scholarly journals Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Science ◽  
2020 ◽  
Vol 371 (6525) ◽  
pp. 172-177 ◽  
Author(s):  
Bas B. Oude Munnink ◽  
Reina S. Sikkema ◽  
David F. Nieuwenhuijse ◽  
Robert Jan Molenaar ◽  
Emmanuelle Munger ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Nonhuman Primates ◽  
Animal Experiments ◽  
Whole Genome ◽  
Infection Period ◽  
Modes Of Transmission ◽  
Whole Genomes ◽  
Sequence Signature ◽  
In The Beginning ◽  
Farm Residents

Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms.

scholarly journals Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms

2020 ◽  
Author(s):  
Bas B. Oude Munnink ◽  
Reina S. Sikkema ◽  
David F. Nieuwenhuijse ◽  
Robert Jan Molenaar ◽  
Emmanuelle Munger ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Early Warning ◽  
Animal Experiments ◽  
Zoonotic Transmission ◽  
Whole Genome ◽  
Infection Period ◽  
Modes Of Transmission ◽  
The Moment ◽  
In The Beginning

AbstractThe zoonotic origin of the SARS-CoV-2 pandemic is still unknown. Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation of outbreaks on 16 mink farms and humans living or working on these farms, using whole genome sequencing. We conclude that the virus was initially introduced from humans and has evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission. We also describe the first animal to human transmissions of SARS-CoV-2 in mink farms.One sentence summarySARS-CoV-2 transmission on mink farms.

scholarly journals Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Myat Htut Nyunt ◽  
Hnin Ohnmar Soe ◽  
Kay Thi Aye ◽  
Wah Wah Aung ◽  
Yi Yi Kyaw ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Early Phase ◽  
International Travel ◽  
Health Concern ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genomic Epidemiology ◽  
Local Spread ◽  
Control And Prevention ◽  
Local Transmission

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigated the mutational and phylogenetic analysis of 30 whole-genome sequences for the virus's genomic characteristics in the specimens collected in the early phase of the pandemic (March–June, 2020) and the sudden surge of local transmission (August–September, 2020). The four samples in the early phase of infection were B.6 lineage and located within a clade of the samples collected at the same time in Singapore and Malaysia, while five returnees by rescue flights showed the lineage B. 1.36.1 (three from India), B.1.1 (one from India) and B.1.80 (one from China). However, there was no evidence of local spread from these returnees. Further, all 19 whole-genome sequences collected in the sudden surge of local transmission showed lineage B.1.36. The surge of the second wave on SARS-CoV-2 infection was linked to the single-introduction of a variant (B.1.36) that may result from the strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

scholarly journals Severity assessment of single-dose Oxford-AstraZeneca vaccinated individuals infected with severe acute respiratory syndrome coronavirus 2 in Southeast Bangladesh

2021 ◽  
pp. 220-226
Author(s):  
Eaftekhar Ahmed Rana ◽  
Pronesh Dutta ◽  
Md. Sirazul Islam ◽  
Tanvir Ahmad Nizami ◽  
Tridip Das ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Quantitative Polymerase Chain Reaction ◽  
Health Indicators ◽  
Good Health ◽  
Health Condition ◽  
Chain Reaction ◽  
Infection Period ◽  
Respiratory Problems ◽  
Polymerase Chain ◽  
Taste And Smell

Background and Aim: A vaccine program for coronavirus illness (coronavirus disease [COVID-19]) is currently underway in numerous regions of the world, including Bangladesh, but no health data on those who have been vaccinated are available at this time. The study aimed to investigate the health condition of people who had received their first dose of the Oxford- AstraZeneca vaccine and were infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Materials and Methods: To detect SARS-CoV-2, a standard virological approach, real-time reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), was used. Several health indicators from vaccinated patients were collected using pre-structured questionnaires during the infection phase. Results: A total of 6146 suspicious samples were analyzed, and 1752 were found to be positive for SARS-CoV-2, with 200 people receiving the first dose of the COVID-19 vaccine. One hundred and sixty-five (82.5%) were not hospitalized among the vaccinated people, and 177 (88.5%) did not have any respiratory problems. Only 8% of patients required further oxygen support, and 199 (99.5%) did not require intensive care unit intervention. Overall, oxygen saturation was recorded at around 96.8% and respiratory difficulties did not extend more than 5 days during the infection period. Among the vaccinated COVID-19-positive people, 113 (56.5%) and 111 (55.5%) had typical physiological taste and smell. Surprisingly, 129 (64.5%) people had diverse comorbidities, with high blood pressure (27.9%) and diabetes (32 [24.8%]) being the most common. The major conclusion of the current study was that 199 (99.5%) of vaccinated patients survived in good health and tested negative for RT-qPCR. Conclusion: According to the findings of this study, administering the first dose of the Oxford-AstraZeneca vaccine considerably reduces health risks during the COVID-19 infection period.

scholarly journals Whole-Genome Sequence of SARS-CoV-2 Isolate Siena-1/2020

2020 ◽  
Vol 9 (39) ◽  
Author(s):  
Maria Grazia Cusi ◽  
David Pinzauti ◽  
Claudia Gandolfo ◽  
Gabriele Anichini ◽  
Gianni Pozzi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Genome Sequence ◽  
Amino Acid Change ◽  
Amplicon Sequencing ◽  
Spike Protein ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Protein Coding

ABSTRACT The complete genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate Siena-1/2020 was obtained by Nanopore sequencing, combining the direct RNA sequencing and amplicon sequencing approaches. The isolate belongs to the B1.1 lineage, which is prevalent in Europe, and contains a mutation in the spike protein coding sequence leading to the D614G amino acid change.

scholarly journals Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution

2019 ◽  
Vol 69 (1) ◽  
pp. 38-60 ◽  
Author(s):  
Rémi Allio ◽  
Céline Scornavacca ◽  
Benoit Nabholz ◽  
Anne-Laure Clamens ◽  
Felix AH Sperling ◽  
...  
Keyword(s):  
Missing Data ◽  
Shotgun Sequencing ◽  
Whole Genome Shotgun ◽  
Amino Acid Sequences ◽  
Molecular Dating ◽  
Whole Genome ◽  
Gene Trees ◽  
Data Set ◽  
Whole Genomes ◽  
Bayesian Mixture Models

Abstract Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.

scholarly journals Divergence-Based Introgression Polarization

2020 ◽  
Vol 12 (4) ◽  
pp. 463-478 ◽  
Author(s):  
Evan S Forsythe ◽  
Daniel B Sloan ◽  
Mark A Beilstein
Keyword(s):  
Genetic Material ◽  
Introgressive Hybridization ◽  
Sequence Divergence ◽  
Whole Genome ◽  
Major Area ◽  
Genome Data ◽  
Whole Genomes ◽  
Potential Sources ◽  
Introgression Event ◽  
Do So

Abstract Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event.

scholarly journals Occurrence and Molecular Characterization of Recombinant Potato virus YNTN Isolates from Sulawesi, Indonesia

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 269-275 ◽  
Author(s):  
Mohamad Chikh-Ali ◽  
Nilsa A. Bosque-Pérez ◽  
Dalton Vander Pol ◽  
Dantje Sembel ◽  
Alexander V. Karasev
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
Potato Cultivar ◽  
Whole Genome ◽  
Chain Reaction ◽  
Recombinant Type ◽  
Whole Genomes ◽  
Polymerase Chain ◽  
First Time

The importance of potato has increased dramatically in Indonesia over the last three decades. During this period, ‘Granola’, a potato cultivar originally from Germany, has become the most common cultivar for fresh consumption in Indonesia. In August 2014, a survey was conducted in Sulawesi, where potato fields cultivated with Granola and its selection, ‘Super John’, were sampled for Potato virus Y (PVY) presence. PVY was found in Sulawesi for the first time. Samples determined to be positive for PVY were subsequently typed to strain using reverse-transcription polymerase chain reaction assays. All PVY isolates sampled were identified as PVYNTN recombinants, with three recombination junctions in P3, VPg, and CP regions of the genome. Three local PVY isolates were subjected to whole-genome sequencing and subsequent sequence analysis. The whole genomes of the Indonesian PVYNTN isolates I-6, I-16, and I-17 were found to be closely related to the European PVYNTN-A. This recombinant type was shown previously to cause potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars. The dependence of potato farmers on mostly a single cultivar, Granola, may have given a competitive advantage to PVYNTN over other PVY strains, resulting in the predominance of the PVYNTN recombinant. The dominance of PVYNTN in Sulawesi, and possibly in Indonesia as a whole, represents a potential risk to any newly introduced potato cultivar to the country, especially cultivars susceptible to PTNRD.

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