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Article: COVID-19 Pandemic in Lebanon: One Year Later, What Have We Learnt?

Koweyes, Jad / Salloum, Tamara / Haidar, Siwar / Merhi, Georgi / Tokajian, Sima

mSystems

2021 Volume 6, Issue 2

Abstract: Lebanon is witnessing an unprecedented crisis with the rapid spread of coronavirus disease 2019 (COVID-19), financial meltdown, economic collapse, and the Beirut Port explosion. The first wave began in February 2020, following which the country ... ...

Abstract	Lebanon is witnessing an unprecedented crisis with the rapid spread of coronavirus disease 2019 (COVID-19), financial meltdown, economic collapse, and the Beirut Port explosion. The first wave began in February 2020, following which the country experienced several episodes and peaks while alternating between lockdowns and phased liftings. One year of the pandemic revealed that effective mitigation could not be separated from the collapse of the ongoing economic, political, and health sectors. Scaling up vaccination, preparedness, and response capacities is essential to control community transmission. The World Health Organization (WHO), National Council for Scientific Research-Lebanon (CNRS-L), nongovernmental organizations (NGOs), and humanitarian responses proved to be the safety net for the country during the current pandemic.
Language	English
Publishing date	2021-04-20
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00351-21
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Article ; Online: SARS-CoV-2 genomic epidemiology: data and sequencing infrastructure.

Merhi, Georgi / Koweyes, Jad / Salloum, Tamara / Khoury, Charbel Al / Haidar, Siwar / Tokajian, Sima

Future microbiology

2022 Volume 17, Page(s) 1001–1007

Abstract: ... Background: ... Genomic surveillance of SARS-CoV-2 is critical in monitoring viral lineages. Available data reveal a significant gap between low- and middle-income countries and the rest of the world. ... Methods: ... The SARS-CoV-2 sequencing costs ... ...

Abstract	Background: Genomic surveillance of SARS-CoV-2 is critical in monitoring viral lineages. Available data reveal a significant gap between low- and middle-income countries and the rest of the world. Methods: The SARS-CoV-2 sequencing costs using the Oxford Nanopore MinION device and hardware prices for data computation in Lebanon were estimated and compared with those in developed countries. SARS-CoV-2 genomes deposited on the Global Initiative on Sharing All Influenza Data per 1000 COVID-19 cases were determined per country. Results: Sequencing costs in Lebanon were significantly higher compared with those in developed countries. Low- and middle-income countries showed limited sequencing capabilities linked to the lack of support, high prices, long delivery delays and limited availability of trained personnel. Conclusion: The authors recommend the mobilization of funds to develop whole-genome sequencing-based surveillance platforms and the implementation of genomic epidemiology to better identify and track outbreaks, leading to appropriate and mindful interventions.
MeSH term(s)	COVID-19/epidemiology ; Genome, Viral ; Genomics ; Humans ; SARS-CoV-2/genetics ; Sequence Analysis
Language	English
Publishing date	2022-07-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2254620-0
ISSN	1746-0921 ; 1746-0913
ISSN (online)	1746-0921
ISSN	1746-0913
DOI	10.2217/fmb-2021-0207
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Article ; Online: Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon.

Kodsi, Ibrahim Al / Rayes, Douaa El / Koweyes, Jad / Khoury, Charbel Al / Rahy, Kelven / Thoumi, Sergio / Chamoun, Marc / Haddad, Hoda / Mokhbat, Jacques / Tokajian, Sima

Virus research

2023 Volume 339, Page(s) 199289

Abstract: Background: Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged ... ...

Abstract	Background: Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. Methods: A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. Results: Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). Conclusions: The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
MeSH term(s)	Animals ; Humans ; Lebanon/epidemiology ; COVID-19/epidemiology ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Seasons
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-12-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2023.199289
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Article ; Online: Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.

Merhi, Georgi / Trotter, Alexander J / de Oliveira Martins, Leonardo / Koweyes, Jad / Le-Viet, Thanh / Abou Naja, Hala / Al Buaini, Mona / Prosolek, Sophie J / Alikhan, Nabil-Fareed / Lott, Martin / Tohmeh, Tatiana / Badran, Bassam / Jupp, Orla J / Gardner, Sarah / Felgate, Matthew W / Makin, Kate A / Wilkinson, Janine M / Stanley, Rachael / Sesay, Abdul K /

Webber, Mark A / Davidson, Rose K / Ghosn, Nada / Pallen, Mark / Hasan, Hamad / Page, Andrew J / Tokajian, Sima

Microbial genomics

2022 Volume 8, Issue 7

Abstract: The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic ... ...

Abstract	The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.
MeSH term(s)	COVID-19/epidemiology ; Genome, Viral/genetics ; Humans ; Lebanon/epidemiology ; Pandemics ; Phylogeny ; Prospective Studies ; Retrospective Studies ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-09-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000838
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

Webber, Mark A / Davidson, Rose K / Ghosn, Nada / Pallen, Mark / Hasan, Hamad / Page, Andrew J / Tokajian, Sima

medRxiv

Abstract: Background: The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. ... ...

Abstract	Background: The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just twenty six SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. Methods: Nine hundred and five SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, gender, nationality and age. Results: Although sixteen PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97% of samples. In the following two months, all samples contained the Alpha variant. However, this had changed dramatically by June and July, when all samples belonged to the Delta variant. Discussion: This study provides a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country9s largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under six weeks.
Keywords	covid19
Language	English
Publishing date	2021-08-11
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.08.10.21261847
Database	COVID19

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Article ; Online: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review

Áine O'Toole / Verity Hill / Oliver G. Pybus / Alexander Watts / Issac I. Bogoch / Kamran Khan / Jane P. Messina / The COVID-19 Genomics UK (COG-UK) consortium / Network for Genomic Surveillance in South Africa (NGS-SA) / Brazil-UK CADDE Genomic Network / Houriiyah Tegally / Richard R. Lessells / Jennifer Giandhari / Sureshnee Pillay / Kefentse Arnold Tumedi / Gape Nyepetsi / Malebogo Kebabonye / Maitshwarelo Matsheka / Madisa Mine /

Sima Tokajian / Hamad Hassan / Tamara Salloum / Georgi Merhi / Jad Koweyes / Jemma L. Geoghegan / Joep de Ligt / Xiaoyun Ren / Matthew Storey / Nikki E. Freed / Chitra Pattabiraman / Pramada Prasad / Anita S. Desai / Ravi Vasanthapuram / Thomas F. Schulz / Lars Steinbrück / Tanja Stadler / Swiss Viollier Sequencing Consortium / Antonio Parisi / Angelica Bianco / Darío García de Viedma / Sergio Buenestado-Serrano / Vítor Borges / Joana Isidro / Sílvia Duarte / João Paulo Gomes / Neta S. Zuckerman / Michal Mandelboim / Orna Mor / Torsten Seemann / Alicia Arnott

Wellcome Open Research, Vol

2 approved]

2021 Volume 6

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 ... ...

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.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Wellcome
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review

Wellcome Open Research, Vol

3 approved]

2021 Volume 6

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.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Wellcome
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

O'Toole, Áine / Hill, Verity / Pybus, Oliver G / Watts, Alexander / Bogoch, Issac I / Khan, Kamran / Messina, Jane P / Tegally, Houriiyah / Lessells, Richard R / Giandhari, Jennifer / Pillay, Sureshnee / Tumedi, Kefentse Arnold / Nyepetsi, Gape / Kebabonye, Malebogo / Matsheka, Maitshwarelo / Mine, Madisa / Tokajian, Sima / Hassan, Hamad / Salloum, Tamara /

Merhi, Georgi / Koweyes, Jad / Geoghegan, Jemma L / de Ligt, Joep / Ren, Xiaoyun / Storey, Matthew / Freed, Nikki E / Pattabiraman, Chitra / Prasad, Pramada / Desai, Anita S / Vasanthapuram, Ravi / Schulz, Thomas F / Steinbrück, Lars / Stadler, Tanja / Parisi, Antonio / Bianco, Angelica / García de Viedma, Darío / Buenestado-Serrano, Sergio / Borges, Vítor / Isidro, Joana / Duarte, Sílvia / Gomes, João Paulo / Zuckerman, Neta S / Mandelboim, Michal / Mor, Orna / Seemann, Torsten / Arnott, Alicia / Draper, Jenny / Gall, Mailie / Rawlinson, William / Deveson, Ira / Schlebusch, Sanmarié / McMahon, Jamie / Leong, Lex / Lim, Chuan Kok / Chironna, Maria / Loconsole, Daniela / Bal, Antonin / Josset, Laurence / Holmes, Edward / St George, Kirsten / Lasek-Nesselquist, Erica / Sikkema, Reina S / Oude Munnink, Bas / Koopmans, Marion / Brytting, Mia / Sudha Rani, V / Pavani, S / Smura, Teemu / Heim, Albert / Kurkela, Satu / Umair, Massab / Salman, Muhammad / Bartolini, Barbara / Rueca, Martina / Drosten, Christian / Wolff, Thorsten / Silander, Olin / Eggink, Dirk / Reusken, Chantal / Vennema, Harry / Park, Aekyung / Carrington, Christine / Sahadeo, Nikita / Carr, Michael / Gonzalez, Gabo / de Oliveira, Tulio / Faria, Nuno / Rambaut, Andrew / Kraemer, Moritz U G

Wellcome open research

2021 Volume 6, Page(s) 121

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.
Language	English
Publishing date	2021-09-17
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.16661.2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: COVID-19 Pandemic in Lebanon: One Year Later, What Have We Learnt?

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Article ; Online: SARS-CoV-2 genomic epidemiology: data and sequencing infrastructure.

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Article ; Online: Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon.

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Article ; Online: Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.

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Article ; Online: Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

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Article ; Online: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review

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Article ; Online: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review

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Article: Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

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