COVID-19 vaccine coverage and the necessity of its urgent development towards Omicron the new SARS CoV-2 B.1.1. 529 variant

A SARS-CoV-2 variant belonging to Pango lineage B.1.1.529 with a significant number of S-gene mutations compared to the original virus was found in early November 2021. On 26th November 2021, the World Health Organization (WHO) designated the mutation as a variant of concern and assigned it the name Omicron. The difference is identified by 30 changes in the spike protein, three minor deletions, and one minor insertion, 15 of which are in the receptor-binding area. The Omicron variant is the most diverging variety discovered in substantial numbers so far during the pandemic, raising significant concerns that it may be associated with significant reductions in vaccination efficacy and an increased risk of reinfections. Omicron pseudo- or live virus isolates are urgently needed to understand better the virus's escape potential against both vaccination, and infection-acquired immunity is urgently required.

Molecular Epidemiology of Rabies in Wild Canidae in Tunisia

Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.

MOLECULAR-GENETIC CHARACTERIZATION OF PARAINFLUENZA-3 VIRUS ISOLATES

This study reports on the molecular-genetic characterization of a field strain of BPIV-3 isolated in the Republic of Tatarstan. M gene fragments of the Russian isolate LD-9 and the vaccine strain PTK/86 were sequenced and aligned with the corresponding sequences of the virus strains presented in GenBank. The results of the phylogenetic analysis showed that the Russian isolate LD-9 (MW52481) and the vaccine strain PTK45/86 belong to the genotype A of the parainfluenza virus-3, as well as the reference strain SF-4. The Russian isolate LD-9 showed 98.3 % similarity with the reference strain SF-4, and the Russian vaccine strain PTK-45/86 was 100 % identical to the reference strain.

Genetic analysis of nucleotide sequences of neuraminidase gene of highly pathogenic avian influenza A/H5N8 virus isolates recovered in the Russian Federation in 2020

Avian influenza is a highly dangerous viral disease that causes huge economic damage to poultry farming. Currently, highly virulent influenza virus with N8 neur- aminidase subtype is quite often detected in populations of domestic and wild birds in various countries of the world. The article provides data on complete nucleotide sequences of the neuraminidase gene of highly pathogenic avian influenza virus isolates recovered in the second half of 2020 from pathological material received from four regions of the Russian Federation. The conducted research showed that the subtype of the isolated virus was N8. According to the phylogenetic analysis, isolates of N8 virus belong to group 8C.4. During the phylogenetic analysis of the neuraminidase, we also took into account data on hemagglutinin classification, according to which H5N8 virus isolates belong to a widespread clade 2.3.4.4. Viruses of the clade were first registered in 2010 in China and they have been circulating up to now. The paper also provides data of a comparative analysis of nucleotide sequences of the studied isolates and the isolates from the international GenBank and GISAID databases, recovered in other countries from 2007 to 2020. During the analysis of the amino acid sequence of the studied isolates, no substitutions were found in the positions that affect resistance to neuraminidase inhibitors. The complete nucleotide sequences of the neuraminidase gene of the avian influenza virus subtype N8 (isolates A/domestic goose/OMSK/1521-1/2020, A/duck/Chelyabinsk/1207-1/2020, A/duck/Saratov/1578-2/2020, A/goose/Tatarstan/1730-2/2020) are published in the international GenBank and GISAID databases. Based on the analysis of the nucleotide sequences of the studied isolates, the article shows gradual evolution of the N8 subtype virus.

Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan

Introduction: The first case of severe acute respiratory syndrome 2 (SARS-CoV-2) was imported to Pakistan in February 2020, since then 8,260 deaths have been witnessed. The virus has been constantly mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS-CoV-2 have been defined globally. In this study, the epidemiology of SARS-CoV-2 was studied and locally transmitted SARS-CoV-2 isolates from Karachi were sequenced to compared and identify any possible variants. Methodology: The real time PCR was performed on nasopharyngeal specimen to confirm SARS-CoV-2 with Orf 1ab and E gene as targets. The virus isolates were sequenced through oxford nanopore technology MinION platform. Isolates from the first and second wave of COVID-19 outbreak in Karachi were compared. Results: The overall positivity rate for PCR was 26.24% with the highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from the second wave of COVID-19. Conclusions: Based on the present findings it is suggested that the locally transmitted virus from Karachi varies from those reported from other parts of Pakistan. Slight variability was also observed between viruses from the first and second wave. Variability in any potential vaccine target may result in failed trials, therefore information on any local viral variants is always useful for effective vaccine design and/or selection.