First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia

Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19-positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest-Omicron recombinant "Kraken" (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5'-untranslated region (5'UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide.

Complete Genomic Characterisation and Mutation Patterns of Iraqi SARS-CoV-2 Isolates

This study was performed for molecular characterisation of the SARS-CoV-2 strains in Iraq and reveal their variants, lineages, clades, and mutation patterns. A total of 912 Iraqi sequences were retrieved from GISAID, which had been submitted from the beginning of the SARS-CoV-2 pandemic to 26 September 2022, along with 12 samples that were collected during the third and fifth waves of the SARS-CoV-2 pandemic. Next-generation sequencing was performed using an Illumina MiSeq system, and phylogenetic analysis was performed for all the Iraqi sequences retrieved from GISAID. Three established global platforms GISAID, Nextstrain, and PANGO were used for the classification of isolates into distinct clades, variants, and lineages. Analysis of the isolates of this study showed that all the sequences from the third wave were clustered in the GK clades and the 21J (Delta) clade according to the GISAID and Nextclade systems, while the PANGO system revealed that six sequences were B.1.617.2 and four sequences were of the AY.33 lineage. Furthermore, the latest e wave in the summer of 2022 was due to thpredominance of the BA.5.2 lineage of the 22B (Omicron) clade in Iraq. Our study revealed patterns of circulation and dominance of SARS-CoV-2 clades and their lineages in the subsequent pandemic waves in the country.

Risk and severity of SARS-CoV-2 reinfections during 2020–2022 in Vojvodina, Serbia: A population-level observational study

Background

Data on the rate and severity of SARS-CoV-2 reinfections in real-world settings are scarce and the effects of vaccine boosters on reinfection risk are unknown.

Methods

In a population-level observational study, registered SARS-CoV-2 laboratory-confirmed Vojvodina residents, between March 6, 2020 and October 31, 2021, were followed for reinfection ≥90 days after primary infection. Data were censored at the end of follow-up (January 31, 2022) or death. The reinfection risk was visualized with Kaplan-Meier plots. To examine the protective effect of vaccination, the subset of individuals with primary infection in 2020 (March 6–December 31) were matched (1:2) with controls without reinfection.

Findings

Until January 31, 2022, 13,792 reinfections were recorded among 251,104 COVID-19 primary infections (5.49%). Most reinfections (86.77%, 11,967/13,792) were recorded in January 2022. Reinfections were mostly mild (99.17%, 13,678/13,792). Hospitalizations were uncommon [1.08% (149/13,792) vs. 3.66% (505/13,792) in primary infection] and COVID-19 deaths were very rare (20/13,792, case fatality rate 0.15%). The overall incidence rate of reinfections was 5.99 (95% CI 5.89–6.09) per 1000 person-months. The reinfection risk was estimated as 0.76% at six months, 1.36% at nine months, 4.96% at 12 months, 16.68% at 15 months, and 18.86% at 18 months. Unvaccinated (OR=1.23; 95%CI=1.14–1.33), incompletely (OR=1.33; 95%CI=1.08–1.64) or completely vaccinated (OR=1.50; 95%CI=1.37–1.63), were modestly more likely to be reinfected compared with recipients of a third (booster) vaccine dose.

Interpretation

SARS-CoV-2 reinfections were uncommon until the end of 2021 but became common with the advent of Omicron. Very few reinfections were severe. Boosters may modestly reduce reinfection risk.

Funding

No specific funding was obtained for this study.

Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq

Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning of the fourth pandemic wave. The samples were sequenced using Illumina Miseq system, and the reference sequences were retrieved from GISAID database. Phylogenetic analysis was performed through Mega software. This study provides an initial sequence analysis and molecular characterization of the first Omicron variant cases recorded in the country. Our analysis revealed many mutations on the spike glycoprotein, especially on the receptor binding domain, with potential impact on immune escape and infectivity. The study findings suggest considering the highly mutated immunogenic epitope of the Omicron variant as a reference for developing a new vaccine for combating the ongoing pandemic.