1
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Ganor Paz Y, Shiloh S, Brosh-Nissimov T, Grupel D, Sorek N, Kustin T, Stern A, Maklakovsky M, Polak M, Sharvit M, Neeman O, Ben Valid T, Tovbin J, Barzilay E. The association between SARS-CoV-2 infection and late pregnancy loss. Int J Gynaecol Obstet 2021; 157:208-209. [PMID: 34778964 PMCID: PMC9087656 DOI: 10.1002/ijgo.14025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 12/02/2022]
Affiliation(s)
- Yael Ganor Paz
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod university Hospital, Ashdod, Israel.,Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Sivan Shiloh
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod university Hospital, Ashdod, Israel
| | - Tal Brosh-Nissimov
- Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.,Infectious Diseases Unit, Samson Assuta Ashdod university Hospital, Ashdod, Israel
| | - Daniel Grupel
- Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.,Infectious Diseases Unit, Samson Assuta Ashdod university Hospital, Ashdod, Israel
| | - Nadav Sorek
- Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.,Microbiology Lab, Samson Assuta Ashdod university Hospital, Ashdod, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Marina Maklakovsky
- Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.,Pathology department, Samson Assuta Ashdod university Hospital, Ashdod, Israel
| | - Mia Polak
- Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.,Pathology department, Samson Assuta Ashdod university Hospital, Ashdod, Israel
| | - Merav Sharvit
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod university Hospital, Ashdod, Israel.,Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Ortal Neeman
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod university Hospital, Ashdod, Israel.,Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Tal Ben Valid
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod university Hospital, Ashdod, Israel
| | - Josef Tovbin
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod university Hospital, Ashdod, Israel.,Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Eran Barzilay
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod university Hospital, Ashdod, Israel.,Faculty of health sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
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2
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Kustin T, Harel N, Finkel U, Perchik S, Harari S, Tahor M, Caspi I, Levy R, Leshchinsky M, Ken Dror S, Bergerzon G, Gadban H, Gadban F, Eliassian E, Shimron O, Saleh L, Ben-Zvi H, Keren Taraday E, Amichay D, Ben-Dor A, Sagas D, Strauss M, Shemer Avni Y, Huppert A, Kepten E, Balicer RD, Netzer D, Ben-Shachar S, Stern A. Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals. Nat Med 2021; 27:1379-1384. [PMID: 34127854 PMCID: PMC8363499 DOI: 10.1038/s41591-021-01413-7] [Citation(s) in RCA: 235] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/26/2021] [Indexed: 12/28/2022]
Abstract
The BNT162b2 mRNA vaccine is highly effective against SARS-CoV-2. However, apprehension exists that variants of concern (VOCs) may evade vaccine protection, due to evidence of reduced neutralization of the VOCs B.1.1.7 and B.1.351 by vaccine sera in laboratory assays. We performed a matched cohort study to examine the distribution of VOCs in infections of BNT162b2 mRNA vaccinees from Clalit Health Services (Israel) using viral genomic sequencing, and hypothesized that if vaccine effectiveness against a VOC is reduced, its proportion among breakthrough cases would be higher than in unvaccinated controls. Analyzing 813 viral genome sequences from nasopharyngeal swabs, we showed that vaccinees who tested positive at least 7 days after the second dose were disproportionally infected with B.1.351, compared with controls. Those who tested positive between 2 weeks after the first dose and 6 days after the second dose were disproportionally infected by B.1.1.7. These findings suggest reduced vaccine effectiveness against both VOCs within particular time windows. Our results emphasize the importance of rigorously tracking viral variants, and of increasing vaccination to prevent the spread of VOCs.
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Affiliation(s)
- Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Noam Harel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Uriah Finkel
- Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel
| | - Shay Perchik
- Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel
| | - Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Maayan Tahor
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Itamar Caspi
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Levy
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michael Leshchinsky
- Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel
| | - Shifra Ken Dror
- Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel
| | - Galit Bergerzon
- Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel
| | - Hala Gadban
- Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel
| | - Faten Gadban
- Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel
| | - Eti Eliassian
- Progenin Laboratories, Jerusalem District, Clalit Health Services, Tel Aviv, Israel
| | - Orit Shimron
- Progenin Laboratories, Jerusalem District, Clalit Health Services, Tel Aviv, Israel
| | - Loulou Saleh
- Microbiology lab, Rabin Medical Center, Beilinson Hospital, Petah Tiqva, Israel
| | - Haim Ben-Zvi
- Microbiology lab, Rabin Medical Center, Beilinson Hospital, Petah Tiqva, Israel
| | | | - Doron Amichay
- Central Laboratory, Clalit Health Services, Tel Aviv, Israel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheba, Israel
| | - Anat Ben-Dor
- Central Laboratory, Clalit Health Services, Tel Aviv, Israel
| | - Dana Sagas
- Microbiology Laboratory, Emek Medical Center, Afula, Israel
| | - Merav Strauss
- Microbiology Laboratory, Emek Medical Center, Afula, Israel
| | - Yonat Shemer Avni
- Laboratory of Clinical Virology, Soroka University Medical Center, Beersheba, Israel
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheba, Israel
| | - Amit Huppert
- The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel HaShomer, Ramat Gan, Israel
- The Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Eldad Kepten
- Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel
| | - Ran D Balicer
- Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel
| | | | - Shay Ben-Shachar
- Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel.
- The Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
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3
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Nahmad AD, Lazzarotto C, Zelikson N, Kustin T, Tenuta M, Huang D, Reuveni I, Horovitz-Fried M, Dotan I, Rosin-Arbesfeld R, Nemazee D, Voss J, Stern A, Tsai S, Barzel A. In-vivo engineering of B cells elicits memory retention and allows for secretion of broadly neutralizing antibodies in mice. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.59.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
A potential single-shot HIV therapy may be transplanted engineered B cells allowing strong secretion of broadly neutralizing antibodies (bNAbs). However, extensive, and expensive ex-vivo manipulations performed in specialized facilities hinders clinical potential of this approach. Furthermore, allogeneic B cell therapy necessitates MHC-II compatibility to receive mandatory T-cell help.
To overcome these limitations, we engineer B cells in-vivo. In particular, we demonstrate that a single, systemic dose of dual AAV, one coding for CRISPR/Cas9 and another coding for a bNAb donor cassette, allows for site specific integration in B cells. Following immunizations, we show memory retention and bNAb secretion at high titers. Antibodies secreted by the engineered B cells were found to be of multiple isotypes and IgGs could neutralize autologous and heterologous pseudoviruses. We found engineered B cell subsets in the spleen and blood. We detected homing of in-vivo engineered cells to germinal centers and bone marrow. Biodistribution of the donor AAV over time and as compared to a CRISPR- group, indicated expansion of engineered B cells in lymphatic tissues. We determined minimal CRISPR/Cas9 off-target cleavage, using unbiased, highly sensitive, CHANGE-Seq analysis. Finally, we diminished on-target, non-productive double-strand breaks at undesired tissues by expressing Cas9 from a B cell specific promoter.
Eliciting a specific, neutralizing serological response to hypervariable viruses is a long-standing challenge in medicine. B cell engineering provides an opportunity to express therapeutic antibodies to generate an adaptive and evolving immunity.
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4
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Abstract
RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based data set spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases toward U rather than A in genomes of all viruses. In +ssRNA viruses, we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In -ssRNA viruses, the genomic mutational bias toward U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses.
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Affiliation(s)
- Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
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5
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Gelbart M, Harari S, Ben-Ari Y, Kustin T, Wolf D, Mandelboim M, Mor O, Pennings PS, Stern A. Drivers of within-host genetic diversity in acute infections of viruses. PLoS Pathog 2020; 16:e1009029. [PMID: 33147296 PMCID: PMC7668575 DOI: 10.1371/journal.ppat.1009029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/16/2020] [Accepted: 10/04/2020] [Indexed: 12/01/2022] Open
Abstract
Genetic diversity is the fuel of evolution and facilitates adaptation to novel environments. However, our understanding of what drives differences in the genetic diversity during the early stages of viral infection is somewhat limited. Here, we use ultra-deep sequencing to interrogate 43 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV. Hundreds to thousands of virus templates were sequenced per sample, allowing us to reveal dramatic differences in within-host genetic diversity among virus populations. We found that increased diversity was mostly driven by presence of multiple divergent genotypes in HIV and CMV samples, which we suggest reflect multiple transmitted/founder viruses. Conversely, we detected an abundance of low frequency hyper-edited genomes in RSV samples, presumably reflecting defective virus genomes (DVGs). We suggest that RSV is characterized by higher levels of cellular co-infection, which allow for complementation and hence elevated levels of DVGs. The few days or weeks following infection with a virus, termed acute infection, are critical for virus establishment. Here we sought to characterize what leads to differences in the genetic diversity of different viruses sampled during acute infection. We performed ultra-deep sequencing of hundreds to thousands viral genomes from forty-three samples spanning three pathogenic human viruses: HIV, RSV and CMV. We found major differences in the genetic diversity of these different viruses, and in different patients infected with the same virus. We investigated the factors responsible for these differences. We found that the DNA virus CMV was less diverse, most likely since it has a lower mutation rate than the RNA viruses HIV and RSV. We also found that the samples with the highest genetic diversity, which included one CMV sample and two HIV samples, bore evidence for multiple genotype infection. In other words, patients from whom these samples were taken were infected with two different “strains” of the virus. Finally, we also found evidence that viral genomes of HIV, and in particular RSV, are edited by the innate immune system of the host, leading to the presence of defective virus genomes.
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Affiliation(s)
- Maoz Gelbart
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ya’ara Ben-Ari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dana Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Lautenberg Center for General and Tumor Immunology, IMRIC, the Faculty of Medicine, the Hebrew University, Jerusalem, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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6
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Miller D, Martin MA, Harel N, Tirosh O, Kustin T, Meir M, Sorek N, Gefen-Halevi S, Amit S, Vorontsov O, Shaag A, Wolf D, Peretz A, Shemer-Avni Y, Roif-Kaminsky D, Kopelman NM, Huppert A, Koelle K, Stern A. Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nat Commun 2020; 11:5518. [PMID: 33139704 DOI: 10.1101/2020.05.21.20104521] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/02/2020] [Indexed: 05/22/2023] Open
Abstract
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Base Sequence
- Basic Reproduction Number/statistics & numerical data
- Betacoronavirus/genetics
- COVID-19
- Child
- Child, Preschool
- Communicable Diseases, Imported/epidemiology
- Communicable Diseases, Imported/virology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/transmission
- Female
- Genome, Viral/genetics
- Humans
- Infant
- Infant, Newborn
- Israel/epidemiology
- Male
- Middle Aged
- Pandemics/prevention & control
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/transmission
- Psychological Distance
- RNA, Viral/genetics
- SARS-CoV-2
- Sequence Analysis, RNA
- United States
- Young Adult
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Affiliation(s)
- Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michael A Martin
- Department of Biology, Emory University, Atlanta, GA, USA
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Noam Harel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Omer Tirosh
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Moran Meir
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nadav Sorek
- Microbiology Laboratory, Assuta Ashdod University-Affiliated Hospital, Ashdod, Israel
| | | | - Sharon Amit
- Clinical Microbiology Laboratory, Sheba Medical Center, Ramat-Gan, Israel
| | - Olesya Vorontsov
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avraham Shaag
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Dana Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel
| | - Yonat Shemer-Avni
- Clinical Virology Laboratory, Soroka Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Naama M Kopelman
- Department of Computer Science, Holon Institute of Technology, Holon, Israel
| | - Amit Huppert
- Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, 52621, Tel Hashomer, Israel
- School of Public Health, The Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta, GA, USA
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
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7
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Miller D, Martin MA, Harel N, Tirosh O, Kustin T, Meir M, Sorek N, Gefen-Halevi S, Amit S, Vorontsov O, Shaag A, Wolf D, Peretz A, Shemer-Avni Y, Roif-Kaminsky D, Kopelman NM, Huppert A, Koelle K, Stern A. Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nat Commun 2020; 11:5518. [PMID: 33139704 PMCID: PMC7606475 DOI: 10.1038/s41467-020-19248-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Base Sequence
- Basic Reproduction Number/statistics & numerical data
- Betacoronavirus/genetics
- COVID-19
- Child
- Child, Preschool
- Communicable Diseases, Imported/epidemiology
- Communicable Diseases, Imported/virology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/transmission
- Female
- Genome, Viral/genetics
- Humans
- Infant
- Infant, Newborn
- Israel/epidemiology
- Male
- Middle Aged
- Pandemics/prevention & control
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/transmission
- Psychological Distance
- RNA, Viral/genetics
- SARS-CoV-2
- Sequence Analysis, RNA
- United States
- Young Adult
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Affiliation(s)
- Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michael A Martin
- Department of Biology, Emory University, Atlanta, GA, USA
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Noam Harel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Omer Tirosh
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Moran Meir
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nadav Sorek
- Microbiology Laboratory, Assuta Ashdod University-Affiliated Hospital, Ashdod, Israel
| | | | - Sharon Amit
- Clinical Microbiology Laboratory, Sheba Medical Center, Ramat-Gan, Israel
| | - Olesya Vorontsov
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avraham Shaag
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Dana Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel
| | - Yonat Shemer-Avni
- Clinical Virology Laboratory, Soroka Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Naama M Kopelman
- Department of Computer Science, Holon Institute of Technology, Holon, Israel
| | - Amit Huppert
- Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, 52621, Tel Hashomer, Israel
- School of Public Health, The Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta, GA, USA
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
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