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Genomic Analysis Reveals a New Dominant Lineage of SARS-CoV-2

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Kamal Saini
Kamal S. has been Journalist and Writer for Business, Hardware and Gadgets at Revyuh.com since 2018. He deals with B2b, Funding, Blockchain, Law, IT security, privacy, surveillance, digital self-defense and network policy. As part of his studies of political science, sociology and law, he researched the impact of technology on human coexistence. Email: kamal (at) revyuh (dot) com

Scientists and health officials throughout the world are raising the alarm about the emergence and spread of more COVID variants, subvariants and third generation subvariants with the worrying mutations, which have been linked to increased fusogenicity, illness severity, and death. Infectivity and transmissibility have also grown in these new BA.2 subvariants and third generation subvariants.

With a population of 8.8 million people (87 percent of whom live in rural regions), Papua New Guinea (PNG) experienced the first wave of COVID-19 in April 2020, which was quickly controlled by August 2020. However, by the end of July, the country had seen an increase in cases, resulting in the second wave of SARS-CoV-2 infection, with roughly 177,774 confirmed cases.

By October 2021, the total number of cases had skyrocketed. Testing for SARS-CoV-2 infection, epidemiological investigations, and disease surveillance throughout the country were hampered due to logistical constraints, affecting the implementation of public health measures to control the illness’s spread.

A PANGO lineage of SARS-CoV-2 was designated as a variant of concern (VOC) by local or international bodies after appropriate pathological, immunological, and epidemiological data. The World Health Organization (WHO) has classed four SARS-CoV-2 lineages as VOC, indicating that they contain an unusually high number of mutations that result in immune evasion and significant transmissibility.

Genomic surveillance has now been deemed a requirement for controlling and managing the pandemic by detecting and identifying novel emerging variations, outbreaks, and disease transmission, allowing for appropriate public health actions to restrict disease spread.

In a recent study, published in the journal Virus Evolution, the researchers characterized the SARS-CoV-2 lineages spreading in Papua New Guinea during the second wave of COVID-19, explained the region’s unique genomic dataset, and investigated the rapid rise of an ill-defined but widespread lineage of SARS-CoV-2 in the Western Pacific region.

A regular genomic system of SARS-CoV-2 from PNG was built for this work. The sequences generated from SARS-CoV-2 infected individuals were subjected to phylogenetic and phylogenomic analysis.

In total, 1,797 SARS-CoV-2 positive samples passed internal quality control (QC) methods, and 1,672 samples were successfully connected to PNG NCC and Ok Tedi Mining Limited (OTML) epidemiological databases.

With continuous shifts between three closely related lineages – AU/B.1.466/B.1.459 – PANGO lineage assignment of 1,797 PNG samples was very unstable. Regardless of sequencing quality or genome coverage, samples had to be reassigned often between these groups.

88 percent of the PNG sequences belonged to the closely related B.1.459, B.1.466.2, AU.1, or AU.3 lineages found in Southeast Asia and the Pacific. Moreover, 5 percent of the sequences belonged to the B.6/B.6.B lineage, whereas 2.4 percent of the sequences belonged to the B or B.1 lineages. In the meantime, only one sample was found to contain a VOC (Delta- B.1.617.2).

Within the clusters, phylogenetic analysis revealed an intermingling of B.1, B.1.466.2, B.1.459, and AU lineages, as well as closely related samples classified as PANGO lineages. Early in 2021, an analysis of the temporal distribution indicated a shift from B.6.8/B.6 lineages to B.1 and B.1.459/B.1.466.2/AU lineages. Other lineages were not found in the 2020 samples.

The clusters were found to be geographically diverse, with each cluster centered on a certain PNG region. The largest cluster, ‘Cluster 2,’ was tied to the Western Province and the OTML mines, while the lesser clusters were linked to the island of New Britain, the National Capital District, and the bigger surrounding provinces, or a spread to New Britain from the highland provinces.

According to the available genomic data, 55 occurrences were introduced into PNG, with only three of them consisting of a single case with no indication of transmission. Importantly, the importation clusters were shown to be consistent with the wide genomic clusters. There were twenty-four importation genomic clusters discovered, each with at least five sequences (the largest having 926 sequences).

Between July 2020 and March 2021, the first imported genomic cluster with a minimum of five genomes was discovered. Between February 2020 and March 2021, it was predicted that imported genome clusters with at least five genomes will be launched. The majority of importation incidents were anticipated to have occurred during March 2021.

PANGO lineages B.1.459, B.1.466.2.3 (AU.3), and B.1.466.2.1 (AU.1) accounted for 90 percent of the genome clusters, with 256, 198, and 387 genomes, respectively.

The application of a coalescent framework for the four major importation genomic clusters indicated a similar coalescent growth rate among clusters — with evidence of epidemic expansion in all clusters. The doubling times of the genomic importation clusters overlapped, with the largest cluster (Cluster A) doubling in nine days and the smallest cluster doubling in eight days (cluster B).

Cluster A had the maximum sampling intensity, with a sampling intensity of less than 0.02 and uncertainty (0.011). These estimates show that the genomic sampling is only a small part of each importation cluster.

Multiple novel introductions were discovered, as well as a rapid spread of B.1.466.2 and associated lineages in Papua New Guinea. Furthermore, the data highlighted the issues that unstable lineage assignments might bring when using genomics to define fast clusters.

Image Credit: Getty

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