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

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          Two-way transmission on mink farms

          Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic virus—one that spilled over from another species to infect and transmit among humans. We know that humans can infect other animals with SARS-CoV-2, such as domestic cats and even tigers in zoos. Oude Munnink et al. used whole-genome sequencing to show that SARS-CoV-2 infections were rife among mink farms in the southeastern Netherlands, all of which are destined to be closed by March 2021 (see the Perspective by Zhou and Shi). Toward the end of June 2020, 68% of mink farm workers tested positive for the virus or had antibodies to SARS-CoV-2. These large clusters of infection were initiated by human COVID-19 cases with viruses that bear the D614G mutation. Sequencing has subsequently shown that mink-to-human transmission also occurred. More work must be done to understand whether there is a risk that mustelids may become a reservoir for SARS-CoV-2.

          Science, this issue p. 172; see also p. [Related article:]120

          Abstract

          Genetic evidence indicates that SARS-CoV-2 transmission occurred from humans to mink as well as from mink to humans on farms in the Netherlands.

          Abstract

          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.

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          A Novel Coronavirus from Patients with Pneumonia in China, 2019

          Summary In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.)
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            A pneumonia outbreak associated with a new coronavirus of probable bat origin

            Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.
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              IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

              Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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                Author and article information

                Journal
                Science
                Science
                SCIENCE
                science
                Science (New York, N.y.)
                American Association for the Advancement of Science
                0036-8075
                1095-9203
                08 January 2021
                10 November 2020
                : 371
                : 6525
                : 172-177
                Affiliations
                [1 ]Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands.
                [2 ]Royal GD, Deventer, Netherlands.
                [3 ]Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands.
                [4 ]Municipal Health Services GGD Brabant-Zuidoost, Eindhoven, Netherlands.
                [5 ]Municipal Health Services GGD Hart voor Brabant, ‘s-Hertogenbosch, Netherlands.
                [6 ]Municipal Health Services GGD Limburg-Noord, Venlo, Netherlands.
                [7 ]Wageningen Bioveterinary Research, Lelystad, Netherlands.
                [8 ]Stichting PAMM, Veldhoven, Netherlands.
                [9 ]Division of Farm Animal Health, Department of Population Health Sciences, Utrecht University, Utrecht, Netherlands.
                [10 ]Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands.
                Author notes
                [* ]Corresponding author: Email: b.oudemunnink@ 123456erasmusmc.nl
                Author information
                https://orcid.org/0000-0002-9394-1189
                https://orcid.org/0000-0003-1310-5031
                https://orcid.org/0000-0003-0336-1226
                https://orcid.org/0000-0002-4428-8988
                https://orcid.org/0000-0002-9004-3850
                https://orcid.org/0000-0002-3142-352X
                https://orcid.org/0000-0002-0193-2710
                https://orcid.org/0000-0002-1749-5789
                https://orcid.org/0000-0002-2923-3233
                https://orcid.org/0000-0003-0292-0946
                https://orcid.org/0000-0003-4361-3846
                https://orcid.org/0000-0002-7498-8002
                https://orcid.org/0000-0002-5204-2312
                Article
                abe5901
                10.1126/science.abe5901
                7857398
                33172935
                a2d8fdf1-6871-49a1-93ac-ed32d78a8774
                Copyright © 2021, American Association for the Advancement of Science

                This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 01 September 2020
                : 05 November 2020
                Funding
                Funded by: ZonMW;
                Award ID: 10150062010005
                Funded by: European Union’s Horizon 2020 research and innovation programme;
                Award ID: 848096
                Funded by: European Union’s Horizon 2020 research and innovation programme;
                Award ID: 101003589
                Funded by: The European Union’s Horizon 2020 research and innovation programme;
                Award ID: 874735
                Funded by: the Netherlands Ministry of Agriculture, Nature and Foods;
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