Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021

Abstract Background Indonesia has started the big project of COVID-19 vaccination program since 13 January 2021 by employing the first shot of vaccine to the President of Indonesia as the outbreak and rapid transmission of COVID-19 have endangered not only Indonesian but the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as of 12 January 2021. Results All data of the isolates were extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver platform was employed to investigate the full-length genome mutation analysis of all isolates. This study also focused on the phylogeny analysis in unlocking the mutation of S protein in Indonesian SARS-CoV-2 isolates. WIV04 isolate that was originated from Wuhan, China was used as the virus reference according to the CoVsurver default. The result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully generated. Every single mutation in S protein was described and then visualized by utilizing BioRender platform. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates. Conclusions To sum up, this study helped to observe the spread of COVID-19 transmission. However, it also proposed that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia.

Download Full-text

An Updated Investigation Prior To COVID-19 Vaccination Program In Indonesia: Full-Length Genome Mutation Analysis Of SARS-CoV-2

10.1101/2021.01.26.426655 ◽

2021 ◽

Author(s):

Reviany V. Nidom ◽

Setyarina Indrasari ◽

Irine Normalina ◽

Astria N. Nidom ◽

Balqis Afifah ◽

...

Keyword(s):

Global Health ◽

Mutation Analysis ◽

Full Length ◽

Vaccination Program ◽

Epidemiological Surveillance ◽

Single Mutation ◽

S Protein ◽

Rapid Transmission ◽

Global Initiative ◽

Full Length Genome

ABSTRACTIntroductionIndonesia kick-started the big project of COVID-19 vaccination program in January 2021 by employed vaccine to the president of Indonesia. The outbreak and rapid transmission of COVID-19 have endangered the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as 12 January 2021.MethodsAll data of isolates was extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver was employed to investigate the full-length genome mutation analysis of all isolates. Furthermore, this study also focused on the unlocking of mutation in Indonesian SARS-CoV-2 isolates S protein. WIV04 isolate that was originated from Wuhan, China was used as a virus reference according to CoVsurver default. All data was visualized using GraphPad Prism software, PyMOL, and BioRender.ResultsThis study result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully discovered. Every single mutation in S protein was described and then visualised by employing BioRender. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates.ConclusionTo sum up, this study helps to observe the spread of the COVID-19 transmission. However, it would like to propose that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia.

Download Full-text

Role of Small Envelope Protein in Sustaining the Intracellular and Extracellular Levels of Hepatitis B Virus Large and Middle Envelope Proteins

Viruses ◽

10.3390/v13040613 ◽

2021 ◽

Vol 13 (4) ◽

pp. 613

Author(s):

Jing Zhang ◽

Yongxiang Wang ◽

Shuwen Fu ◽

Quan Yuan ◽

Qianru Wang ◽

...

Keyword(s):

Envelope Proteins ◽

Full Length ◽

M Protein ◽

Intracellular Level ◽

S Protein ◽

L Protein ◽

M Proteins ◽

B Virus ◽

Subviral Particle ◽

Genotype A

Hepatitis B virus (HBV) expresses co-terminal large (L), middle (M), and small (S) envelope proteins. S protein drives virion and subviral particle secretion, whereas L protein inhibits subviral particle secretion but coordinates virion morphogenesis. We previously found that preventing S protein expression from a subgenomic construct eliminated M protein. The present study further examined impact of S protein on L and M proteins. Mutations were introduced to subgenomic construct of genotype A or 1.1mer replication construct of genotype A or D, and viral proteins were analyzed from transfected Huh7 cells. Mutating S gene ATG to prevent expression of full-length S protein eliminated M protein, reduced intracellular level of L protein despite its blocked secretion, and generated a truncated S protein through translation initiation from a downstream ATG. Truncated S protein was secretion deficient and could inhibit secretion of L, M, S proteins from wild-type constructs. Providing full-length S protein in trans rescued L protein secretion and increased its intracellular level from mutants of lost S gene ATG. Lost core protein expression reduced all the three envelope proteins. In conclusion, full-length S protein could sustain intracellular and extracellular L and M proteins, while truncated S protein could block subviral particle secretion.

Download Full-text

Full-length genome characterization of a novel alphapartitivirus detected in the ectomycorrhizal fungus Hygrophorus penarioides

Virus Genes ◽

10.1007/s11262-020-01814-9 ◽

2021 ◽

Author(s):

Ergin Sahin ◽

Ilgaz Akata

Keyword(s):

Ectomycorrhizal Fungus ◽

Full Length ◽

Genome Characterization ◽

Full Length Genome

Download Full-text

Next Generation Sequencing of Near-Full Length Genome of Norovirus GII.4 from Botswana

Virus Research ◽

10.1016/j.virusres.2021.198491 ◽

2021 ◽

pp. 198491

Author(s):

Kgomotso Makhaola ◽

Sikhulile Moyo ◽

Lemme P. Kebaabetswe

Keyword(s):

Next Generation Sequencing ◽

Full Length ◽

Next Generation ◽

Norovirus Gii ◽

Full Length Genome ◽

Generation Sequencing

Download Full-text

Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

Viruses ◽

10.3390/v13081556 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1556

Author(s):

Monika J. Hjortaas ◽

Elena Fringuelli ◽

Adérito L. Monjane ◽

Aase B. Mikalsen ◽

Christine M. Jonassen ◽

...

Keyword(s):

Full Length ◽

Genomic Diversity ◽

Last Common Ancestor ◽

Source Of Infection ◽

New Variant ◽

Genotype 2 ◽

Boat Traffic ◽

Horizontal Spread ◽

Full Length Genome

Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.

Download Full-text