Sequential viral introductions and spread of BA.1 drove the Omicron wave across Pakistani provinces

Raza, Sayed Ali; Ashraf, Javaria; Kanji, Akbar; Rehman, Yusra; Trovão, Nídia Sequeira; Thielen, Peter; Yameen, Maliha; Kanwar, Samiah; Khan, Waqasuddin; Kabir, Furqan; Nisar, Muhammad Imran; Merritt, Brian B.; Hasan, Rumina; Spiro, David; Rasmussen, Zeba; Bashir, Uzma; Hasan, Zahra

doi:10.1101/2023.03.25.23287718

Cited by 1 publication

(1 citation statement)

References 19 publications

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“…Multifarious studies have characterised the initial introduction of SARS-CoV-2 to specific regions (Gonzalez-Reiche et al 2020;Dı ´ez-Fuertes et al 2020;Deng et al 2020;Gámbaro et al 2020;Bedford et al 2020;Moreno et al 2020;Maurano et al 2020;Paiva et al 2020;Komissarov et al 2021;Muenchhoff et al 2021;da Silva Filipe et al 2021;Lobiuc et al 2021;Murall et al 2021;Juscamayta-López et al 2021;Githinji et al 2021;du Plessis et al 2021;Tordoff et al 2021;Mallon et al 2021;Lemieux et al 2021;McBroome et al 2022;Borges et al 2022), or variants of SARS-CoV-2 to regions (Stefanelli et al 2020;Tang et al 2021;Toovey et al 2021;Alpert et al 2021;Elliott et al 2022;Michaelsen et al 2022;Fonager et al 2022;Nasir et al 2022;Bukhari et al 2023). A previous phylogenetic analysis of 225 Irish genomes from two pandemic waves suggested that multiple introductions of SARS-CoV-2 to Ireland from outside had taken place (Mallon et al 2021).…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 introductions to the island of Ireland

Rice

Troendle

Bridgett

et al. 2023

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an unprecedented impact on the people of Ireland as waves of infection spread across the island during the global coronavirus disease 2019 (COVID-19) pandemic. Viral whole-genome sequencing (WGS) has provided insights into SARS-CoV-2 molecular mechanisms of pathogenicity and evolution and contributed to the development of anti-virals and vaccines. High levels of WGS have enabled effective SARS-CoV-2 genomic surveillance on the island of Ireland, leading to the generation of a sizeable data set with potential to provide additional insights into viral epidemiology. Because Ireland is an island, accurate documentation of travel rates to and from other regions, both by air and by sea, are available. Furthermore, the two distinct political jurisdictions on the island allow comparison of the impact of varying public health responses on viral dynamics, including SARS-CoV-2 introduction events. Using phylogenomic analysis incorporating sample collection date and location metadata, we identify multiple introduction and spreading events for all major viral lineages to the island of Ireland during the period studied (March 2020-June 2022). The majority of SARS-CoV-2 introductions originated from England, with frequent introductions from USA and northwestern Europe. The clusters of sequences predicted to derive from discrete introduction events ("introduction clusters") vary greatly in size, with some involving only one or two cases and others comprising thousands of samples. When introduction cluster samples are mapped sequentially by collection date, they appear predominantly in previously affected or adjacent areas. This mirroring of the phylogenetic relationships by the geospatiotemporal propagation of SARS-CoV-2 validates our analytic approach. By downsampling, we estimate the power to detect introductions to Ireland as a function of sequencing levels. Per capita normalisation of both sequencing levels and detected introductions accounts for biases due to differing sequencing efforts and total populations. This approach showed similar rates of introductions for all major lineages into Northern Ireland (NI) and Republic of Ireland (RoI) with the exception of Delta, which was higher in NI which is likely attributable to higher travel per capita. However, there were similar rates of Delta infection within NI and RoI, suggesting that although travel restrictions will reduce risk of introducing novel variants to the region, they may not substantially decrease total incidence. Our generalisable methodology to study introduction dynamics and optimal sequencing levels will assist public health authorities to select the most appropriate control measures and viral sequencing strategy.

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