Genomic epidemiology and phylogeographic dynamics of SARS-CoV-2 during the sixth wave and post-sixth wave in Pakistan

Abstract

Background: We aim to fill a genomic surveillance gap by exploring the diversity of SARS-CoV-2 during the sixth wave (June–September 2022) and the post-sixth wave period (since October 2022) in Pakistan. Materials and methods: We sequenced 1398 samples (Ct <30) using Illumina COVIDSeq assay and analyzed them using CDC USA guidelines and Nextstrain. Results: The predominant variant during the sixth wave was BA.5.2 (62.43%), impacting Islamabad and Karachi. Post-sixth wave, a resurgence occurred from January 2023 to May 2023, driven by XBB.1.9.1 (16.13%), XBB.1.19.1 (15.62%) and XBB.1.5 (8.49%), with either Islamabad or Karachi, estimated as initial transmission point. Conclusion: The study highlights the link between phylogeography, regional case surges, impact of relaxed policies and vaccination efforts, providing vital insights for future strategies.

Plain language summary

This study looks at the different types of the COVID-19 virus that were spreading in Pakistan during an outbreak between June and September 2022 and the period after that from October 2022 onwards. During this sixth wave of infection, a version of the virus called BA.5.2 was the most common. This variant likely caused more COVID-19 cases, mostly in the cities of Islamabad and Karachi between June and July 2022. After the sixth wave, from November 2022 to March 2023, there was another rise in COVID-19 cases. This increase was mainly caused by new versions of the virus, such as XBB.1.9.1, XBB.1.19.1 and XBB.1.5. We think that Islamabad or Karachi may be where these new variants started spreading. This study shows a link between the genetics of the COVID-19 virus, the rise in cases in different regions of Pakistan and the effect of policies and vaccination. It gives valuable information to help plan better ways to deal with the changing COVID-19 situation.

Article highlights

Background & rationale

• As the COVID-19 pandemic enters its fourth year, new challenges arise from different SARS-CoV-2 variants, especially the rising threat of Omicron XBB variants.

• This study aims to fill the genomic surveillance gap by exploring SARS-CoV-2 diversity during the sixth wave (June–September 2022) and post-sixth wave period (since October 2022) in Pakistan.

Materials & methods

• Around 1398 samples (Ct<30) were successfully sequenced using the Illumina COVIDSeq assay from 1500 collected nasopharyngeal/oropharyngeal swabs.

• Data analysis followed CDC USA guidelines, and phylogeographic analysis utilized Nextstrain.

Results

Sixth-wave dynamics

• The predominant variant during the Sixth wave was BA.5.2 (62.43%, n = 901). Phylogeographic analysis suggested the marked effect of the BA.5.2 variant on increased case numbers and positivity rates, particularly in Islamabad and Karachi, with a noticeable rise between June and July 2022.

Post-sixth wave resurgence

• During post-sixth wave, a resurgence occurred from January to May 2023, driven by XBB.1.9.1 (16.13%), XBB.1.19.1 (15.62%) and XBB.1.5 (8.49%).

• Either Islamabad or Karachi was estimated as the initial transmission point for these variants.

Conclusion & implication

• The study highlights the link between phylogeography, regional case surges, relaxed policies and vaccination efforts, providing vital insights.

• It guides future strategies amid rapid evolution and XBB variant prevalence, emphasizing continuous genomic surveillance.

Keywords: :

• Epidemiological waves
• Genomic surveillance
• NGS
• Omicron XBB variants
• Pakistan
• phylogeographical analysis
• post sixth wave
• public health response
• sixth wave

Author contributions

Conceptualization: M Umair, M Salman and A Ikram; methodology: SA Haider, Z Jamal and M Ammar; formal analysis: Z Jamal, SA Haider and Z Rehman; resources: M Umair, M Salman, and A Ikram; writing—original draft preparation: Z Jamal and SA Haider; writing—review and editing: Z Jamal, SA Haider and M Umair. Z Jamal and SA Haider have contributed equally as first authors. All authors have read and agreed to the published version of the manuscript.

Financial disclosure

This study was partially funded by the ‘Enhanced Sequencing Support – SARS-CoV-2 Pakistan’ project of the Bill & Melinda Gates Foundation (BMGF) and the SARS-CoV-2 Genomic Sequencing Grant provided by the AHF Global Public Health Institute at the University of Miami. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Competing interests disclosure

The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Writing disclosure

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

This study was approved by the Internal Review Board of the National Institute of Health (NIH), Islamabad, under the approval code PHLD/VIR/COVID-19/2022. For investigations involving human subjects, informed written consent has been obtained from the participants involved and an explanation of how this was obtained is included in the manuscript.

Additional information

Funding

This study was partially funded by the ‘Enhanced Sequencing Support – SARS-CoV-2 Pakistan’ project of the Bill & Melinda Gates Foundation (BMGF) and the SARS-CoV-2 Genomic Sequencing Grant provided by the AHF Global Public Health Institute at the University of Miami.