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Erster O, Bar-Or I, Azar R, Assraf H, Kabat A, Mannasse B, Moshayoff V, Fleishon S, Preis SA, Yishai R, Teijman-Yarden N, Aguvaev I, Matar R, Aydenzon A, Mandelboim M, Zuckerman NS, Sofer D, Lustig Y. Incursion of SARS-CoV-2 BA.2.86.1 variant into Israel: National-scale wastewater surveillance using a novel quantitative real-time PCR assay. Sci Total Environ 2024:173164. [PMID: 38735317 DOI: 10.1016/j.scitotenv.2024.173164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
The emergence of the SARS-CoV-2 variant BA.2.86.1 raised a considerable concern, due to the large number of potentially virulent mutations. In this study, we developed a novel assay that specifically detects variant BA.2.86.1, and used it to screen environmental samples from wastewater treatment sites across Israel. By using a multiplex assay that included a general SARS-CoV-2 reaction, together with the BA.2.86.1-specific reaction and a control reaction, we quantified the absolute number of viral copies in each sample and its relative abundance, compared with the total copy number of circulating SARS-CoV-2. Evaluation of the new reactions showed that they are both sensitive and specific, detecting down to four copies per reaction, and maintain specificity in the presence of Omicron variants BA.1, 2 and 4 RNA. Examination of 279 samples from 30 wastewater collection sites during August-September 2023 showed that 35 samples (12.5 %) were positive, from 18 sites. Quantitative analysis of the samples showed that the relative abundance of variant BA.2.86.1 with respect to the total viral load of SARS-CoV-2 was very low and consisted between 0.01 % and 0.6 % of the total SARS-CoV-2 circulation. This study demonstrates the importance of combining wastewater surveillance with the development of specialized diagnostic assays, when clinical testing is insufficient. This approach may be useful for timely response by public health authorities in future outbreaks.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel.
| | - Itay Bar-Or
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Hadar Assraf
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Vardit Moshayoff
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Shay Fleishon
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Ruth Yishai
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Irina Aguvaev
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roaa Matar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Alex Aydenzon
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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2
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Bucris E, Indenbaum V, Levin T, Kanaaneh Y, Friedman K, Kushnir T, Sheffer R, Savion M, Salama M, Di-Castro N, Labay K, Butera M, Shihada B, Mor Z, Lustig Y, Zuckerman NS. Rapid molecular epidemiology investigations into two recent measles outbreaks in Israel detected from October 2023 to January 2024. Euro Surveill 2024; 29:2400202. [PMID: 38639095 PMCID: PMC11027474 DOI: 10.2807/1560-7917.es.2024.29.16.2400202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 04/20/2024] Open
Abstract
Between late 2023 and early 2024, two measles outbreaks occurred in Israel, each caused by importation of measles virus strains of respective B3 and D8 genotypes. In this study, we validate transmission pathways uncovered by epidemiological investigations using a rapid molecular approach, based on complete measles virus genomes. The presented findings support this rapid molecular approach in complementing conventional contact tracing and highlight its potential for informing public health interventions.
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Affiliation(s)
- Efrat Bucris
- These authors contributed equally to the manuscript
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
| | - Victoria Indenbaum
- These authors contributed equally to the manuscript
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
| | - Tal Levin
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
| | - Yara Kanaaneh
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
| | - Keren Friedman
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
| | - Tatyana Kushnir
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
| | - Rivka Sheffer
- Tel Aviv District Health Office, Ministry of Health, Tel Aviv, Israel
| | - Michal Savion
- Tel Aviv District Health Office, Ministry of Health, Tel Aviv, Israel
| | - Matanelle Salama
- Tel Aviv District Health Office, Ministry of Health, Tel Aviv, Israel
| | - Noa Di-Castro
- District Health Office, Ministry of Health, Tiberias, Israel
| | - Kozita Labay
- District Health Office, Ministry of Health, Tiberias, Israel
| | - Maya Butera
- District Health Office, Ministry of Health, Tiberias, Israel
| | - Baraah Shihada
- District Health Office, Ministry of Health, Tiberias, Israel
| | - Zohar Mor
- School of Health Sciences, Ashkelon Academic College, Ashkelon, Israel
- Division of Epidemiology, Ministry of Health, Jerusalem, Israel
| | - Yaniv Lustig
- These authors contributed equally to the manuscript
- Faculty of Medicine, Department of Epidemiology and Preventive Medicine, Tel-Aviv University, Tel Aviv, Israel
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
| | - Neta S Zuckerman
- These authors contributed equally to the manuscript
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat-Gan, Israel
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3
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Zuckerman NS, Bucris E, Keidar-Friedman D, Amsalem M, Brosh-Nissimov T. Nirmatrelvir Resistance-de Novo E166V/L50V Mutations in an Immunocompromised Patient Treated With Prolonged Nirmatrelvir/Ritonavir Monotherapy Leading to Clinical and Virological Treatment Failure-a Case Report. Clin Infect Dis 2024; 78:352-355. [PMID: 37596935 DOI: 10.1093/cid/ciad494] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Resistance of SARS-CoV-2 to antivirals was shown to develop in immunocompromised individuals receiving remdesivir. We describe an immunocompromised patient who was treated with repeated and prolonged courses of nirmatrelvir and developed de-novo E166V/L50F mutations in the Mpro region. These mutations were associated with clinical and virological treatment failure.
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Affiliation(s)
- Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Tel Hashomer, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Tel Hashomer, Israel
| | - Danielle Keidar-Friedman
- Microbiology Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
- Emerging Infectious Diseases Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Muriel Amsalem
- Microbiology Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Tal Brosh-Nissimov
- Infectious Diseases Unit, Samson Assuta Ashdod University Hospital, Ashdod, Israel
- Faculty of Health Sciences, Ben Gurion University in the Negev, Beer Sheba, Israel
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4
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Wagner T, Levy I, Elbirt D, Shahar E, Olshtain-Pops K, Elinav H, Chowers M, Istomin V, Riesenberg K, Geva D, Zuckerman NS, Wax M, Shirazi R, Gozlan Y, Matus N, Girshengorn S, Marom R, Mendelson E, Mor O, Turner D. Factors Associated with Virological Failure in First-Line Antiretroviral Therapy in Patients Diagnosed with HIV-1 between 2010 and 2018 in Israel. Viruses 2023; 15:2439. [PMID: 38140680 PMCID: PMC10748212 DOI: 10.3390/v15122439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the progress in contemporary antiretroviral therapy (ART) and the continuous changes in treatment guidelines, virological failure (VF) is still an ongoing concern. The goal of this study was to assess factors related to VF after first-line ART. A longitudinal cohort retrospective study of individuals on first-line ART diagnosed with HIV-1 in 2010-2018 and followed-up for a median of two years was conducted. Demographics, baseline and longitudinal CD4 counts, treatment regimens, adherence and VF were recorded. The Cox proportional hazards regression and mixed models were used. A cohort of 1130 patients were included. Overall, 80% were males and 62% were Israeli-born individuals. Compared to individuals diagnosed in 2010-2014, when treatment was initiated according to CD4 levels, those diagnosed in 2015-2018 were older and had lower baseline CD4 counts. VF was recorded in 66 (5.8%) patients. Diagnosis with CD4 <200 cells/mmᶟ with AIDS-defining conditions (HR = 2.75, 95%CI:1.52-4.97, p < 0.001) and non-integrase strand transfer inhibitor regimens (non-INSTI, HR = 1.80, 95%CI:1.01-3.24, p = 0.047) increased VF risk. No impact of baseline resistance was observed. We concluded that the early detection of HIV-1 infection and usage of INSTI-based regimens are recommended to reduce VF.
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Affiliation(s)
- Tali Wagner
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- National HIV-1 and Viral Hepatitis Reference Laboratory, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Itzchak Levy
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Infectious Disease Unit, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Daniel Elbirt
- Faculty of Medicine, Hadassah Braun School of Public Health & Community Medicine, The Hebrew University, Jerusalem 9112102, Israel; (D.E.); (H.E.)
- Immunology, Kaplan Medical Center, Rehovot 76100, Israel
| | - Eduardo Shahar
- Immunology Unit, Rambam Health Care Campus, Haifa 3109601, Israel;
- Rappaport Faculty of Medicine, Institute of Technology, Technion, Haifa 3109601, Israel
| | | | - Hila Elinav
- Faculty of Medicine, Hadassah Braun School of Public Health & Community Medicine, The Hebrew University, Jerusalem 9112102, Israel; (D.E.); (H.E.)
- Hadassah Medical Center, Jerusalem 9112102, Israel;
| | - Michal Chowers
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Infectious Diseases, Meir Medical Center, Kfar Saba 4428164, Israel
| | | | - Klaris Riesenberg
- Goldman Medical School, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba 8410501, Israel;
- Infectious Disease Institute, Soroka Medical Center, Beersheba 84101, Israel
| | - Dikla Geva
- Integristat Ltd., Tel Aviv 69051, Israel;
| | - Neta S. Zuckerman
- National HIV-1 and Viral Hepatitis Reference Laboratory, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Marina Wax
- National HIV-1 and Viral Hepatitis Reference Laboratory, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Rachel Shirazi
- National HIV-1 and Viral Hepatitis Reference Laboratory, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Yael Gozlan
- National HIV-1 and Viral Hepatitis Reference Laboratory, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Natasha Matus
- Ichilov Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (N.M.); (S.G.); (R.M.)
| | - Shirley Girshengorn
- Ichilov Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (N.M.); (S.G.); (R.M.)
| | - Rotem Marom
- Ichilov Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (N.M.); (S.G.); (R.M.)
| | - Ella Mendelson
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- National HIV-1 and Viral Hepatitis Reference Laboratory, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Orna Mor
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- National HIV-1 and Viral Hepatitis Reference Laboratory, Chaim Sheba Medical Center, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Dan Turner
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Ichilov Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (N.M.); (S.G.); (R.M.)
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5
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Zuckerman NS, Schwartz E, Pandey P, Erster O, Halpern O, Bucris E, Morad-Eliyahu H, Wax M, Lustig Y. Dengue Types 1 and 3 Identified in Travelers Returning from Kathmandu, Nepal, during the October 2022 Outbreak Are Related to Strains Recently Identified in India. Viruses 2023; 15:2334. [PMID: 38140575 PMCID: PMC10921925 DOI: 10.3390/v15122334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Phylogenetic analysis of dengue serotypes 1 and 3, which were diagnosed in travelers and Nepalese infected in Kathmandu during the October 2022 outbreak, revealed that both serotypes were clustered closest to the sequences sampled in India. This suggests both serotypes may have originated in India.
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Affiliation(s)
- Neta S. Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; (O.E.); (O.H.); (E.B.); (H.M.-E.); (M.W.); (Y.L.)
| | - Eli Schwartz
- The Center for Travel and Tropical Medicine, Sheba Medical Center, Tel Hashomer 52621, Israel;
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 39040, Israel
| | - Prativa Pandey
- CIWEC Hospital and Travel Medicine Center, Kathmandu 44600, Nepal;
| | - Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; (O.E.); (O.H.); (E.B.); (H.M.-E.); (M.W.); (Y.L.)
| | - Osnat Halpern
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; (O.E.); (O.H.); (E.B.); (H.M.-E.); (M.W.); (Y.L.)
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; (O.E.); (O.H.); (E.B.); (H.M.-E.); (M.W.); (Y.L.)
| | - Hagar Morad-Eliyahu
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; (O.E.); (O.H.); (E.B.); (H.M.-E.); (M.W.); (Y.L.)
| | - Marina Wax
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; (O.E.); (O.H.); (E.B.); (H.M.-E.); (M.W.); (Y.L.)
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel; (O.E.); (O.H.); (E.B.); (H.M.-E.); (M.W.); (Y.L.)
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 39040, Israel
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6
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Weil M, Sofer D, Shulman LM, Weiss L, Levi N, Aguvaev I, Cohen Z, Kestin K, Vasserman R, Elul M, Fratty IS, Zuckerman NS, Erster O, Yishai R, Hecht L, Alroy-Preis S, Mendelson E, Bar-Or I. Environmental surveillance detected type 3 vaccine-derived polioviruses in increasing frequency at multiple sites prior to detection of a poliomyelitis case. Sci Total Environ 2023; 871:161985. [PMID: 36739034 DOI: 10.1016/j.scitotenv.2023.161985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Israel conducts routine environmental (15 sites) and acute flaccid paralysis (AFP) surveillance for poliovirus. During September 2021, increasing numbers of wastewater samples collected from more than one site in the Jerusalem region proved positive for ambiguous type 3 vaccine-derived poliovirus (aVDPV3), while environmental samples from remaining sampling sites were negative. In late February 2022, a VDPV3, genetically related to the Jerusalem environmental surveillance samples, was isolated from a stool sample collected from a non-immunodeficient, non-immunized child from Jerusalem who developed AFP, indicating that the aVDPV3s were circulating (cVDPV3s) rather than immunodeficiency-related VDPV3s (iVDPVs). In response to these isolations, the Israel Ministry of Health launched a catch-up immunization program.
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Affiliation(s)
- Merav Weil
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Lester M Shulman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Leah Weiss
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Nofar Levi
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Irina Aguvaev
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Zvi Cohen
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Klil Kestin
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rinat Vasserman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Elul
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ilana S Fratty
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; The Israel Center for Disease Control, Israel Ministry of Health, Ramat-Gan, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ruth Yishai
- Department of Laboratories, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Lior Hecht
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Itay Bar-Or
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.
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7
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Zuckerman NS, Shulman LM. Next-Generation Sequencing in the Study of Infectious Diseases. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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8
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun 2022; 13:7003. [PMID: 36385137 PMCID: PMC9667854 DOI: 10.1038/s41467-022-33713-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.
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Affiliation(s)
- Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Instituto Todos pela Saúde, São Paulo, SP, Brazil.
| | | | - Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gabriel W Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Lucy E Matkin
- Department of Biology, University of Oxford, Oxford, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Fernando R Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Ben Branda
- GISAID Global Data Science Initiative, Munich, Germany
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C Sabino
- Instituto Todos pela Saúde, São Paulo, SP, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Royal Veterinary College, Hawkshead, UK
| | | | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Marc A Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK.
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
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9
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Brosh-Nissimov T, Benshalom-Tirosh N, Bucris E, Morad H, Zuckerman NS, Tepperberg Oikawa M. Recurrent congenital cytomegalovirus infection in a sequential pregnancy with severe sequelae, and a possible association with prophylactic valacyclovir treatment: a case report. Int J Infect Dis 2022; 125:93-95. [PMID: 36229004 DOI: 10.1016/j.ijid.2022.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
Recurrent congenital cytomegalovirus infections in consecutive pregnancies are rarely reported. Due to the risk of fetal infection from preconception maternal infection, a 6-month interval after primary maternal infection is generally advised before a new conception. Recently, high-dose valacyclovir treatment was shown to prevent fetal infection in first trimester primary infections. We present a case of first trimester primary infection treated with high-dose valacyclovir but resulting in polymerase chain reaction-confirmed fetal infection. Cytomegalovirus-specific immunoglobulin G titers remained very low during treatment and rose only after cessation of antiviral treatment. Six months after primary seroconversion, in a sequential pregnancy, recurrent fetal infection was diagnosed and resulted in severe fetal sequella. Whole genome sequencing of both amniotic fluid isolates proved them to be identical. Both pregnancies were terminated. We hypothesize that valacyclovir treatment, although unsuccessful in preventing fetal infection, had delayed the adaptive maternal immune response and might have contributed to fetal infection during the sequential pregnancy. We suggest that a longer delay might be warranted after valacyclovir treatment and before a new conception.
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Affiliation(s)
- Tal Brosh-Nissimov
- Infectious Diseases Unit, Samson Assuta Ashdod University Hospital, Ashdod, Israel; Faculty of Health Sciences, Ben Gurion University in the Negev, Beer Sheva, Israel.
| | - Neta Benshalom-Tirosh
- Faculty of Health Sciences, Ben Gurion University in the Negev, Beer Sheva, Israel; Department of Obstetrics and Gynecology, Samson Assuta Ashdod University Hospital, Ashdod, Israel.
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Tel Hashomer, Israel.
| | - Hagar Morad
- Central Virology Laboratory, Ministry of Health, Tel Hashomer, Israel.
| | - Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Tel Hashomer, Israel.
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10
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Zuckerman NS, Bar-Or I, Sofer D, Bucris E, Morad H, Shulman LM, Levi N, Weiss L, Aguvaev I, Cohen Z, Kestin K, Vasserman R, Elul M, Fratty IS, Geva M, Wax M, Erster O, Yishai R, Hecht-Sagie L, Alroy-Preis S, Mendelson E, Weil M. Emergence of genetically linked vaccine-originated poliovirus type 2 in the absence of oral polio vaccine, Jerusalem, April to July 2022. Euro Surveill 2022; 27. [PMID: 36111556 PMCID: PMC9479469 DOI: 10.2807/1560-7917.es.2022.27.37.2200694] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report an emergence and increase in poliovirus type 2 detection via routine wastewater surveillance in three non-overlapping regions in the Jerusalem region, Israel, between April and July 2022. Sequencing showed genetic linkage among isolates and accumulation of mutations over time, with two isolates defined as vaccine-derived polioviruses (VDPV). This demonstrates the emergence and potential circulation of type 2 VDPV in a high-income country with high vaccine coverage and underscores the importance of routine wastewater surveillance during the polio eradication.
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Affiliation(s)
- Neta S Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Itay Bar-Or
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Hagar Morad
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Lester M Shulman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Nofar Levi
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Leah Weiss
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Irina Aguvaev
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Zvi Cohen
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Klil Kestin
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rinat Vasserman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Elul
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ilana S Fratty
- The Israel Center for Disease Control, Israel Ministry of Health, Ramat-Gan, Israel
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Miranda Geva
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Marina Wax
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ruth Yishai
- Department of Laboratories, Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | | | - Ella Mendelson
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Merav Weil
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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11
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Wagner T, Zuckerman NS, Wax M, Shirazi R, Gozlan Y, Girshengorn S, Marom R, Mendelson E, Turner D, Mor O. HIV-1 Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs) in Israel, 2010-2018. Viruses 2022; 14:v14091970. [PMID: 36146776 PMCID: PMC9502407 DOI: 10.3390/v14091970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Monitoring HIV-1 circulating recombinant forms (CRFs) and unique recombinant forms (URFs) is important for disease surveillance. Recombination may affect prevention efforts and interfere with the diagnosis and treatment of HIV-1 infection. Here, we characterized the epidemiology of HIV-1 CRFs and URFs in Israel. Partial pol sequences from treatment naïve patients diagnosed in 2010−2018 were assessed using the recombinant identification program (RIP), the recombinant detection program (RDP5), and using the maximum-likelihood phylogenetic method, using 410 reference sequences obtained from the Los Alamos database. CRFs and URFs were identified in 11% (213/1940) of all sequenced cases. The median age at diagnosis was 38 (30−47) years, 61% originated from Israel, and 82% were male. The most common were CRF02_AG (30.5%), CRF01_AE (16.9%), and the more complex forms CRF01_AE/CRF02_AG/A3 (10.8%) and B/F1 (7%). A significant increase in their overall proportion was observed in recent years (8.1% in 2010−2012, 20.3% in 2016−2018, p < 0.001). This increase was most prominent in individuals carrying CRF02_AG (2.5% in 2010−2015, 9.8% in 2016−2018, p < 0.001). Men who have sex with men (MSM) was the most common risk group; however, those infected with the secondary recombinant CRF02_AG/A6 were mainly injecting drug users (IDUs). The most common resistance mutations were K103N (5/213, 2.3%) and E138A (18/213, 8.5%) in the reverse transcriptase. Only E138A was more frequent in the recombinants compared with the classic subtypes and was significantly associated with a specific secondary CRF, CRF02_AG/A4. We concluded that CRFs and URFs were mainly detected in Israeli-born MSM and that an increase in the overall proportion of such HIV-1 sequences could be observed in more recent years.
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Affiliation(s)
- Tali Wagner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 5262112, Israel
- Correspondence: (T.W.); (O.M.); Tel.: +972-3-5302458 (T.W. & O.M.)
| | - Neta S. Zuckerman
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Marina Wax
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Yael Gozlan
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Shirley Girshengorn
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel
| | - Rotem Marom
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel
| | - Ella Mendelson
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 5262112, Israel
| | - Dan Turner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel
| | - Orna Mor
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 5262112, Israel
- Correspondence: (T.W.); (O.M.); Tel.: +972-3-5302458 (T.W. & O.M.)
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12
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Bar-Or I, Indenbaum V, Weil M, Elul M, Levi N, Aguvaev I, Cohen Z, Levy V, Azar R, Mannasse B, Shirazi R, Bucris E, Mor O, Sela Brown A, Sofer D, Zuckerman NS, Mendelson E, Erster O. National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel. Viruses 2022; 14:1229. [PMID: 35746700 PMCID: PMC9227326 DOI: 10.3390/v14061229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
In this report, we describe a national-scale monitoring of the SARS-CoV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December 2020 and March 2021, a complete shift in the SC-2 variant circulation was observed, where the B.1.1.7 replaced the A19 in all examined test points. We further show that the normalized viral load (NVL) values and the average new cases per week reached a peak in January 2021 and then decreased gradually in almost all test points, in parallel with the progression of the national vaccination campaign, during February-March 2021. This study demonstrates the importance of monitoring SC-2 variant by using a combination of inclusive and selective PCR tests on a national scale through wastewater sampling, which is far more amendable for high-throughput monitoring compared with sequencing. This approach may be useful for real-time dynamics surveillance of current and future variants, such as the Omicron (BA.1, BA.2) and other variants.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Victoria Indenbaum
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Merav Weil
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Michal Elul
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Nofar Levi
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Irina Aguvaev
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Zvi Cohen
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Virginia Levy
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Roberto Azar
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Batya Mannasse
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Rachel Shirazi
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Efrat Bucris
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
- Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Alin Sela Brown
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Danit Sofer
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Ella Mendelson
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
- Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Oran Erster
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
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13
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Glatman-Freedman A, Gur-Arie L, Sefty H, Kaufman Z, Bromberg M, Dichtiar R, Rosenberg A, Pando R, Nemet I, Kliker L, Mendelson E, Keinan-Boker L, Zuckerman NS, Mandelboim M. The impact of SARS-CoV-2 on respiratory syndromic and sentinel surveillance in Israel, 2020: a new perspective on established systems. Euro Surveill 2022; 27. [PMID: 35451365 PMCID: PMC9027148 DOI: 10.2807/1560-7917.es.2022.27.16.2100457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background The COVID-19 pandemic presented new challenges for the existing respiratory surveillance systems, and adaptations were implemented. Systematic assessment of the syndromic and sentinel surveillance platforms during the pandemic is essential for understanding the value of each platform in the context of an emerging pathogen with rapid global spread. Aim We aimed to evaluate systematically the performance of various respiratory syndromic surveillance platforms and the sentinel surveillance system in Israel from 1 January to 31 December 2020. Methods We compared the 2020 syndromic surveillance trends to those of the previous 3 years, using Poisson regression adjusted for overdispersion. To assess the performance of the sentinel clinic system as compared with the national SARS-CoV-2 repository, a cubic spline with 7 knots and 95% confidence intervals were applied to the sentinel network's weekly percentage of positive SARS-CoV-2 cases. Results Syndromic surveillance trends changed substantially during 2020, with a statistically significant reduction in the rates of visits to physicians and emergency departments to below previous years' levels. Morbidity patterns of the syndromic surveillance platforms were inconsistent with the progress of the pandemic, while the sentinel surveillance platform was found to reflect the national circulation of SARS-CoV-2 in the population. Conclusion Our findings reveal the robustness of the sentinel clinics platform for the surveillance of the main respiratory viruses during the pandemic and possibly beyond. The robustness of the sentinel clinics platform during 2020 supports its use in locations with insufficient resources for widespread testing of respiratory viruses.
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Affiliation(s)
- Aharona Glatman-Freedman
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lea Gur-Arie
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Hanna Sefty
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Zalman Kaufman
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Michal Bromberg
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rita Dichtiar
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Alina Rosenberg
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Rakefet Pando
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Ital Nemet
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Limor Kliker
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Ella Mendelson
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Lital Keinan-Boker
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,School of Public Health, University of Haifa, Israel
| | - Neta S Zuckerman
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Michal Mandelboim
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | -
- The Israeli Respiratory Viruses Surveillance Network (IRVSN) members are listed under Acknowledgements
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14
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Fass E, Zizelski Valenci G, Rubinstein M, Freidlin PJ, Rosencwaig S, Kutikov I, Werner R, Ben-Tovim N, Bucris E, Erster O, Zuckerman NS, Mor O, Mendelson E, Dveyrin Z, Rorman E, Nissan I. HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene. Front Med (Lausanne) 2022; 8:798130. [PMID: 35087848 PMCID: PMC8787038 DOI: 10.3389/fmed.2021.798130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022] Open
Abstract
The changing nature of the SARS-CoV-2 pandemic poses unprecedented challenges to the world's health systems. Emerging spike gene variants jeopardize global efforts to produce immunity and reduce morbidity and mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and is susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Tight monitoring of spike protein gene variants is key to mitigating COVID-19 spread and generation of vaccine escape mutants. Currently, SARS-CoV-2 sequencing methods are labor intensive and expensive. When sequence demands are high sequencing resources are quickly exhausted. Consequently, most SARS-CoV-2 strains are sequenced in only a few developed countries and rarely in developing regions. This poses the risk that undetected, dangerous variants will emerge. In this work, we present HiSpike, a method for high-throughput cost effective targeted next generation sequencing of the spike gene. This simple three-step method can be completed in < 30 h, can sequence 10-fold more samples compared to conventional methods and at a fraction of their cost. HiSpike has been validated in Israel, and has identified multiple spike variants from real-time field samples including Alpha, Beta, Delta and the emerging Omicron variants. HiSpike provides affordable sequencing options to help laboratories conserve resources for widespread high-throughput, near real-time monitoring of spike gene variants.
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Affiliation(s)
- Ephraim Fass
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Mor Rubinstein
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Paul J. Freidlin
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Shira Rosencwaig
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Inna Kutikov
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Robert Werner
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Nofar Ben-Tovim
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
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15
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Wagner T, Zuckerman NS, Halperin T, Chemtob D, Levy I, Elbirt D, Shachar E, Olshtain-Pops K, Elinav H, Chowers M, Itsomin V, Riesenberg K, Wax M, Shirazi R, Gozlan Y, Matus N, Girshengorn S, Marom R, Mendelson E, Turner D, Mor O. Epidemiology and Transmitted HIV-1 Drug Resistance among Treatment-Naïve Individuals in Israel, 2010-2018. Viruses 2021; 14:v14010071. [PMID: 35062274 PMCID: PMC8779053 DOI: 10.3390/v14010071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/22/2023] Open
Abstract
Despite the low prevalence of HIV-1 in Israel, continuous waves of immigration may have impacted the local epidemic. We characterized all people diagnosed with HIV-1 in Israel in 2010–2018. The demographics and clinical data of all individuals (n = 3639) newly diagnosed with HIV-1 were retrieved. Subtypes, transmitted drug-resistance mutations (TDRM), and phylogenetic relations, were determined in >50% of them. In 39.1%, HIV-1 transmission was through heterosexual contact; 34.3% were men who have sex with men (MSM); and 10.4% were people who inject drugs. Many (>65%) were immigrants. Israeli-born individuals were mostly (78.3%) MSM, whereas only 9% of those born in Sub-Saharan Africa (SSA), Eastern Europe and Central Asia (EEU/CA), were MSM. The proportion of individuals from SSA decreased through the years 2010–2018 (21.1% in 2010–2012; 16.8% in 2016–2018) whereas those from EEU/CA increased significantly (21% in 2010–2012; 27.8% in 2016–2018, p < 0.001). TDRM were identified in 12.1%; 3.7, 3.3 and 6.6% had protease inhibitors (PI), nucleotide reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI) TDRM, respectively, with the overall proportion remaining stable in the studied years. None had integrase TDRM. Subtype B was present in 43.9%, subtype A in 25.2% (A6 in 22.8 and A1 in 2.4%) and subtype C in 17.1% of individuals. Most MSM had subtype B. Subtype C carriers formed small clusters (with one unexpected MSM cluster), A1 formed a cluster mainly of locally-born patients with NNRTI mutations, and A6 formed a looser cluster of individuals mainly from EEU. Israelis, <50 years old, carrying A1, had the highest risk for having TDRM. In conclusion, an increase in immigrants from EEU/CA and a decrease in those from SSA characterized the HIV-1 epidemic in 2010–2018. Baseline resistance testing should still be recommended to identify TDRM, and improve surveillance and care.
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Affiliation(s)
- Tali Wagner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Neta S. Zuckerman
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Tami Halperin
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Daniel Chemtob
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Tuberculosis and AIDS Department, Ministry of Health, Jerusalem 9101002, Israel
| | - Itzchak Levy
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, Infectious Disease Unit, Ramat Gan 5262112, Israel
| | - Daniel Elbirt
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Immunology, Kaplan Medical Center, Rehovot 76100, Israel
| | - Eduardo Shachar
- Immunology Unit, Rambam Health Care Campus, Haifa 3109601, Israel;
- Rappaport Faculty of Medicine, Institute of Technology, Technion, Haifa 3200003, Israel
| | | | - Hila Elinav
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Hadassah Medical Center, Jerusalem 9112102, Israel;
| | - Michal Chowers
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Infectious Diseases, Meir Medical Center, Kfar Saba 4428164, Israel
| | | | - Klaris Riesenberg
- Faculty of Health Sciences, Goldman Medical School, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel;
- Soroka Medical Center, Infectious Disease Institute, Beer-Sheva 84101, Israel
| | - Marina Wax
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Rachel Shirazi
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Yael Gozlan
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Natasha Matus
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Shirley Girshengorn
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Rotem Marom
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Ella Mendelson
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Dan Turner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Orna Mor
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
- Correspondence: ; Tel.: +972-3-530-2458
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16
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MU, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. medRxiv 2021:2021.08.21.21262393. [PMID: 34462754 PMCID: PMC8404891 DOI: 10.1101/2021.08.21.21262393] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.
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Affiliation(s)
- Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Elizaveta Semenova
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Mathematics, Imperial College London, London, UK
| | - Gytis Dudas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Gabriel W. Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
| | | | - Lucy E. Matkin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
| | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales 2145, Australia
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Tulio de Oliveira
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | | | | | | | - Fernando R. Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N. Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D. Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Royal Veterinary College, Hawkshead, United Kingdom
| | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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17
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Singer SR, Angulo FJ, Swerdlow DL, McLaughlin JM, Hazan I, Ginish N, Anis E, Mendelson E, Mor O, Zuckerman NS, Erster O, Southern J, Pan K, Mircus G, Lipsitch M, Haas EJ, Jodar L, Levy Y, Alroy-Preis S. Effectiveness of BNT162b2 mRNA COVID-19 vaccine against SARS-CoV-2 variant Beta (B.1.351) among persons identified through contact tracing in Israel: A prospective cohort study. EClinicalMedicine 2021; 42:101190. [PMID: 34870134 PMCID: PMC8628463 DOI: 10.1016/j.eclinm.2021.101190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND SARS-CoV-2 variant Beta (B.1.351) was designated as a Variant of Concern (VoC) after becoming the dominant strain in South Africa and spreading internationally. BNT162b2 showed lower levels of neutralizing antibodies against Beta than against other strains raising concerns about effectiveness of vaccines against infections caused by Beta. We estimated BNT162b2 vaccine effectiveness (VE) against Beta infections in Israel, a country with high vaccine uptake. METHODS The Ministry of Health (MoH) identified Beta cases through mandatory reporting of SARS-CoV-2 cases and whole genome sequencing (WGS) of specimens from vaccination-breakthrough infections, reinfections, arriving international travelers, and a selection of other infected persons. A cohort analysis was conducted of exposure events of contacts of primary Beta cases. WGS was conducted on available PCR-positive specimens collected from contacts. VE estimates with 95% confidence intervals (CIs) against confirmed and probable Beta infections were determined by comparing infection risk between unvaccinated and fully-vaccinated (≥7 days after the second dose) contacts, and between unvaccinated and partially-vaccinated (<7 days after the second dose) contacts. FINDINGS MoH identified 310 Beta cases through Jun 27, 2021. During the study period (Dec 11, 2020 - Mar 25, 2021), 164 non-institutionalized primary Beta cases, with 552 contacts aged ≥16 years, were identified. 343/552 (62%) contacts were interviewed and tested. 71/343 (21%) contacts were PCR-positive. WGS was performed on 7/71 (10%) PCR-positive specimens; all were Beta. Among SARS-CoV-2-infected contacts, 48/71 (68%) were symptomatic, 10/71 (14%) hospitalized, and 2/71 (3%) died. Fully-vaccinated VE against confirmed or probable Beta infections was 72% (95% CI -5 - 97%; p=0·04) and against symptomatic confirmed or probable Beta infections was 100% (95% CI 19 - 100%; p=0·01). There was no evidence of protection in partially-vaccinated contacts. INTERPRETATION In a prospective observational study, two doses of BNT162b2 were effective against confirmed and probable Beta infections. Through the end of June 2021, introductions of Beta did not interrupt control of the pandemic in Israel. FUNDING Israel Ministry of Health and Pfizer.
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Affiliation(s)
- Shepherd R. Singer
- Public Health Services, Israel Ministry of Health, Jerusalem, Israel
- Hadassah Braun School of Public Health, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | | | | | | | | | | | - Emilia Anis
- Public Health Services, Israel Ministry of Health, Jerusalem, Israel
- Hadassah Braun School of Public Health, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oran Erster
- Central Virology Laboratory, Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | | | | | | | - Eric J. Haas
- Public Health Services, Israel Ministry of Health, Jerusalem, Israel
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | | | | | - Sharon Alroy-Preis
- Public Health Services, Israel Ministry of Health, Jerusalem, Israel
- Corresponding author and reprint requests: Sharon Alroy-Preis, Public Health Services, Israel Ministry of Health, Yirmiyahu Street 39, Jerusalem 9101002, P.O.B. 1176, Israel.
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18
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Erster O, Mendelson E, Levy V, Kabat A, Mannasse B, Asraf H, Azar R, Ali Y, Shirazi R, Bucris E, Bar-Ilan D, Mor O, Mandelboim M, Sofer D, Fleishon S, Zuckerman NS. Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Microbiol Spectr 2021; 9:e0050621. [PMID: 34612692 PMCID: PMC8510166 DOI: 10.1128/spectrum.00506-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/19/2021] [Indexed: 11/20/2022] Open
Abstract
Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health decision making and to provide valuable data for epidemiological and policy decision making. We developed a multiplex reverse transcriptase quantitative PCR (RT-qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions-one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, one that detects the 242 to 244 deletion, which is specific to variant B.1.351, and the fourth reaction, which identifies the human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants and not with other major known variants. The assay's specificity was tested against a panel of respiratory pathogens (n = 16), showing high specificity toward SC-2 RNA. The assay's sensitivity was assessed using both in vitro transcribed RNA and clinical samples and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole-genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide-circulating SC-2 variants. IMPORTANCE This study describes the design and utilization of a multiplex reverse transcriptase quantitative PCR (RT-qPCR) to identify SARS-COV-2 (SC2) RNA in general and, specifically, to detect whether it is of lineage B.1.1.7 or B.1.351. Implementation of this method in diagnostic and research laboratories worldwide may help the efforts to contain the COVID-19 pandemic. The method can be easily scaled up and be used in high-throughput laboratories, as well as small ones. In addition to immediate help in diagnostic efforts, this method may also help in epidemiological studies focused on the spread of emerging SC-2 lineages.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Virginia Levy
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Hadar Asraf
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Yaniv Ali
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Shai Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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19
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Erster O, Mendelson E, Levy V, Kabat A, Mannasse B, Asraf H, Azar R, Ali Y, Shirazi R, Bucris E, Bar-Ilan D, Mor O, Mandelboim M, Sofer D, Fleishon S, Zuckerman NS. Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Microbiol Spectr 2021; 9:e0050621. [PMID: 34612692 DOI: 10.1101/2021.05.19.21257439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health decision making and to provide valuable data for epidemiological and policy decision making. We developed a multiplex reverse transcriptase quantitative PCR (RT-qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions-one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, one that detects the 242 to 244 deletion, which is specific to variant B.1.351, and the fourth reaction, which identifies the human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants and not with other major known variants. The assay's specificity was tested against a panel of respiratory pathogens (n = 16), showing high specificity toward SC-2 RNA. The assay's sensitivity was assessed using both in vitro transcribed RNA and clinical samples and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole-genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide-circulating SC-2 variants. IMPORTANCE This study describes the design and utilization of a multiplex reverse transcriptase quantitative PCR (RT-qPCR) to identify SARS-COV-2 (SC2) RNA in general and, specifically, to detect whether it is of lineage B.1.1.7 or B.1.351. Implementation of this method in diagnostic and research laboratories worldwide may help the efforts to contain the COVID-19 pandemic. The method can be easily scaled up and be used in high-throughput laboratories, as well as small ones. In addition to immediate help in diagnostic efforts, this method may also help in epidemiological studies focused on the spread of emerging SC-2 lineages.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Virginia Levy
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Hadar Asraf
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Yaniv Ali
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Shai Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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20
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Mor O, Zuckerman NS, Hazan I, Fluss R, Ash N, Ginish N, Mendelson E, Alroy-Preis S, Freedman L, Huppert A. BNT162b2 vaccine effectiveness was marginally affected by the SARS-CoV-2 beta variant in fully vaccinated individuals. J Clin Epidemiol 2021; 142:38-44. [PMID: 34715314 PMCID: PMC8553421 DOI: 10.1016/j.jclinepi.2021.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 11/04/2022]
Abstract
Objective To evaluate the effectiveness of the Pfizer BNT162b2 vaccine against the SARS-Cov-2 Beta variant. Study Design and Setting Israel's mass vaccination program, using two doses of the Pfizer BNT162b2 vaccine, successfully curtailed the Alpha variant outbreak during winter 2020–2021, However, the virus may mutate and partially evade the immune system. To monitor this, sequencing of selected positive swab samples of interest was initiated. Comparing vaccinated with unvaccinated PCR positive persons, we estimated the odds ratio for a vaccinated case to have the Beta vs. the Alpha variant, using logistic regression, controlling for important confounders. Results There were 19 cases of Beta variant (3.2%) among those vaccinated more than 14 days before the positive sample and 79 (3.4%) among the unvaccinated. The estimated odds ratio was 1.26 (95% CI: 0.65–2.46). Assuming the effectiveness against the Alpha variant to be 95%, the estimated effectiveness against the Beta variant was 94% (95% CI: 88%–98%). Conclusion Despite concerns over the Beta variant, the BNT162b2 vaccine seemed to provide substantial immunity against both the Beta and the Alpha variants. From 14 days following the second vaccine dose, the effectiveness of BNT162b2 vaccine was at most marginally affected by the Beta variant.
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Affiliation(s)
- Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 5262100, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 5262100, Israel
| | - Itay Hazan
- Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Ronen Fluss
- The Biostatistical and Biomathematical Unit, Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Ramat Gan 5265601, Israel
| | - Nachman Ash
- Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Netanel Ginish
- Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 5262100, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Sharon Alroy-Preis
- Public Health Services, Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Laurence Freedman
- The Biostatistical and Biomathematical Unit, Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Ramat Gan 5265601, Israel
| | - Amit Huppert
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel; The Biostatistical and Biomathematical Unit, Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Ramat Gan 5265601, Israel.
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21
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Abstract
A nosocomial outbreak of SARS-CoV-2 Delta variant infected 42 patients, staff and family members; 39 were fully vaccinated. The attack rate was 10.6% (16/151) among exposed staff and reached 23.7% (23/97) among exposed patients in a highly vaccinated population, 16–26 weeks after vaccination (median: 25 weeks). All cases were linked and traced to one patient. Several transmissions occurred between individuals wearing face masks. Fourteen of 23 patients became severely sick or died, raising a question about possible waning immunity.
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Affiliation(s)
- Pnina Shitrit
- Infection Control Unit, Meir Medical Center, Kfar Saba, Israel.,Sackler Medical School, Tel-Aviv University, Tel-Aviv Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Bat-Sheva Gottesman
- Sackler Medical School, Tel-Aviv University, Tel-Aviv Israel.,Infectious Disease Unit, Meir Medical Center, Kfar Saba, Israel
| | - Michal Chowers
- Sackler Medical School, Tel-Aviv University, Tel-Aviv Israel.,Infectious Disease Unit, Meir Medical Center, Kfar Saba, Israel
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22
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Bar-Or I, Weil M, Indenbaum V, Bucris E, Bar-Ilan D, Elul M, Levi N, Aguvaev I, Cohen Z, Shirazi R, Erster O, Sela-Brown A, Sofer D, Mor O, Mendelson E, Zuckerman NS. Detection of SARS-CoV-2 variants by genomic analysis of wastewater samples in Israel. Sci Total Environ 2021; 789:148002. [PMID: 34323811 PMCID: PMC8142738 DOI: 10.1016/j.scitotenv.2021.148002] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 05/12/2023]
Abstract
Investigation of SARS-CoV-2 spread and identification of variants in sewers has been demonstrated to accurately detect prevalence of viral strains and is advantageous to clinical sampling in population catchment size. Herein, we utilized an established nationwide system of wastewater sampling and viral concentration approaches to perform large-scale surveillance of SARS-CoV-2 variants in nine different locations across Israel that were sampled from August 2020 to February 2021 and sequenced (n = 58). Viral sequences obtained from the wastewater samples had high coverages of the genome, and mutation analyses successfully identified the penetration of the B.1.1.7 variant into Israel in December 2020 in the central and north regions, and its spread into additional regions in January and February 2021, corresponding with clinical sampling results. Moreover, the wastewater analysis identified the B.1.1.7 variant in December 2020 in regions in which non-sufficient clinical sampling was available. Other variants of concern examined, including P.1 (Brazil/Manaus), B.1.429 (USA/California), B.1.526 (USA/New York), A.23.1 (Uganda) and B.1.525 (Unknown origin), did not show consistently elevated frequencies. This study exemplifies that surveillance by sewage is a robust approach which allows to monitor the diversity of SARS-CoV-2 strains circulating in the community. Most importantly, this approach can pre-identify the emergence of epidemiologically or clinically relevant mutations/variants, aiding in public health decision making.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Merav Weil
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Victoria Indenbaum
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Elul
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Nofar Levi
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Irina Aguvaev
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Zvi Cohen
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Alin Sela-Brown
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.
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23
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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24
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Mor O, Mandelboim M, Fleishon S, Bucris E, Bar-Ilan D, Linial M, Nemet I, Kliker L, Lustig Y, Mendelson ES, Zuckerman NS. The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Vaccines (Basel) 2021; 9:937. [PMID: 34452062 PMCID: PMC8402656 DOI: 10.3390/vaccines9080937] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Emerging SARS-CoV-2 variants may threaten global vaccination efforts and the awaited reduction in outbreak burden. In this study, we report a novel variant carrying the L452R mutation that emerged from a local B.1.362 lineage, B.1.362+L452R. The L452R mutation is associated with the Delta and Epsilon variants and was shown to cause increased infection and reduction in neutralization in pseudoviruses. Indeed, the B.1.362+L452R variant demonstrated a X4-fold reduction in neutralization capacity of sera from BNT162b2-vaccinated individuals compared to a wild-type strain. The variant infected 270 individuals in Israel between December 2020 and March 2021, until diminishing due to the gain in dominance of the Alpha variant in February 2021. This study demonstrates an independent, local emergence of a variant carrying a critical mutation, L452R, which may have the potential of becoming a variant of concern and emphasizes the importance of routine surveillance and detection of novel variants among efforts undertaken to prevent further disease spread.
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Affiliation(s)
- Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Shay Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Ital Nemet
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Limor Kliker
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Yaniv Lustig
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | | | - Ella S. Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
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25
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Mor O, Mandelboim M, Fleishon S, Bucris E, Bar-Ilan D, Linial M, Nemet I, Kliker L, Lustig Y, Mendelson ES, Zuckerman NS. The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Vaccines (Basel) 2021; 9. [PMID: 34452062 DOI: 10.1101/2021.07.03.21259957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 05/20/2023] Open
Abstract
Emerging SARS-CoV-2 variants may threaten global vaccination efforts and the awaited reduction in outbreak burden. In this study, we report a novel variant carrying the L452R mutation that emerged from a local B.1.362 lineage, B.1.362+L452R. The L452R mutation is associated with the Delta and Epsilon variants and was shown to cause increased infection and reduction in neutralization in pseudoviruses. Indeed, the B.1.362+L452R variant demonstrated a X4-fold reduction in neutralization capacity of sera from BNT162b2-vaccinated individuals compared to a wild-type strain. The variant infected 270 individuals in Israel between December 2020 and March 2021, until diminishing due to the gain in dominance of the Alpha variant in February 2021. This study demonstrates an independent, local emergence of a variant carrying a critical mutation, L452R, which may have the potential of becoming a variant of concern and emphasizes the importance of routine surveillance and detection of novel variants among efforts undertaken to prevent further disease spread.
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Affiliation(s)
- Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Shay Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ital Nemet
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Limor Kliker
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Ella S Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
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26
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Zuckerman NS, Bucris E, Erster O, Mandelboim M, Adler A, Burstein S, Protter N, Szwarcwort-Cohen M, Mendelson E, Mor O. Prolonged detection of complete viral genomes demonstrated by SARS-CoV-2 sequencing of serial respiratory specimens. PLoS One 2021; 16:e0255691. [PMID: 34351998 PMCID: PMC8341697 DOI: 10.1371/journal.pone.0255691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/21/2021] [Indexed: 11/19/2022] Open
Abstract
Accurate and timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is clinically essential, and is required also to monitor confirmed cases aiming to prevent further spread. Positive real-time PCR results at late time points following initial diagnosis may be clinically misleading as this methodology cannot account for the infection capabilities and the existence of whole genome sequences. In this study, 47 serial respiratory samples were tested by Allplex-nCoV test (Seegene), a triplex of three assays targeting the SARS-CoV-2 RdRP, E and N genes and subsequently assessed by next generation sequencing (NGS). COVID19 patients were tested at an early stage of the disease, when all these viral gene targets were positive, and at an advanced stage, when only the N gene target was positive in the Allplex-nCoV test. The corresponding NGS results showed the presence of complete viral genome copies at both early and advanced stages of the disease, although the total number of mapped sequences was lower in samples from advanced disease stages. We conclude that reduced viral transmission at this late disease stage may result from the low quantities of complete viral sequences and not solely from transcription favoring the N gene.
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Affiliation(s)
- Neta S. Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim 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
| | - Amos Adler
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Clinical Microbiology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | | | | | | | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim 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, Chaim 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
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27
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Zuckerman NS, Fleishon S, Bucris E, Bar-Ilan D, Linial M, Bar-Or I, Indenbaum V, Weil M, Lustig Y, Mendelson E, Mandelboim M, Mor O, Zuckerman N. A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Vaccines (Basel) 2021; 9:616. [PMID: 34201088 PMCID: PMC8228438 DOI: 10.3390/vaccines9060616] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/20/2021] [Accepted: 06/03/2021] [Indexed: 11/30/2022] Open
Abstract
The routine detection, surveillance, and reporting of novel SARS-CoV-2 variants is crucial, as these threaten to hinder global vaccination efforts. Herein we report a novel local variant with a non-synonymous mutation in the spike (S) protein P681H. This local Israeli variant was not associated with a higher infection rate or higher prevalence. Furthermore, the local variant was successfully neutralized by sera from fully vaccinated individuals at a comparable level to the B.1.1.7 variant and an Israel wild-type strain. While it is not a variant of concern, routine monitoring by sequencing is still required.
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Affiliation(s)
- Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Shay Fleishon
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Efrat Bucris
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Dana Bar-Ilan
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Itay Bar-Or
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Victoria Indenbaum
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Merav Weil
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Yaniv Lustig
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
| | - Ella Mendelson
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Neta Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (S.F.); (E.B.); (D.B.-I.); (I.B.-O.); (V.I.); (M.W.); (Y.L.); (E.M.); (M.M.); (O.M.); (N.Z.)
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28
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Pando R, Stern S, Nemet I, Glatman-Freedman A, Sefty H, Zuckerman NS, Drori Y, Friedman N, McCauley JW, Keinan-Boker L, Mendelson E, Daniels RS, Mandelboim M. Diversity in the Circulation of Influenza A(H3N2) Viruses in the Northern Hemisphere in the 2018-19 Season. Vaccines (Basel) 2021; 9:375. [PMID: 33924296 PMCID: PMC8069444 DOI: 10.3390/vaccines9040375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 11/23/2022] Open
Abstract
While vaccination is considered the most effective means to prevent influenza infection, its seasonal effectiveness varies, depending on the circulating influenza strains. Here, we characterized the circulation of influenza strains in October-2018 and March-2019 around the world. For this, we used nasopharyngeal samples collected from outpatient and hospitalized patients in Israel and data reported in ECDC, CDC, and WHO databases. Influenza A(H3N2) was dominant in Israel, while in Europe, Asia, and USA, A(H1N1)pdm09 virus circulated first, and then the A(H3N2) virus also appeared. Phylogenetic analysis indicated that A(H3N2) viruses circulating in Israel belonged to clade-3C.3a, while in Europe, Asia, and USA, A(H3N2) viruses belonged to subclade-3C.2a1, but were later replaced by clade-3C.3a viruses in USA. The vaccine A(H3N2) components of that year, A/Singapore/INFIMH-16-0019/2016-(H3N2)-like-viruses, belonged to clade-3C.2a1. The circulation of different influenza subtypes and clades of A(H3N2) viruses in a single season highlights the need for universal influenza vaccines.
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Affiliation(s)
- Rakefet Pando
- The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Ramat-Gan 52621, Israel; (R.P.); (A.G.-F.); (H.S.); (N.S.Z.); (L.K.-B.)
- Chaim Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Ramat-Gan 52621, Israel; (S.S.); (I.N.); (Y.D.); (N.F.); (E.M.)
| | - Shahar Stern
- Chaim Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Ramat-Gan 52621, Israel; (S.S.); (I.N.); (Y.D.); (N.F.); (E.M.)
| | - Ital Nemet
- Chaim Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Ramat-Gan 52621, Israel; (S.S.); (I.N.); (Y.D.); (N.F.); (E.M.)
| | - Aharona Glatman-Freedman
- The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Ramat-Gan 52621, Israel; (R.P.); (A.G.-F.); (H.S.); (N.S.Z.); (L.K.-B.)
- Department of Epidemiology and Preventive Medicine, Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Hanna Sefty
- The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Ramat-Gan 52621, Israel; (R.P.); (A.G.-F.); (H.S.); (N.S.Z.); (L.K.-B.)
| | - Neta S. Zuckerman
- The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Ramat-Gan 52621, Israel; (R.P.); (A.G.-F.); (H.S.); (N.S.Z.); (L.K.-B.)
| | - Yaron Drori
- Chaim Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Ramat-Gan 52621, Israel; (S.S.); (I.N.); (Y.D.); (N.F.); (E.M.)
| | - Nehemya Friedman
- Chaim Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Ramat-Gan 52621, Israel; (S.S.); (I.N.); (Y.D.); (N.F.); (E.M.)
| | - John W. McCauley
- Worldwide Influenza Center, The Francis Crick Institute, London NW1 1AT, UK; (J.W.M.); (R.S.D.)
| | - Lital Keinan-Boker
- The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Ramat-Gan 52621, Israel; (R.P.); (A.G.-F.); (H.S.); (N.S.Z.); (L.K.-B.)
- School of Public Health, University of Haifa, Haifa 3498838, Israel
| | - Ella Mendelson
- Chaim Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Ramat-Gan 52621, Israel; (S.S.); (I.N.); (Y.D.); (N.F.); (E.M.)
- Department of Epidemiology and Preventive Medicine, Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Rodney S. Daniels
- Worldwide Influenza Center, The Francis Crick Institute, London NW1 1AT, UK; (J.W.M.); (R.S.D.)
| | - Michal Mandelboim
- Chaim Sheba Medical Center, Central Virology Laboratory, Ministry of Health, Ramat-Gan 52621, Israel; (S.S.); (I.N.); (Y.D.); (N.F.); (E.M.)
- Department of Epidemiology and Preventive Medicine, Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 6997801, Israel
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Zuckerman NS, Pando R, Bucris E, Drori Y, Lustig Y, Erster O, Mor O, Mendelson E, Mandelboim M. Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. Viruses 2020; 12:v12080854. [PMID: 32764372 PMCID: PMC7472171 DOI: 10.3390/v12080854] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 has become a major global concern as of December 2019, particularly affecting healthcare workers. As person-to-person transmission is airborne, crowded closed spaces have high potential for rapid virus spread, especially early in the pandemic when social distancing and mask wearing were not mandatory. This retrospective study thoroughly investigates a small-scale SARS-CoV-2 outbreak in Israel’s central virology laboratory (ICVL) in mid-March 2020, in which six staff members and two related family members were infected. Suspicions regarding infection by contaminated surfaces in ICVL facilities were nullified by SARS-CoV-2 negative real time polymerase chain reaction (PCR) of work surfaces swipe tests. Complete SARS-CoV-2 genomes were sequenced and mutation analyses showed inclusion of all samples to clades 20B and 20C, possessing the spike mutation D614G. Phylogenetic analysis clarified transmission events, confirming S1 as having infected at least three other staff members and refuting the association of a staff member’s infected spouse with the ICVL transmission cluster. Finally, serology tests exhibited IgG and IgA antibodies in all infected individuals and revealed the occurrence of asymptomatic infections in additional staff members. This study demonstrates the advantages of molecular epidemiology in elucidating transmission events and exemplifies the importance of good laboratory practice, distancing and mask wearing in preventing SARS-CoV-2 spread, specifically in healthcare facilities.
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Affiliation(s)
- Neta S. Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
| | - Rakefet Pando
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
- The Israel Center for Disease Control, Israel Ministry of Health, P.O. Box 5265601, Tel-Hashomer, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
| | - Yaron Drori
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, P.O. Box 39040, Tel-Aviv, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
| | - Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, P.O. Box 39040, Tel-Aviv, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, P.O. Box 39040, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; (N.S.Z.); (R.P.); (E.B.); (Y.D.); (Y.L.); (O.E.); (O.M.); (E.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, P.O. Box 39040, Tel-Aviv, Israel
- Correspondence: ; Tel.: +972-3-530-2455
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McIntyre D, Zuckerman NS, Field M, Mehr R, Stott DI. The V(H) repertoire and clonal diversification of B cells in inflammatory myopathies. Eur J Immunol 2014; 44:585-96. [PMID: 24343314 DOI: 10.1002/eji.201343315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 07/24/2013] [Accepted: 12/11/2013] [Indexed: 01/12/2023]
Abstract
The contribution of antigen-driven B-cell adaptive immune responses within the inflamed muscle of inflammatory myopathies (IMs) is largely unknown. In this study, we investigated the immunoglobulin V(H) gene repertoire, somatic hypermutation, clonal diversification, and selection of infiltrating B cells in muscle biopsies from IM patients (dermatomyositis and polymyositis), to determine whether B cells and/or plasma cells contribute to the associated pathologies of these diseases. The data reveal that Ig V(H) gene repertoires of muscle-infiltrating B cells deviate from the normal V(H) gene repertoire in individual patients, and differ between different types of IMs. Analysis of somatic mutations revealed clonal diversification of muscle-infiltrating B cells and evidence for a chronic B-cell response within the inflamed muscle. We conclude that muscle-infiltrating B cells undergo selection, somatic hypermutation and clonal diversification in situ during antigen-driven immune responses in patients with IMs, providing insight into the contribution of B cells to the pathological mechanisms of these disorders.
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Affiliation(s)
- Donna McIntyre
- Institute of Infection, Immunity and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, Scotland, UK
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Yu H, Simons DL, Segall I, Carcamo-Cavazos V, Schwartz EJ, Yan N, Zuckerman NS, Dirbas FM, Johnson DL, Holmes SP, Lee PP. PRC2/EED-EZH2 complex is up-regulated in breast cancer lymph node metastasis compared to primary tumor and correlates with tumor proliferation in situ. PLoS One 2012; 7:e51239. [PMID: 23251464 PMCID: PMC3519681 DOI: 10.1371/journal.pone.0051239] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [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: 06/16/2011] [Accepted: 11/05/2012] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Lymph node metastasis is a key event in the progression of breast cancer. Therefore it is important to understand the underlying mechanisms which facilitate regional lymph node metastatic progression. METHODOLOGY/PRINCIPAL FINDINGS We performed gene expression profiling of purified tumor cells from human breast tumor and lymph node metastasis. By microarray network analysis, we found an increased expression of polycomb repression complex 2 (PRC2) core subunits EED and EZH2 in lymph node metastatic tumor cells over primary tumor cells which were validated through real-time PCR. Additionally, immunohistochemical (IHC) staining and quantitative image analysis of whole tissue sections showed a significant increase of EZH2 expressing tumor cells in lymph nodes over paired primary breast tumors, which strongly correlated with tumor cell proliferation in situ. We further explored the mechanisms of PRC2 gene up-regulation in metastatic tumor cells and found up-regulation of E2F genes, MYC targets and down-regulation of tumor suppressor gene E-cadherin targets in lymph node metastasis through GSEA analyses. Using IHC, the expression of potential EZH2 target, E-cadherin was examined in paired primary/lymph node samples and was found to be significantly decreased in lymph node metastases over paired primary tumors. CONCLUSIONS/SIGNIFICANCE This study identified an over expression of the epigenetic silencing complex PRC2/EED-EZH2 in breast cancer lymph node metastasis as compared to primary tumor and its positive association with tumor cell proliferation in situ. Concurrently, PRC2 target protein E-cadherin was significant decreased in lymph node metastases, suggesting PRC2 promotes epithelial mesenchymal transition (EMT) in lymph node metastatic process through repression of E-cadherin. These results indicate that epigenetic regulation mediated by PRC2 proteins may provide additional advantage for the outgrowth of metastatic tumor cells in lymph nodes. This opens up epigenetic drug development possibilities for the treatment and prevention of lymph node metastasis in breast cancer.
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Affiliation(s)
- Hongxiang Yu
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Diana L. Simons
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, United States of America
- Department of Cancer Immunotherapeutics and Tumor Immunology, City of Hope Cancer Center, Duarte, California, United States of America
| | - Ilana Segall
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Valeria Carcamo-Cavazos
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Erich J. Schwartz
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ning Yan
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Neta S. Zuckerman
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, United States of America
- Department of Cancer Immunotherapeutics and Tumor Immunology, City of Hope Cancer Center, Duarte, California, United States of America
| | - Frederick M. Dirbas
- Department of Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Denise L. Johnson
- Department of Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Peter P. Lee
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, United States of America
- Department of Cancer Immunotherapeutics and Tumor Immunology, City of Hope Cancer Center, Duarte, California, United States of America
- * E-mail:
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Zuckerman NS, Yu H, Simons DL, Bhattacharya N, Carcamo-Cavazos V, Yan N, Dirbas FM, Johnson DL, Schwartz EJ, Lee PP. Altered local and systemic immune profiles underlie lymph node metastasis in breast cancer patients. Int J Cancer 2012; 132:2537-47. [PMID: 23136075 DOI: 10.1002/ijc.27933] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 10/10/2012] [Indexed: 12/14/2022]
Abstract
Cancer-mediated immune dysfunction contributes to tumor progression and correlates with patient outcome. Metastasis to tumor draining lymph nodes (TDLNs) is an important step in breast cancer progression and is used to predict patient outcome and survival. Although lymph nodes are important immune organs, the role of immune cells in TDLNs has not been thoroughly investigated. We hypothesized that the host immune response in node negative (NN) patients is more intact and thereby can resist tumor invasion compared to node positive (NP) patients. As such, lymph node metastasis requires breakdown of the host immune response in addition to escape of cancer cells from the tumor. To investigate the immunological differences between NN and NP breast cancer patients, we purified and profiled immune cells from the three major compartments where cancer and immune cells interact: tumor, TDLNs and peripheral blood. Significant down-regulation of genes associated with immune-related pathways and up-regulation of genes associated with tumor-promoting pathways was consistently observed in NP patients' TDLNs compared to NN patients. Importantly, these signatures were seen even in NP patients' tumor-free TDLNs, suggesting that such immune changes are not driven solely by local tumor invasion. Furthermore, similar patterns were also observed in NP patients' tumor and blood immune cells, suggesting that immunological differences between NN and NP patients are systemic. Together, these findings suggest that alterations in overall immune function may underlie risk for LN metastasis in breast cancer patients.
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Affiliation(s)
- Neta S Zuckerman
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
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Zuckerman NS, McCann KJ, Ottensmeier CH, Barak M, Shahaf G, Edelman H, Dunn-Walters D, Abraham RS, Stevenson FK, Mehr R. Ig gene diversification and selection in follicular lymphoma, diffuse large B cell lymphoma and primary central nervous system lymphoma revealed by lineage tree and mutation analyses. Int Immunol 2010; 22:875-87. [PMID: 21059768 DOI: 10.1093/intimm/dxq441] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Follicular lymphoma (FL), diffuse large B cell lymphoma (DLBCL) and primary central nervous system lymphoma are B cell malignancies. FL and DLBCL have a germinal center origin. We have applied mutational analyses and a novel algorithm for quantifying shape properties of mutational lineage trees to investigate the nature of the diversification, somatic hypermutation and selection processes that affect B cell clones in these malignancies and reveal whether they differ from normal responses. Lineage tree analysis demonstrated higher diversification and mutations per cell in the lymphoma clones. This was caused solely by the longer diversification times of the malignant clones, as their recent diversification processes were similar to those of normal responses, implying similar mutation frequencies. Since previous analyses of antigen-driven selection were shown to yield false positives, we performed a corrected analysis of replacement and silent mutation patterns, which revealed selection against replacement mutations in the framework regions, responsible for the structural integrity of the B cell receptor, but not for positive selection for replacements in the complementary determining regions. Most replacements, however, were neutral or conservative, suggesting that if at all selection operates in these malignancies it is for structural B cell receptor integrity but not for antigen binding.
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Affiliation(s)
- Neta S Zuckerman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Zuckerman NS, Hazanov H, Barak M, Edelman H, Hess S, Shcolnik H, Dunn-Walters D, Mehr R. Somatic hypermutation and antigen-driven selection of B cells are altered in autoimmune diseases. J Autoimmun 2010; 35:325-35. [PMID: 20727711 DOI: 10.1016/j.jaut.2010.07.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [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: 07/01/2010] [Revised: 07/20/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022]
Abstract
B cells have been found to play a critical role in the pathogenesis of several autoimmune (AI) diseases. A common feature amongst many AI diseases is the formation of ectopic germinal centers (GC) within the afflicted tissue or organ, in which activated B cells expand and undergo somatic hypermutation (SHM) and antigen-driven selection on their immunoglobulin variable region (IgV) genes. However, it is not yet clear whether these processes occurring in ectopic GCs are identical to those in normal GCs. The analysis of IgV mutations has aided in revealing many aspects concerning B cell expansion, mutation and selection in GC reactions. We have applied several mutation analysis methods, based on lineage tree construction, to a large set of data, containing IgV productive and non-productive heavy and light chain sequences from several different tissues, to examine three of the most profoundly studied AI diseases - Rheumatoid Arthritis (RA), Multiple Sclerosis (MS) and Sjögren's Syndrome (SS). We have found that RA and MS sequences exhibited normal mutation spectra and targeting motifs, but a stricter selection compared to normal controls, which was more apparent in RA. SS sequence analysis results deviated from normal controls in both mutation spectra and indications of selection, also showing differences between light and heavy chain IgV and between different tissues. The differences revealed between AI diseases and normal control mutation patterns may result from the different microenvironmental influences to which ectopic GCs are exposed, relative to those in normal secondary lymphoid tissues.
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Affiliation(s)
- Neta S Zuckerman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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Zuckerman NS, Howard WA, Bismuth J, Gibson K, Edelman H, Berrih-Aknin S, Dunn-Walters D, Mehr R. Ectopic GC in the thymus of myasthenia gravis patients show characteristics of normal GC. Eur J Immunol 2010; 40:1150-61. [DOI: 10.1002/eji.200939914] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Barak M, Zuckerman NS, Edelman H, Unger R, Mehr R. IgTree: creating Immunoglobulin variable region gene lineage trees. J Immunol Methods 2008; 338:67-74. [PMID: 18706908 DOI: 10.1016/j.jim.2008.06.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/21/2008] [Accepted: 06/23/2008] [Indexed: 11/19/2022]
Abstract
Lineage trees describe the microevolution of cells within an organism. They have been useful in the study of B cell affinity maturation, which is based on somatic hypermutation of immunoglobulin genes in germinal centers and selection of the resulting mutants. Our aim was to create and implement an algorithm that can generate lineage trees from immunoglobulin variable region gene sequences. The IgTree program implements the algorithm we developed, and generates lineage trees. Original sequences found in experiments are assigned to either leaves or internal nodes of the tree. Each tree node represents a single mutation separating the sequences. The mutations that separate the sequences from each other can be point mutations, deletions or insertions. The program can deal with gaps and find potential reversion mutations. The program also enumerates mutation frequencies and sequence motifs around each mutation, on a per-tree basis. The algorithm has proven useful in several studies of immunoglobulin variable region gene mutations.
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Affiliation(s)
- Michal Barak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Shahaf G, Barak M, Zuckerman NS, Swerdlin N, Gorfine M, Mehr R. Antigen-driven selection in germinal centers as reflected by the shape characteristics of immunoglobulin gene lineage trees: a large-scale simulation study. J Theor Biol 2008; 255:210-22. [PMID: 18786548 DOI: 10.1016/j.jtbi.2008.08.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [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: 03/09/2008] [Revised: 08/03/2008] [Accepted: 08/04/2008] [Indexed: 01/12/2023]
Abstract
During the immune response, the generation of memory B lymphocytes in germinal centers involves affinity maturation of the cells' antigen receptors, based on somatic hypermutation of receptor genes and antigen-driven selection of the resulting mutants. Affinity maturation is vital for immune protection, and is the basis of humoral immune learning and memory. Lineage trees of somatically hypermutated immunoglobulin genes often serve to qualitatively illustrate claims concerning the dynamics of affinity maturation in germinal centers. Here, we derive the quantitative relationships between parameters characterizing affinity maturation dynamics (proliferation, differentiation and mutation rates, initial affinity of the Ig to the antigen, and selection thresholds) and the mathematical properties of lineage trees, using a computer simulation which combines mathematical models for all mature B cell populations, stochastic models of hypermutation and selection, lineage tree generation and measurement of graphical tree characteristics. We identified seven key lineage tree properties, and found correlations of these with initial clone affinity and with the selection threshold. These two parameters were found to be the main factors affecting lineage tree shapes in both primary and secondary response trees. The results also confirm that recycling from centrocytes back to centroblasts is highly likely.
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Affiliation(s)
- Gitit Shahaf
- Mina & Everard Goodman Faculty of Life Sciences, Building 212, Bar-Ilan University, Ramat-Gan 52900, Israel
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Steiman-Shimony A, Edelman H, Hutzler A, Barak M, Zuckerman NS, Shahaf G, Dunn-Walters D, Stott DI, Abraham RS, Mehr R. Lineage tree analysis of immunoglobulin variable-region gene mutations in autoimmune diseases: chronic activation, normal selection. Cell Immunol 2007; 244:130-6. [PMID: 17434468 DOI: 10.1016/j.cellimm.2007.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 01/31/2007] [Indexed: 11/21/2022]
Abstract
Autoimmune diseases show high diversity in the affected organs, clinical manifestations and disease dynamics. Yet they all share common features, such as the ectopic germinal centers found in many affected tissues. Lineage trees depict the diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. We previously developed an algorithm for quantifying the graphical properties of IGV gene lineage trees, allowing evaluation of the dynamical interplay between SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we apply this method to ectopic GC B cell clones from patients with Myasthenia Gravis, Rheumatoid Arthritis, and Sjögren's Syndrome, using data scaling to minimize the effects of the large variability due to methodological differences between groups. Autoimmune trees were found to be significantly larger relative to normal controls. In contrast, comparison of the measurements for tree branching indicated that similar selection pressure operates on autoimmune and normal control clones.
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Affiliation(s)
- Avital Steiman-Shimony
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 212, Box 61, Ramat-Gan 52900, Israel
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Manske MK, Zuckerman NS, Timm MM, Maiden S, Edelman H, Shahaf G, Barak M, Dispenzieri A, Gertz MA, Mehr R, Abraham RS. Corrigendum to “Quantitative analysis of clonal bone marrow CD19+ B cells: Use of B cell lineage trees to delineate their role in the pathogenesis of light chain amyloidosis” [Clin. Immunol. 120 (2006) 106–120]. Clin Immunol 2007. [DOI: 10.1016/j.clim.2006.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abraham RS, Manske MK, Zuckerman NS, Sohni A, Edelman H, Shahaf G, Timm MM, Dispenzieri A, Gertz MA, Mehr R. Novel Analysis of Clonal Diversification in Blood B Cell and Bone Marrow Plasma Cell Clones in Immunoglobulin Light Chain Amyloidosis. J Clin Immunol 2006; 27:69-87. [PMID: 17192818 DOI: 10.1007/s10875-006-9056-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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: 09/13/2006] [Accepted: 11/03/2006] [Indexed: 11/24/2022]
Abstract
Immunoglobulin light chain amyloidosis (AL) is characterized by a limited clonal expansion of plasma cells and amyloid formation. Here, we report restriction in the diversity of VL gene usage with a dominance of clonally related B cells in the peripheral blood (PB) isotype-specific repertoire of AL patients. A rigorous quantification of lineage trees reveals presence of intraclonal variations in the PB clones compared to the bone marrow (BM) clones, which suggests a common precursor that is still subject to somatic mutation. When compared to normal BM and PB B cells, AL clones showed significant but incomplete impairment of antigenic selection, which could not be detected by conventional R and S mutation analysis. Therefore, graphical analysis of B cell lineage trees and mathematical quantification of tree properties provide novel insights into the process of B cell clonal evolution in AL.
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Affiliation(s)
- Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
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Manske MK, Zuckerman NS, Timm MM, Maiden S, Edelman H, Shahaf G, Barak M, Dispenzieri A, Gertz MA, Mehr R, Abraham RS. Quantitative analysis of clonal bone marrow CD19+ B cells: use of B cell lineage trees to delineate their role in the pathogenesis of light chain amyloidosis. Clin Immunol 2006; 120:106-20. [PMID: 16515886 DOI: 10.1016/j.clim.2006.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [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: 12/07/2005] [Revised: 01/04/2006] [Accepted: 01/18/2006] [Indexed: 11/28/2022]
Abstract
Light chain amyloidosis (AL) is a bone marrow (BM) plasma cell neoplasia with systemic deposition of Ig light chain amyloid fibrils. Here, we report the identification of clonal CD19 B cells in the BM and the use of a novel mathematical algorithm to generate B cell lineage trees of the clonal CD19 B cells and CD138 plasma cells from the BM of AL patients to delineate the relationship between these two clonal populations. The CD19+ clonal B cells in the BM of AL patients related to the clonal plasma cells represent a pre-plasma cell precursor population. The B cell lineage trees from AL patients also show significant differences in clonal diversification and antigenic selection compared to clones from normal, healthy controls. These data provide a robust example of the use of graphical quantification methods in delineating the role of neoplastic precursors in the pathogenesis of hematopoietic malignancies.
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Affiliation(s)
- Michelle K Manske
- Division of Hematology, Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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