Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021

Abstract

The outbreak of coronavirus disease 2019 (COVID-19), by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly developed into a worldwide pandemic. Mutations in the SARS-CoV-2 genome may affect various aspects of the disease including fatality ratio. In this study, 553,518 SARS-CoV-2 genome sequences isolated from patients from continents for the period 1 December 2020 to 15 March 2021 were comprehensively analyzed and a total of 82 mutations were identified concerning the reference sequence. In addition, associations between the mutations and the case fatality ratio (CFR), cases per million and deaths per million, were examined. The mutations having the highest frequencies among different continents were Spike_D614G and NSP12_P323L. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed a positive correlation to CFR. While the NSP13_Y541C, NSP3_T73I and NSP3_Q180H mutations demonstrated a negative correlation to CFR. The Spike_D614G and NSP12_P323L mutations showed a positive correlation to deaths per million. The NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to deaths per million. The NSP12_P323L and Spike_D614G mutations showed a positive correlation to the number of cases per million. In contrast, NS8_L84S and NSP12_A97V mutations showed a negative correlation to the number of cases per million. In addition, among the identified clades, none showed a significant correlation to CFR. The G, GR, GV, S clades showed a significant positive correlation to deaths per million. The GR and S clades showed a positive correlation to number of cases per million. The clades having the highest frequencies among continents were G, followed by GH and GR. These findings should be taken into consideration during epidemiological surveys of the virus and vaccine development.

Selective Pressure and Evolution of SARS-CoV-2 Lineages BF.7 and BQ.1.1 Circulating in Italy from July to December 2022

“…As regards the data on nsp3, the Q180H and N1329D mutations were identified at a low frequency (2.59%) in Italian genomes of the BF.7 lineage. In particular, literature data showed that the frequency of the Q180H mutation ranged from 0.05% to 1.18% in SARS-CoV-2 genomes collected in Africa, Asia, Australia, Europe, North America, and South America [31,32]. The same authors identified the mutation Q180H with a significant negative correlation with a case fatality ratio.…”

Pathological changes in oral epithelium and the expression of SARS-CoV-2 entry receptors, ACE2 and furin

“…Due to the occasional presence of a gradual escalation in epithelial changes in adjacent areas even in the same sample, diagnostic entities were grouped as following: epithelial hyperplasia-to-mild dysplasia and moderate-tosevere dysplasia. As the SARS-CoV-2 is primarily a virus of the respiratory tract [1][2][3], we included samples of upper respiratory mucosa (nose and maxillary sinus), collected from cases of inflammatory conditions, which served as controls. All cases comprised of tissues that were referred to the oral pathology laboratory before the COVID-19 pandemic.…”

“…The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was first reported in December 2019 in Wuhan, China, was found to be responsible for the coronavirus disease 2019 (COVID-19) that became a worldwide pandemic [1]. This is an enveloped single stranded RNA virus with a complete genome of about 30,000 nucleotides, that translates both structural and non-structural proteins [2].…”

Development of Lateral Flow Immunochromatographic Test for Rapid Detection of SARS-CoV-2 Virus Antigens in Clinical Specimens

“…COVID-19 has been recorded in most countries of the world, with noticed high transmission and morbidity rates that triggered the alarm for public health to respond to emerging diseases [ 5 ]. The World Health Organization (WHO) declared the COVID-19 outbreak a worldwide pandemic on 11 March 2020.…”