Genome characterization based on the Spike-614 and NS8-84 loci of SARS-CoV-2 reveals two major possible onsets of the COVID-19 pandemic.

The global COVID-19 pandemic has lasted for 3 years since its outbreak, however its origin is still unknown. Here, we analyzed the genotypes of 3.14 million SARS-CoV-2 genomes based on the amino acid 614 of the Spike (S) and the amino acid 84 of NS8 (nonstructural protein 8), and identified 16 linkage haplotypes. The GL haplotype (S_614G and NS8_84L) was the major haplotype driving the global pandemic and accounted for 99.2% of the sequenced genomes, while the DL haplotype (S_614D and NS8_84L) caused the pandemic in China in the spring of 2020 and accounted for approximately 60% of the genomes in China and 0.45% of the global genomes. The GS (S_614G and NS8_84S), DS (S_614D and NS8_84S), and NS (S_614N and NS8_84S) haplotypes accounted for 0.26%, 0.06%, and 0.0067% of the genomes, respectively. The main evolutionary trajectory of SARS-CoV-2 is DS→DL→GL, whereas the other haplotypes are minor byproducts in the evolution. Surprisingly, the newest haplotype GL had the oldest time of most recent common ancestor (tMRCA), which was May 1 2019 by mean, while the oldest haplotype DS had the newest tMRCA with a mean of October 17, indicating that the ancestral strains that gave birth to GL had been extinct and replaced by the more adapted newcomer at the place of its origin, just like the sequential rise and fall of the delta and omicron variants. However, the haplotype DL arrived and evolved into toxic strains and ignited a pandemic in China where the GL strains had not arrived in by the end of 2019. The GL strains had spread all over the world before they were discovered, and ignited the global pandemic, which had not been noticed until the virus was declared in China. However, the GL haplotype had little influence in China during the early phase of the pandemic due to its late arrival as well as the strict transmission controls in China. Therefore, we propose two major onsets of the COVID-19 pandemic, one was mainly driven by the haplotype DL in China, the other was driven by the haplotype GL globally.

Characterization of the chloroplast genome of Chlorolobion braunii ITBB-AG6 isolated from a treatment pond of sanitary sewage.

Sphaeropleales is an order of fast-growing microalgae with high oil content and high efficiency in sewage treatment, in which photosynthesis plays a critical role. We isolated a strain of Sphaeropleales, Chlorolobion braunii ITBB-AG6 from an azolla community in a sewage pond, and sequenced its chloroplast genome. The complete genome has a length of 154 kb with a GC content of 31.7%. A total of 89 genes were annotated, including 56 protein-coding genes, 30 tRNA genes, and three rRNA genes. Out of the protein coding genes, 64.3% are involved in photosynthesis, 28.6% are involved in protein synthesis, and 7.1% are involved in ATP synthesis. Transfer RNA genes for 20 amino acids were identified, in which tRNA genes for methionine, leucine, and arginine are tripled, whereas tRNA genes for glutamic acid, glycine, serine, and threonine are doubled. Terminal inverted repeats of 27.9 kb containing 10 genes related to photosynthesis and chloroplast division are present in the genome, suggesting that photosynthesis was strengthened in the evolutionary history. Phylogenetic analysis indicates that C. braunii ITBB-AG6 falls in the family Selenastraceae and is most closely related to Monoraphidium neglectum.

The mitochondrial genome of the endophyte Edenia gomezpompae CRI Eg3 isolated from sweet potato.

Edenia gomezpompae CRI Eg3 was isolated from the leaves of sweet potato. Its complete mitogenome contains 37,226 bp, with a G + C content of 26.1%. A total of 51 genes were annotated, including 16 protein-coding genes, 33 tRNA genes, and 2 rRNA (s-rRNA, L-rRNA) genes. The most significant character of this mitogenome is its free of group I introns in the CDS regions. Phylogenetic analysis using the mitogenomes of relative fungal species indicated that CRI Eg3 is closely related to Shiraia bambusicola, and they clustered in the Pleosporales lineage. This is the first genome reported in the genus Edenia.

The chloroplast genome of a unicellular green alga strain isolated from the rubber processing wastewater.

Chlorella vulgaris ITBBA3-12 has a role in the purification of the rubber processing wastewater. Its complete chloroplast genome contains 168369 bp, with a G + C content of 33.0%. A total of 147 genes were annotated, including 113 protein-coding genes, three rRNA (rrn23, rrn16, and rrn5) genes, and 31 tRNA genes. The significant feature of the chloroplast genome is that the genes encoding subunit V (petG), VI (petL), and apocytochrome f (petA) of the cytochrome b6/f complex are in triplicate, which was not observed in the other C. vulgaris strains. Phylogenetic analysis using the chloroplast genomes of Chlorophyta species indicated that ITBBA3-12 is closely related to C. vulgaris strain UTEX259 and NJ-7, and they clustered in the Chlorella lineage.