ABSTRACT
Background: A newly emerged SARS-CoV-2 variant B.1.1.529 has worried health policymakers worldwide due to the presence of a large number of mutations in its genomic sequence, especially in the spike protein region. World Health Organization (WHO) has designated it as a global variant of concern (VOC) and has named as Omicron. A surge in new COVID-19 cases has been reported from certain geographical locations, primarily in South Africa (SA) following the emergence of Omicron. Materials and methods: We performed an in silico analysis of the complete genomic sequences of Omicron available on GISAID (until 2021-12-6) to predict the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period of 01 Oct-29 Nov 2021) with the current epidemiological data (new COVID-19 cases and deaths) from SA to understand whether the Omicron has an epidemiological advantage over existing variants. Results: Compared to the current list of global VOCs/VOIs (as per WHO) Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with Alpha variant for the complete sequence as well as for RBM. The mutations were found primarily condensed in the spike region (28-48) of the virus. Further, the mutational analysis showed enrichment for the mutations decreasing ACE2-binding affinity and RBD protein expression, in contrast, increasing the propensity of immune escape. An inverse correlation of Omicron with Delta variant was noted (r=-0.99, p< .001, 95% CI: -0.99 to -0.97) in the sequences reported from SA post-emergence of the new variant, later showing a decrease. There has been a steep rise in the new COVID-19 cases in parallel with the increase in the proportion of Omicron since the first case (74-100%), on the contrary, the incidences of new deaths have not been increased (r=-0.04, p>0.05, 95% CI =-0.52 to 0.58). Conclusions: Omicron may have greater immune escape ability than the existing VOCs/VOIs. However, there are no clear indications coming out from the predictive mutational analysis that the Omicron may have higher virulence/lethality than other variants, including Delta. The higher ability for immune escape may be a likely reason for the recent surge in Omicron cases in SA.
Subject(s)
COVID-19 , DeathABSTRACT
ImportanceHigher risks of contracting infection, developing severe illness and mortality are known facts in aged and male sex if exposed to the wild type SARS-CoV-2 strains (Wuhan and B.1 strains). Now, accumulating evidence suggests greater involvement of lower age and narrowing the age and sex based differences for the severity of symptoms in infections with emerging SARS-CoV-2 variants. Delta variant (B.1.617.2) is now a globally dominant SARS-CoV-2 strain, however, current evidence on demographic characteristics for this variant are limited. Recently, delta variant caused a devastating second wave of COVID-19 in India. We performed a demographic characterization of COVID-19 cases in Indian population diagnosed with SARS-CoV-2 genomic sequencing for delta variant. ObjectiveTo determine demographic characteristics of delta variant in terms of age and sex, severity of the illness and mortality rate, and post-vaccination infections. DesignA cross sectional study SettingDemographic characteristics, including vaccination status (for two complete doses) and severity of the illness and mortality rate, of COVID-19 cases caused by wild type strain (B.1) and delta variant (B.1.617.2) of SARS-CoV-2 in Indian population were studied. ParticipantsCOVID-19 cases for which SARS-CoV-2 genomic sequencing was performed and complete demographic details (age, sex, and location) were available, were included. ExposuresSARS-CoV-2 infection with Delta (B.1.617.2) variant and wild type (B.1) strain. Main Outcomes and MeasuresThe patient metadata containing details for demographic and vaccination status (two complete doses) of the COVID-19 patients with confirmed delta variant and WT (B.1) infections were analyzed [total number of cases (N) =9500, Ndelta=6238, NWT=3262]. Further, severity of the illness and mortality were assessed in subsets of patients. Final data were tabulated and statistically analyzed to determine age and sex based differences in chances of getting infection and the severity of illness, and post-vaccination infections were compared between wild type and delta variant strains. Graphs were plotted to visualize the trends. ResultsWith delta variant, in comparison to wild type (B.1) strain, higher proportion of lower age groups, particularly <20 year (0-9 year: 4.47% vs. 2.3%, 10-19 year: 9% vs. 7%) were affected. The proportion of women contracting infection were increased (41% vs. 36%). The higher proportion of total young (0-19 year, 10% vs. 4%) (p=.017) population and young (14% vs. 3%) as well as adult (20-59 year, 75% vs. 55%) women developed symptoms/hospitalized with delta variant in comparison to B.1 infection (p< .00001). The mean age of contracting infection [Delta, men=37.9 ({+/-}17.2) year, women=36.6 ({+/-}17.6) year; B.1, men=39.6 ({+/-}16.9) year and women= 40.1 ({+/-}17.4) year (p< .001)] as well as developing symptoms/hospitalization [Delta, men=39.6({+/-} 17.4) year, women=35.6 ({+/-}16.9) year; B.1, men=47({+/-}18) year and women= 49.5({+/-}20.9) year (p< .001)] was considerably lower. The total mortality was about 1.8 times higher (13% vs. 7%). Risk of death increased irrespective of the sex (Odds ratio: 3.034, 95% Confidence Interval: 1.7-5.2, p<0.001), however, increased proportion of women (32% vs. 25%) were died. Further, multiple incidences of delta infections were noted following complete vaccination. Conclusions and RelevanceThe increased involvement of young (0-19 year) and women, lower mean age for contracting infection and symptomatic illness/hospitalization, higher mortality, and frequent incidences of post-vaccination infections with delta variant compared to wild type strain raises significant epidemiological concerns. Key PointsO_ST_ABSQuestionC_ST_ABSDid SARS-CoV-2 B.1.617.2 (Delta) variant infections show varied demographic characteristics in comparison to wild type strains? FindingsIn this cross sectional study viral genomic sequences of 9500 COVID-19 patients were analyzed. As the key findings, increased involvement of young (0-19 year) and women, lower mean age for contracting infection and symptomatic illness/hospitalization, higher mortality, and frequent incidences of post-vaccination infections with delta variant in comparison to wild type (WT) strain (B.1) were observed. MeaningThe findings of this study suggest that delta variant has varied demographic characteristics reflecting increased involvement of the young and women, and increased lethality in comparison to wild type strains.
Subject(s)
COVID-19 , Hepatitis D , InfectionsABSTRACT
COVID-19 pandemic has been a global health emergency due to its association with severe pneumonia and high rate of mortality. In the current study, we reported the direct evidence for the variable level of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infection on several types of oral epithelial cells isolated from the aspirated oropharyngeal and bronchoalveolar secretions of severely infected and intubated patients using cytology, confocal based immunofluorescence imaging (IF), scanning electron microscope (SEM) and transmission electron microscopic (TEM) studies. Cytological analysis showed the presence of keratinised and non-keratinised oral epithelial cells with viral inclusion bodies in stratum granulosum and intermedium cells. IF imaging using SARS-CoV-2 spike protein specific antibody confirmed the presence of virus inside the stratum spinosum/granulosum (keratinised) and stratum intermedium/superficial cells (non-keratinised). No SARS-CoV-2 viruses were seen in stratum corneum cells. SEM analysis also confirms the absence of virus like structure on stratum corneum surface while viruses like structure were seen on the stratum spinosum/granulosum/stratum/intermedium and stratum superficial cells. This advanced microscopic study confirms directly that the virus tends to infect and multiply in the metabolically active or sub-basal cells of oral epithelium and absent in the inactive keratinised stratum corneum from shedding zones of oral mucosa.
ABSTRACT
The pandemic of the coronavirus disease, 2019 (COVID-19) has caused millions to suffer from the disease and to die globally. Global epidemiological statistics reflect, significantly more numbers of men, aged, those suffering from co-morbidities, and people facing socio-economic inequalities, such as, racial/ethnic minorities, have been affected by COVID-19. Why the disease affects more to these specific population groups is intriguing the researchers globally. Emerging literature in COVID-19 indicates crucial role of factors intrinsic to the host behind such poor outcomes in selected individuals. Our comprehensive review of existing literature unravels a range of host factors which could have decisive role in patient outcomes in COVID-19, in terms of contracting infections, disease severity, and mortality, such as: age, sex, co-morbidities, genetic and phenotypic factors (e.g. polymorphisms or mutations, blood group etc.), clinical and laboratory parameters (at the time of hospital admission), cross protection from previous respiratory virus infections and childhood vaccinations, gut-microbiome, life style, habits and behavior (smoking and substance abuse), and socio-economic and systemic inequalities. In this article, we discuss in brief the most definitive and updated evidence for each of these host factors.
Subject(s)
COVID-19 , Anisocoria , Coronavirus InfectionsABSTRACT
Recent epidemiological studies analysing sex disaggregated patient data in COVID-19 across the world revealed a distinct sex bias in the disease morbidity as well as the mortality— both being higher for the men. Similar antecedents have been known for the previous viral infections, including from coronaviruses, such as severe acute respiratory syndrome (SARS) and middle-east respiratory syndrome (MERS). A sound understanding of the molecular mechanisms leading the biological sex bias in the survival outcomes of the patients in relation to COVID-19 will act as an essential requisite for developing a sex differentiated approach for therapeutic management of this disease. Recent studies which have explored molecular mechanism(s) behind sex-based differences in COVID-19 pathogenesis are scarce, however, existing evidence, for other viral infections, provides important clues in this regard. In attempt to consolidate the available knowledge on this issue, we performed a systematic review of the existing empirical knowledge and recent experimental studies following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The online literature sources including PubMed, Medline (EBSCO & Ovid), Google Scholar, Science Direct, Scopus, Bio Medical and Web of Science (WoS) were searched for the relevant data. Additionally, published literatures were also explored extensively. The time period taken to review the COVID-19 specific data was from December 1, 2019 to November 20, 2020. The qualitative analysis of the collected data unravelled multiple molecular mechanisms, such as sex-linkage of viral host cell entry receptor and immune genes, sex hormone and gut microbiome mediated immune-modulation, as the possible reasons for the sex-based differences in patient outcomes in COVID-19.