Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach

Viral metagenomics, also known as virome studies, have yielded an unprecedented number of novel sequences, essential in recognizing and characterizing the etiological agent and the origin of emerging infectious diseases. Several tools and pipelines have been developed, to date, for the identification and assembly of viral genomes. Assembly pipelines often result in viral genomes contaminated with host genetic material, some of which are currently deposited into public databases. In the current report, we present a group of deposited sequences that encompass ribosomal RNA (rRNA) contamination. We highlight the detrimental role of chimeric next generation sequencing reads, between host rRNA sequences and viral sequences, in virus genome assembly and we present the hindrances these reads may pose to current methodologies. We have further developed a refining pipeline, the Zero Waste Algorithm (ZWA) that assists in the assembly of low abundance viral genomes. ZWA performs context-depended trimming of chimeric reads, precisely removing their rRNA moiety. These, otherwise discarded, reads were fed to the assembly pipeline and assisted in the construction of larger and cleaner contigs making a substantial impact on current assembly methodologies. ZWA pipeline may significantly enhance virus genome assembly from low abundance samples and virus metagenomics approaches in which a small number of reads determine genome quality and integrity.

For years now the study of viruses and their genetic composition has been important in their identification and classification. Especially in these times of the pandemic turmoil, accurate knowledge of a virus’ exact genetic composition can help identify its strengths and weaknesses allowing us to track its evolution and assist in the development of vaccines and antiviral agents. The reconstruction of these genomic sequences is called the assembly process, a bioinformatics approach which can be complicated and full of pitfalls. This work identifies one such issue, concerning artifacts introduced in viral genomes from the new technologies of nucleic acid sequencing. The proposed algorithm helps alleviate this problem by tentatively removing these problematic regions while keeping the vast majority of the genetic information required to produce a more complete viral genome. This work is anticipated to assist in the submission of higher integrity and accuracy viral genomes in public databases used for novel virus identification and characterization.

A Second Genome Sequence of an Enterovirus C99 Detected in a Healthy Chimpanzee

We report the nearly complete genome sequence of an enterovirus 99 strain (Cpz-IJC08) detected in a healthy chimpanzee from the Tchimpounga Sanctuary, Republic of Congo. According to the phylogeny, Cpz-IJC08 clustered with Cpz-IJC04, a previously identified chimpanzee enterovirus from the same sanctuary, isolated in animals with signs of acute flaccid paralysis.

We report the nearly complete genome sequence of an enterovirus 99 strain (Cpz-IJC08) detected in a healthy chimpanzee from the Tchimpounga Sanctuary in the Republic of Congo. According to the phylogeny, Cpz-IJC08 clustered with Cpz-IJC04, a previously identified chimpanzee enterovirus from the same sanctuary, isolated from an animal with signs of acute flaccid paralysis.

Complete Genome Sequences of Igbo-Ora and Babanki Alphavirus Strains Isolated in the Central African Republic in the 1960s and 1970s

Vector-borne viruses are becoming increasingly important from a public health standpoint with the emergence or reemergence of viruses and extension of the areas at risk. Here, we report the whole-genome sequences of two alphaviruses, namely, one Igbo-Ora virus and one Babanki virus, that were isolated several decades ago in Africa from human serum.

Vector-borne viruses are becoming increasingly important from a public health standpoint with the emergence or reemergence of viruses and extension of the areas at risk. Here, we report the whole-genome sequences of two alphaviruses, namely, one Igbo-Ora virus and one Babanki virus, that were isolated several decades ago in Africa from human serum.

Complete Genome Sequence of an Equine Arteritis Virus Strain Isolated from a Lipizzaner Stallion in 2015 in Serbia

Here, we report the first whole-genome sequence of an equine arteritis virus (EAV) strain, RS1, isolated from the semen of a Lipizzaner stallion held in the Vojvodina region of Serbia.

Here, we report the first whole-genome sequence of an equine arteritis virus (EAV) strain, RS1, isolated from the semen of a Lipizzaner stallion held in the Vojvodina region of Serbia.

Complete Genome Sequence of the Tataguine Virus, Isolated in the Central African Republic in 1972 from a Human with an Acute Febrile Syndrome

Tataguine virus (TATV) is an orthobunyavirus that causes febrile illnesses in Africa. Here, we report the complete genome sequences of TATV strain HB72P583, isolated in the Central African Republic in 1972.

Tataguine virus (TATV) is an orthobunyavirus that causes febrile illnesses in Africa. Here, we report the complete genome sequences of TATV strain HB72P583, isolated in the Central African Republic in 1972. Several genetic variations were detected in the small (S), medium (M), and large (L) segments relative to a TATV strain isolated in Nigeria in 1966.

Complete Genome Sequences of Two Chikungunya Viruses Isolated in the Central African Republic in the 1970s and 1980s

Some arboviruses threaten human global health with potentially explosive emergence. Analysis of whole-genome sequences of decades-old isolates might contribute to the understanding of the complex dynamics which drive their circulation and emergence. Here, we report the whole-genome sequences of two Chikungunya viruses isolated in the Central African Republic in the 1970s and 1980s.