Pig as a reservoir of CRISPR type TST4
            <i>Salmonella enterica</i>
            serovar Typhimurium monophasic variant during 2009–2017 in China

Xie, Xiaolei; Wang, Zhenyu; Zhang, Kai; Li, Yang; Hu, Yachen; Pan, Zhiming; Chen, Xiang; Li, Qiuchun; Jiao, Xinan

doi:10.1080/22221751.2019.1699450

Cited by 74 publications

(93 citation statements)

References 18 publications

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“…Multiple studies report major structural variations (SVs) in the SARS-CoV-2 genome 16 – 19 , namely the 382 nt deletion in the open reading frame 8 ( ORF8 ), associated with changes in the replicative fitness 17 and milder infections 18 . Therefore, we investigated if similar ORF8 deletions could be detected from the cases examined by Twist capture sequencing.…”

Section: Resultsmentioning

confidence: 99%

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

Kim

Deveson

Pang

et al. 2021

Sci Rep

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Accumulating evidence supports the high prevalence of co-infections among Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients, and their potential to worsen the clinical outcome of COVID-19. However, there are few data on Southern Hemisphere populations, and most studies to date have investigated a narrow spectrum of viruses using targeted qRT-PCR. Here we assessed respiratory viral co-infections among SARS-CoV-2 patients in Australia, through respiratory virome characterization. Nasopharyngeal swabs of 92 SARS-CoV-2-positive cases were sequenced using pan-viral hybrid-capture and the Twist Respiratory Virus Panel. In total, 8% of cases were co-infected, with rhinovirus (6%) or influenzavirus (2%). Twist capture also achieved near-complete sequencing (> 90% coverage, > tenfold depth) of the SARS-CoV-2 genome in 95% of specimens with Ct < 30. Our results highlight the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture, for SARS-CoV-2 whole-genome sequencing without amplicon generation and the simultaneous identification of viral co-infections with ease.

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Section: Resultsmentioning

confidence: 99%

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

Kim

Deveson

Pang

et al. 2021

Sci Rep

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“…Presence of the viral genomic RNA and its integrity was determined using qPCR as it was previously used for the detection of SARS-CoV-2 in environmental samples [ 13 , 22 , 23 ]. Genomic approaches are shown to be highly sensitive in detecting viral RNA and multiple targets are used for generating PCR amplicon [ 13 , 24 ]. Importantly, detection of genomic RNA through RT-qPCR does not constitute for the presence of an ‘infectious’ virus but shows the presence of viral genomic RNA.…”

Section: Resultsmentioning

confidence: 99%

Inactivation of Human Coronavirus by Titania Nanoparticle Coatings and UVC Radiation: Throwing Light on SARS-CoV-2

Khaiboullina

Uppal

Dhabarde

et al. 2020

Viruses

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The newly identified pathogenic human coronavirus, SARS-CoV-2, led to an atypical pneumonia-like severe acute respiratory syndrome (SARS) outbreak called coronavirus disease 2019 (abbreviated as COVID-19). Currently, nearly 77 million cases have been confirmed worldwide with the highest numbers of COVID-19 cases in the United States. Individuals are getting vaccinated with recently approved vaccines, which are highly protective in suppressing COVID-19 symptoms but there will be a long way before the majority of individuals get vaccinated. In the meantime, safety precautions and effective disease control strategies appear to be vital for preventing the virus spread in public places. Due to the longevity of the virus on smooth surfaces, photocatalytic properties of “self-disinfecting/cleaning” surfaces appear to be a promising tool to help guide disinfection policies for controlling SARS-CoV-2 spread in high-traffic areas such as hospitals, grocery stores, airports, schools, and stadiums. Here, we explored the photocatalytic properties of nanosized TiO2 (TNPs) as induced by the UV radiation, towards virus deactivation. Our preliminary results using a close genetic relative of SAR-CoV-2, HCoV-NL63, showed the virucidal efficacy of photoactive TNPs deposited on glass coverslips, as examined by quantitative RT-qPCR and virus infectivity assays. Efforts to extrapolate the underlying concepts described in this study to SARS-CoV-2 are currently underway.

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“…This is consistent with the fact that the epidemic outbreak in France, Italy, Germany, UK, Finland, Belgium, and Sweden (Coronavirus update (Live) n.d. ) preceded that in Poland by over two weeks, during which border restrictions were not yet imposed. By the time COVID-19 struck Poland, all major coronavirus clades were already present in Europe (Mercatelli and Giorgio 2020 ; Worobey et al 2020 ; Yang et al 2020 ; Mavian et al 2020a ; Pachetti et al 2020 ). With no rigorous epidemiological interview (history of travel, contacts of infected individuals, etc.…”

Section: Discussionmentioning

confidence: 99%

“…Many papers concerning analyses of SARS-CoV-2 diversity in different countries or world regions have been published during the last few months, e.g., world (Mercatelli and Giorgio 2020 ; Yang et al 2020 ), Europe and USA (Worobey et al 2020 ), France (Gambaro et al 2020 ), Germany (Walker et al 2020 ), Italy (Licastro et al 2020 ; Stefanelli et al 2020 ), Iceland (Gudbjartsson et al 2020 ), Croatia (Jurak et al 2020 ), USA (Brufsky 2020 ), Chile (Rodriguez-Morales et al 2020 ; Castillo et al 2020 ), India (Somasundaram et al 2020 ), Australia (Eden et al 2020 ), and more focusing on other non-European populations. Slavic countries, including Poland, remain underrepresented in these studies, mostly since SARS-CoV-2 genomes have only recently become available.…”

Section: Introductionmentioning

confidence: 99%

European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

et al. 2021

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To provide a comprehensive analysis of the SARS-CoV-2 sequence diversity in Poland in the European context. All publicly available (n = 115; GISAID database) whole-genome SARS-Cov-2 sequences from Polish samples, including those obtained during coronavirus testing performed in our COVID-19 Lab, were examined. Multiple sequence alignment of Polish isolates, phylogenetic analysis (ML tree), and multidimensional scaling (based on the pairwise DNA distances) were complemented by the comparison of the coronavirus clades frequency and diversity in the subset of over 5000 European GISAID sequences. Approximately seventy-seven percent of isolates in the European dataset carried frequent and ubiquitously found haplotypes; the remaining haplotype diversity was population-specific and resulted from population-specific mutations, homoplasies, and recombinations. Coronavirus strains circulating in Poland represented the variability found in other European countries. The prevalence of clades circulating in Poland was shifted in favor of GR, both in terms of the diversity (number of distinct haplotypes) and the frequency (number of isolates) of the clade. Polish-specific haplotypes were rare and could be explained by changes affecting common European strains. The analysis of the whole viral genomes allowed detection of several tight clusters of isolates, presumably reflecting local outbreaks. New mutations, homoplasies, and, to a smaller extent, recombinations increase SARS-CoV-2 haplotype diversity, but the majority of these variants do not increase in frequency and remains rare and population-specific. The spectrum of SARS-CoV-2 haplotypes in the Polish dataset reflects many independent transfers from a variety of sources, followed by many local outbreaks. The prevalence of the sequences belonging to the GR clade among Polish isolates is consistent with the European trend of the GR clade frequency increase.

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Pig as a reservoir of CRISPR type TST4 Salmonella enterica serovar Typhimurium monophasic variant during 2009–2017 in China

Cited by 74 publications

References 18 publications

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

Inactivation of Human Coronavirus by Titania Nanoparticle Coatings and UVC Radiation: Throwing Light on SARS-CoV-2

European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

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