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Article ; Online: Robust expansion of phylogeny for fast-growing genome sequence data.

Ye, Yongtao / Shum, Marcus H / Tsui, Joseph L / Yu, Guangchuang / Smith, David K / Zhu, Huachen / Wu, Joseph T / Guan, Yi / Lam, Tommy Tsan-Yuk

PLoS computational biology

2024 Volume 20, Issue 2, Page(s) e1011871

Abstract: Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of de novo inference. 'TIPars' was developed for such challenge integrating parsimony analysis with pre-computed ... ...

Abstract	Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of de novo inference. 'TIPars' was developed for such challenge integrating parsimony analysis with pre-computed ancestral sequences. It took about 21 seconds to insert 100 SARS-CoV-2 genomes into a 100k-taxa reference tree using 1.4 gigabytes. Benchmarking on four datasets, TIPars achieved the highest accuracy for phylogenies of moderately similar sequences. For highly similar and divergent scenarios, fully parsimony-based and likelihood-based phylogenetic placement methods performed the best respectively while TIPars was the second best. TIPars accomplished efficient and accurate expansion of phylogenies of both similar and divergent sequences, which would have broad biological applications beyond SARS-CoV-2. TIPars is accessible from https://tipars.hku.hk/ and source codes are available at https://github.com/id-bioinfo/TIPars.
MeSH term(s)	Phylogeny ; Likelihood Functions ; Genome ; Software ; SARS-CoV-2/genetics
Language	English
Publishing date	2024-02-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1011871
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders.

Nature communications

2024 Volume 15, Issue 1, Page(s) 1126

Abstract: Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration ... ...

Abstract	Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.
MeSH term(s)	Animals ; Animals, Wild ; Birds ; Influenza A virus/genetics ; Influenza in Birds/transmission ; Phylogeny ; Poultry ; Animal Migration
Language	English
Publishing date	2024-02-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45462-1
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Article ; Online: COVID-19 pandemic re-shaped the global dispersal of seasonal influenza viruses

Chen, Zhiyuan / Tsui, Joseph L.-H. / Gutierrez, Bernardo / Moreno, Simon Busch / Plessis, Louis du / Deng, Xiaowei / Cai, Jun / Bajaj, Sumali / Suchard, Marc A. / Pybus, Oliver G. / Lemey, Philippe / Kraemer, Moritz U. G. / Yu, Hongjie

medRxiv

Abstract: Understanding how the global dispersal patterns of seasonal influenza viruses were perturbed during and after the COVID-19 pandemic is needed to inform influenza intervention and vaccination strategies in the post-pandemic period. Although global human ... ...

Abstract	Understanding how the global dispersal patterns of seasonal influenza viruses were perturbed during and after the COVID-19 pandemic is needed to inform influenza intervention and vaccination strategies in the post-pandemic period. Although global human mobility has been identified as a key driver of influenza dispersal, alongside climatic and evolutionary factors, the impact of international travel restrictions on global influenza transmission and recovery remains unknown. Here we combine molecular, epidemiological, climatic, and international travel data within a phylodynamic framework to show that, despite human mobility remaining the principal driver of global influenza virus dissemination, the pandemic9s onset led to a shift in the international population structure and migration network of seasonal influenza lineages. We find that South Asia and Africa played important roles as exporters and phylogenetic trunk locations of influenza in 2020 and 2021, and we highlight the association between population movement, antigenic drift and persistence during the intensive non-pharmaceutical interventions (NPIs) phase. The influenza B/Yamagata lineage disappeared in a context of reduced relative genetic diversity, moderate lineage turnover, and lower positive selection pressure. Our results demonstrate that mobility perturbations reshaped the global dispersal dynamics of influenza viruses, with potential implications for vaccine design and genomic surveillance programmes. As the risk of future pandemics persists, our study provides an opportunity to assess the impact of NPIs during the pandemic on respiratory infectious diseases beyond the interplay between SARS-CoV-2 and influenza viruses.
Keywords	covid19
Language	English
Publishing date	2023-12-24
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.12.20.23300299
Database	COVID19

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Article ; Online: Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern

Cell. 20232023 July 07, June 07, v. 186, no. 15 p.3277-3290.e16

2023

Abstract: The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in ... ...

Abstract	The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%–2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; air transportation ; genomics ; monitoring ; phylogeny ; phylogeography ; India ; South Africa ; mobility ; travel ; SARS-CoV-2 ; global dispersal ; phylogenetics ; variants
Language	English
Dates of publication	2023-0607
Size	p. 3277-3290.e16.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.06.001
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern.

Cell

2023 Volume 186, Issue 15, Page(s) 3277–3290.e16

Abstract	The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
MeSH term(s)	Humans ; Air Travel ; COVID-19 ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2023-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.06.001
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Article ; Online: Routes of importation and spatial dynamics of SARS-CoV-2 variants during localised interventions in Chile

Gutierrez, Bernardo / Tsui, Joseph L.-H. / Pullano, Giulia / Mazzoli, Mattia / Gangavarapu, Karthik / Inward, Rhys P.D. / Bajaj, Sumali / Evans Pena, Rosario / Busch-Moreno, Simon / Suchard, Marc A. / Pybus, Oliver G. / Dunner, Alejandra / Puentes, Rodrigo / Ayala, Salvador / Fernandez, Jorge / Araos, Rafael / Ferres, Leo / Colizza, Vittoria / Kraemer, Moritz U.G.

medRxiv

Abstract: South America suffered large SARS-CoV-2 epidemics between 2020 and 2022 caused by multiple variants of interest and concern, some causing substantial morbidity and mortality. However, their transmission dynamics are poorly characterised. The epidemic ... ...

Abstract	South America suffered large SARS-CoV-2 epidemics between 2020 and 2022 caused by multiple variants of interest and concern, some causing substantial morbidity and mortality. However, their transmission dynamics are poorly characterised. The epidemic situation in Chile enables us to investigate differences in the distribution and spread of variants Alpha, Gamma, Lambda, Mu and Delta. Chile implemented non-pharmaceutical interventions and an integrated genomic and epidemiological surveillance system that included airport and community surveillance to track SARS-CoV-2 variants. Here we combine viral genomic data and anonymised human mobility data from mobile phones to characterise the routes of importation of different variants into Chile, the relative contributions of airport-based importations to viral diversity versus land border crossings and test the impact of the mobility network on the diffusion of viral lineages within the country. We find that Alpha, Lambda and Mu were identified in Chile via airport surveillance six, four and five weeks ahead of their detection via community surveillance, respectively. Further, some variants that originated in South America were imported into Chile via land rather than international air travel, most notably Gamma. Different variants exhibited similar trends of viral dissemination throughout the country following their importation, and we show that the mobility network predicts the time of arrival of imported lineages to different Chilean comunas. Higher stringency of local NPIs was also associated with fewer domestic viral importations. Our results show how genomic surveillance combined with high resolution mobility data can help predict the multi-scale geographic expansion of emerging infectious diseases.
Keywords	covid19
Language	English
Publishing date	2024-01-22
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.01.18.24301504
Database	COVID19

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Article ; Online: Routes of importation and spatial dynamics of SARS-CoV-2 variants during localised interventions in Chile

Gutierrez, Bernardo / Tsui, Joseph L.-H. / Pullano, Giulia / Mazzoli, Mattia / Gangavarapu, Karthik / Inward, Rhys / Bajaj, Sumali / Evans Pena, Rosario / Busch Moreno, Simon / Suchard, Marc A. / Pybus, Oliver G. / Dunner, Alejandra / Puentes, Rodrigo / Ayala, Salvador / Fernandez, Jorge / Araos, Rafael / Ferres, Leo / Colizza, Vittoria / Kraemer, Moritz U.G.

medRxiv

Abstract	South America suffered large SARS-CoV-2 epidemics between 2020 and 2022 caused by multiple variants of interest and concern, some causing substantial morbidity and mortality. However, their transmission dynamics are poorly characterised. The epidemic situation in Chile enables us to investigate differences in the distribution and spread of variants Alpha, Gamma, Lambda, Mu and Delta. Chile implemented non-pharmaceutical interventions and an integrated genomic and epidemiological surveillance system that included airport and community surveillance to track SARS-CoV-2 variants. Here we combine viral genomic data and anonymised human mobility data from mobile phones to characterise the routes of importation of different variants into Chile, the relative contributions of airport-based importations to viral diversity versus land border crossings and test the impact of the mobility network on the diffusion of viral lineages within the country. We find that Alpha, Lambda and Mu were identified in Chile via airport surveillance six, four and five weeks ahead of their detection via community surveillance, respectively. Further, some variants that originated in South America were imported into Chile via land rather than international air travel, most notably Gamma. Different variants exhibited similar trends of viral dissemination throughout the country following their importation, and we show that the mobility network predicts the time of arrival of imported lineages to different Chilean comunas. Higher stringency of local NPIs was also associated with fewer domestic viral importations. Our results show how genomic surveillance combined with high resolution mobility data can help predict the multi-scale geographic expansion of emerging infectious diseases.
Keywords	covid19
Language	English
Publishing date	2024-01-22
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.01.18.24301504
Database	COVID19

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Article: Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel.

medRxiv : the preprint server for health sciences

2022

Abstract: In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third ... ...

Abstract	In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance. Highlights: Global phylogenetic analysis reveals relationship between air travel and speed of dispersal of SARS-CoV-2 variants of concern (VOCs)Omicron VOC spread to 5x more countries within 100 days of its emergence compared to all other VOCsOnward transmission and dissemination of VOCs Delta and Omicron was primarily from secondary hubs rather than initial country of detection during a time of increased global air travelAnalysis highlights highly connected countries identified as major global and regional exporters of VOCs.
Language	English
Publishing date	2022-11-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.11.22.22282629
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Article ; Online: Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong.

Nature communications

2022 Volume 13, Issue 1, Page(s) 736

Abstract: Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23- ... ...

Abstract	Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases. Community outbreaks were caused by novel introductions rather than a resurgence of circulating strains. Thus, local outbreak prevention requires strong border control and community surveillance, especially during periods of less stringent social restriction. Non-adherence to prolonged preventative measures may explain sustained local transmission observed during wave four in late 2020 and early 2021. We also found that, due to a tight transmission bottleneck, transmission of low-frequency single nucleotide variants between hosts is rare.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Genomics ; Hong Kong/epidemiology ; Humans ; Public Health ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology ; Travel
Language	English
Publishing date	2022-02-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28420-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel

medRxiv

Abstract	In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance.
Keywords	covid19
Language	English
Publishing date	2022-11-27
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.11.22.22282629
Database	COVID19

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