Genomic analysis reveals a new dominant lineage of SARS-CoV-2

Scientists and health officials around the world are raising concerns about the emergence and spread of more COVID variants, subverts and third-generation subverts with alarming mutations, associated with fusogenicity, disease severity and death. Infection and contagiousness have also increased in these new BA.2 subverters and third generation subverts.

With a population of 8.8 million (87% of whom live in rural areas), Papua New Guinea (PNG) experienced the first wave of COVID-19 in April 2020, which was quickly controlled by August 2020. Towards the end of July, however, the country saw an increase in cases, resulting in a second wave of SARS-CoV-2 infections, with about 177,774 confirmed cases.

By October 2021, the total number of cases had skyrocketed. SARS-CoV-2 infection testing, epidemiological investigations, and disease surveillance across the country have been hampered by logical limitations that affect the implementation of public health measures to control the spread of the disease.

A PANGO strain of SARS-CoV-2 was designated as a form of concern (VOC) by local or international organizations after receiving relevant pathological, immunological, and epidemiological information. The World Health Organization (WHO) has classified four SARS-CoV-2 strains as VOCs, indicating that they contain unusually high numbers of mutations leading to immune dysfunction and significant infectivity.

Genomic surveillance is now considered a requirement for controlling and managing epidemics by detecting and identifying new emerging varieties, outbreaks, and disease infections, allowing appropriate public health measures to prevent the spread of the disease.

In a recent study published in the Journal of Virus Evolution, researchers identified the SARS-CoV-2 lineage that spread to Papua New Guinea during the second wave of Covid-19, explained the region’s unique genomic dataset, and investigated rapid growth. Mis-defined but widespread lineage of SARS-CoV-2 in the western Pacific.

A regular genomic system of SARS-CoV-2 from PNG was created for this purpose. Sequences from SARS-CoV-2 infected individuals underwent phylogenetic and phylogenomic analysis.

In total, 1,797 SARS-CoV-2 positive samples passed the Internal Quality Control (QC) procedure and 1,672 samples were successfully linked to PNG NCC and Ok Tedi Mining Limited (OTML) epidemiological databases.

The recruitment of three closely related clans – AU / B.1.466 / B.1.459 – 1,797 PNG specimens of the Pango clan was extremely volatile. Regardless of sequencing quality or genome coverage, samples often had to be redistributed within these groups.

Eighty-eight percent of the PNG sequences found in Southeast Asia and the Pacific belong to the closely related B.1.459, B.1.466.2, AU.1, or AU.3 lineages. In addition, 5 percent of the sequences belong to the B.6 / B.6.B lineage, while 2.4 percent of the sequences belong to the B or B.1 lineage. So far, VOC (Delta-B.1.617.2) has been found in only one sample.

Among the clusters, phylogenetic analysis has classified B.1, B.1.466.2, B.1.459, and AU lineage, as well as closely related specimens, as Pango lineage. At the beginning of 2021, an analysis of the temporal distribution indicates a shift from B.6.8 / B.6 lineage to B.1 and B.1.459 / B.1.466.2 / AU lineage. No other genera were found in the 2020 samples.

Clusters are found to be geographically diverse, with each cluster centering on a specific PNG region. The largest cluster, ‘Cluster 2,’ was bounded by the Western Province and OTML mines, while the smaller clusters were attached to or spread over New Britain’s islands, the National Capital District, and the larger neighboring provinces. From the hill provinces.

According to available genomic data, 55 cases were introduced in PNG, of which only three consisted of a single case where there was no indication of infection. Importantly, import clusters were shown to be compatible with broad genomic clusters. Twenty-four imported genomic clusters have been discovered there, each containing at least five sequences (the largest containing 926 sequences).

Between July 2020 and March 2021, the first imported genomic clusters with a minimum of five genomes were discovered. Between February 2020 and March 2021, it was predicted that imported genome clusters with at least five genomes would be launched. Most of the imports were estimated to have occurred in March 2021.

B.1.459, B.1.466.2.3 (AU.3), and B.1.466.2.1 (AU.1) of the PANGO lineage are responsible for 90 percent of the genome cluster with 256, 198, and 387 genomes, respectively.

The application of an integrated structure for the four major import genomic clusters indicates a similar integrated growth rate between the clusters – with evidence of epidemic spread across all clusters. Genomic import clusters overlapped twice, the largest cluster (Cluster A) doubled in nine days and the smallest cluster doubled in eight days (Cluster B).

Cluster A had the highest sampling intensity, with sampling intensity less than 0.02 and uncertainty (0.011). These hypotheses show that the genomic sample is a small fraction of each import cluster.

Multiple fancy acquaintances have been discovered, as well as B.1.466.2 in Papua New Guinea and the rapid spread of related lineages. Furthermore, the data highlighted issues that could lead to erratic lineage assignments when using genomics to quickly define clusters.

Image Credit: Getty

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