, 1686

The authors wish to make the following correction to this paper [...]

A Confirmed Case of SARS-CoV-2 Pneumonia With Negative Routine Reverse Transcriptase–Polymerase Chain Reaction and Virus Variation in Guangzhou, China

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia is a newly recognized disease, and its diagnosis is primarily confirmed by routine reverse transcriptase -polymerase chain reaction (RT-PCR) detection of SARS-CoV-2. Methods However, we report a confirmed case of SARS-CoV-2 pneumonia with a negative routine RT-PCR. Results This case was finally diagnosed by nanopore sequencing combined with antibody of SARS-CoV-2. Simultaneously, the ORF and NP gene variations of SARS-CoV-2 were found. Conclusions This case highlighted that false-negative results could be present in routine RT-PCR diagnosis, especially with virus variation. Currently, nanopore pathogen sequencing and antibody detection have been found to be effective in clinical diagnosis.

Disparate evolution of virus populations in upper and lower airways of mechanically ventilated patients

In routine surveillance and diagnostic testing, influenza virus samples are typically collected only from the upper respiratory tract (URT) due to the invasiveness of sample collection from the lower airways. Very little is known about virus variation in the lower respiratory tract (LRT) and it remains unclear if the virus populations at different sites of the human airways may develop to have divergent genetic signatures. We used deep sequencing of serially obtained matched nasopharyngeal swabs and endotracheal aspirates from four mechanically ventilated patients with influenza A/H3N2 infections. A physical barrier separating both compartments of the respiratory tract introduced as part of the medical procedures enabled us to track and compare the genetic composition of the virus populations during isolated evolution in the same host. Amino acid variants reaching majority proportions emerged during the course of infection in both nasopharyngeal swabs and endotracheal aspirates, and amino acid variation was observed in all influenza virus proteins. Genetic variation of the virus populations differed between the URT and LRT and variants were frequently uniquely present in either URT or LRT virus populations of a patient. These observations indicate that virus populations in spatially distinct parts of the human airways may follow different evolutionary trajectories. Selectively sampling from the URT may therefore fail to detect potentially important emerging variants.ImportanceInfluenza viruses are rapidly mutating pathogens that easily adapt to changing environments. Although advances in sequencing technology make it possible to identify virus variants at very low proportions of the within-host virus population, several aspects of intrahost viral evolution have not been studied because sequentially collected samples and samples from the lower respiratory tract are not routinely obtained for influenza surveillance or clinical diagnostic purposes. Importantly, how virus populations evolve in different parts of the human respiratory tract remains unknown. Here we used serial clinical specimens collected from mechanically ventilated influenza patients to compare how virus populations develop in the upper and lower respiratory tract. We show that virus populations in the upper and lower respiratory tract may evolve along distinct evolutionary pathways, and that current sampling and surveillance regimens likely capture only part of the complete intrahost virus variation.

PLAGA JUSTYNIANA. CESARSTWO WOBEC EPIDEMII

JUSTINIANIC PLAGUE. ROMAN EMPIRE TOWARDS THE EPIDEMIC Summary The first certain epidemic of pestilences was so called “the Justinianic Plague” that had broken out in VI century in the Byzantine Empire and lasted through two centuries. It is recognized that in the years of 541-750 there had been eighteen strikes of pestilences. Two waves of the plague took place during the reign of Justinian. The first one broke out in Pelusium in 541, the second – in 558. The Justinianic Plague was recognized as bubonic plague indeed since one of its main symptom was bubo. Such a diagnosis was confirmed by the World Health Organization. It is estimated that in the time of the outbreak had been dying 10.000 of people every day and had died 25 million in total resulting in decreasing the population of ¼. In XX century there had been theories (Ch. Duncan, S. Scott) that the outbreak in the Justinian Times was not caused by bubonic plague but by its virus variation. However, the thesis of Duncan and Scott has not been shared by the contemporary science. The most basic rules against spreading the diseases have not been known by the ancient Romans. However, the Emperor had taken steps in order to decrease the effects of the outbreak by implementing the medical rules in regards to proceedings of burring the bodies. He set up a referendarius to be responsible for this task and provided him with money and personnel. In 544 Justinian issued an edict (Nov. 122) in which he claimed that the pestilences had ended. But generally, Justinian’s legislation demonstrates rather little interest for the situation caused by the plague.