•Overall, higher SARS-CoV-2 RNA loads are seen for the delta variant compared to the alpha variant within 2 days after symptoms onset.•SARS-CoV-2 RNA loads were higher for the delta than the alpha ...variant, in both asymptomatic adults and children.•For COVID-19 patients, SARS-CoV-2 delta RNA loads were higher in non-vaccinated individuals compared with vaccinated participants.•Asymptomatic vaccinated and unvaccinated individuals displayed similar SARS-CoV-2 delta RNA loads.
Every year, species of the Mycobacterium tuberculosis complex (MTBC) kill more people than any other infectious disease caused by a single agent. As a consequence of its global distribution and ...parallel evolution with the human host the bacteria is not genetically homogeneous. The observed genetic heterogeneity has relevance at different phenotypic levels, from gene expression to epidemiological dynamics. However, current systems biology datasets have focused on the laboratory reference strain H37Rv. By using large expression datasets testing the role of almost two hundred transcription factors, we have constructed computational models to grab the expression dynamics of Mycobacterium tuberculosis H37Rv genes. However, we have found that many of those transcription factors are deleted or likely dysfunctional across strains of the MTBC. As a result, we failed to predict expression changes in strains with a different genetic background when compared with experimental data. These results highlight the importance of designing systems biology approaches that take into account the genetic diversity of tubercle bacilli, or any other pathogen, if we want to identify universal targets for vaccines, diagnostics and treatments.
A sequence-based analysis of seven housekeeping and virulence-related genes shows that the species Vibrio vulnificus is subdivided into three phylogenetic lineages that do not correspond with the ...biotypes and that biotype 2 is polyphyletic. These results support the reclassification of biotype 2 as a pathovar that would group the strains with pathogenic potential to develop vibriosis in fish.
Abstract
Hepatitis C virus (HCV) reinfection may hamper HCV elimination in prisons. We aimed to (i) determine the reinfection rate in people treated for HCV in Catalan prisons, (ii) measure ...reinfection in people entering prisons, and (iii) characterize the molecular epidemiology of HCV in prisons and people who inject drugs (PWID) in the community. Re-HCV was a prospective study in eight prisons (2019–2020) including two groups: (1) people cured with treatment in prison and followed-up every 6 months, and (2) people testing HCV-RNA positive at incarceration. Bio-behavioral data were collected. HCV isolates were sequenced and phylogenetically analyzed with those of PWID in the community. Reinfection follow-up after treatment was achieved in 97 individuals (103.05 person-years). Two reinfections were detected, resulting in an incidence ≤ 10/100 person-years. Among people entering prison, 2% (359/17,732) were viremic, of which 334 (93.0%) were included, and 44 (13.5%) presented with reinfection (84.7% being PWID). Frequently, HCV isolates in prisons and PWID in the community were phylogenetically related. Although HCV reinfection is low after treatment, it is common in people entering Catalan prisons. To maintain a low HCV prevalence in prisons, harm-reduction services and test-and-treat programs for PWID should be strengthened both inside and outside prisons.
Abstract
A third Comirnaty vaccine dose increased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor-binding domain antibody levels (median, 93-fold) and neutralizing antibody ...titers against Wuhan-Hu-1 (median, 57-fold), Beta (me 22-fold), Delta, (median, 43-fold), and Omicron (median, 8-fold) variants, but had less impact on S-reactive T-cell immunity in nursing home residents.
Abstract
The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium ...Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
•Based on the analysis of the HN, M, N, and P genes one hypothetical subgenotype was found (subgenotype A4).•Recombination events identified by RDP4 analysis are described for the first time for ...BPIV-3.•Previously reported sequences were found to be miss-classified.
Bovine parainfluenza-3 virus (BPIV-3) is one of the main viruses associated with bovine respiratory disease complex (BRDC) worldwide. BPIV-3 infect the bovine respiratory tract causing from subclinical infections to severe pneumonia with significant economic losses in the cattle industry. BPIV-3 is a RNA virus with high genetic variability, nevertheless, the contribution of recombination events to its variability has not been assessed so far. In this study the 25 complete genome sequences (CGS) reported so far and 215 partial sequences of different viral genes of BPIV-3 were analyzed to determine their genotypes and subgenotypes, distribution, and the existence of potential recombination events. Based on the analysis of the HN, M, N, and P genes one hypothetical subgenotype was found (subgenotype A4). Four recombination events between sequences of swine and cattle were detected by RDP4 analysis in conjunction with phylogenetic incongruences in the L gene. In addition, 9 sequences reported from Argentina were found to be miss-classified. These results reveal that homologous recombination events have a relevant role in the evolution of BPIV-3 and highlight the importance of implement advanced molecular characterization to better understand the variability and evolution of BPIV-3 as a component of BRDC.
Abstract
A 77-year-old man (case R) with previous diagnosis of a mild COVID-19 episode was hospitalized 35 days later. On day 23 postadmission, he developed a second COVID-19 episode, now severe, and ...finally died. Initially, case R’s COVID-19 recurrence was interpreted as a reinfection due to the exposure to a SARS-CoV-2 RT-PCR–positive roommate. However, whole-genome sequencing indicated that case R’s recurrence corresponded to a reactivation of the strain involved in his first episode. Case R’s reactivation had major consequences, leading to a more severe episode, and causing subsequent transmission to another 2 hospitalized patients, 1 of them with fatal outcome.
Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of ...such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus.
We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak.
We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.
The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic ...and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138
strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to
. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.
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