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SARS-CoV-2 has been highly susceptible to mutations since its emergence in Wuhan, China, and its subsequent propagation due to containing an RNA as its genome. The emergence of variants with improved transmissibility still poses a grave threat to global health. The spike protein mutation is mainly responsible for higher transmissibility and risk severity. This study retrieved SARS-CoV-2 variants structural and nonstructural proteins (NSPs) sequences from several geographic locations, including Africa, Asia, Europe, Oceania, and North and South America. First, multiple sequence alignments with BioEdit and protein homology modeling were performed using the SWISS Model. Then the structure visualization and structural analysis were performed by superimposing against the Wuhan sequence by Pymol to retrieve the RMSD values. Sequence alignment revealed familiar, uncommon regional among variants and, interestingly, a few unique mutations in Beta, Delta, and Omicron. Structural analysis of such unique mutations revealed that they caused structural deviations in Beta, Delta, and Omicron spike proteins. In addition, these variants were more severe in terms of hospitalization, sickness, and higher mortality, which have a substantial relationship with the structural deviations because of those unique mutations. Such evidence provides insight into the SARS-CoV-2 spike protein vulnerability toward mutation and their structural and functional deviations, particularly in Beta, Delta, and Omicron, which might be the cause of their broader coverage. This knowledge can help us with regional vaccine strain selection, virus pathogenicity testing, diagnosis, and treatment with more specific vaccines. [ABSTRACT FROM AUTHOR]

Older people in nursing homes (NH) have been hit particularly hard by the COVID-19 pandemic. We conducted a retrospective study of three outbreaks of COVID-19, occurring during the waves of the initial pre-Alpha, Delta and Omicron SARS-CoV-2 variants, in one NH in suburban Belgrade, Serbia. All staff and 95% residents were vaccinated in February 2021, mostly with BBIBP-CorV, and two thirds were boosted with a third dose in August 2021. COVID-19 was diagnosed by positive PCR and/or antigen test. After the first outbreak, 80 affected individuals were tested for SARS-CoV-2 specific antibodies. The first outbreak involved 64/126 (50.8%) residents and 45/64 (70.3%) staff, the second 22/75 (29.3%) residents and 3/40 (7.5%) staff, and the third involved 36/110 (32.7%) residents and 19/56 (33.9%) staff. Clinical presentation ranged from asymptomatic to severe, with severe cases referred to hospital ICUs. Deaths occurred only in residents, and the case fatality rate was 31.2%, 9.1% and 0%, respectively in outbreaks 1, 2 and 3. Specific IgG antibodies were detected in all 35 residents and 44 of the 45 staff, and higher IgG levels were detected in the residents (417.3±273.5) than in the staff (201.9±192.9, p<0.0001) despite a double difference in age (79.0±7.4 vs. 40.1±11.5 years). Outbreaks 2 and 3 involved four and 23 breakthrough infections, respectively. Older individuals mounted a good immunological response to SARS-CoV-2 infection and vaccination, which prevented significant mortality and severe morbidity in the subsequent outbreaks, despite a significant number of breakthrough infections. [ABSTRACT FROM AUTHOR]

The clinical presentation of COVID-19 and the specific antibody responses associated with SARS-CoV-2 variants have not been investigated during the emergence of Omicron variants in Bangladesh. The Delta and Omicron variants were identified by post-PCR melting curve analysis of the spike (S) protein receptor binding domain amplicons. Anti-S-protein immunoglobulin-G anti-nucleocapsid (N)-protein immunoglobulin-G and immunoglobulin-A levels were measured by ELISA. The Delta variant was found in 40 out of 40 (100%) SARS-CoV-2 RT-PCR positive COVID-19 patients between 13 September and 23 October 2021 and Omicron variants in 90 out of 90 (100%) RT-PCR positive COVID-19 patients between 9 January and 10 February 2022. The Delta variant associated with hospitalization (74%, 80%, and 40%) and oxygen support (60%, 57%, and 40%) in the no vaccine, dose-1, and dose-2 vaccinated cases, respectively, whereas the Omicron COVID-19 required neither hospitalization nor oxygen support (0%, p < 0.0001). Fever, cough, and breathlessness were found at a significantly higher frequency among the Delta than Omicron variants (p < 0.001). The viral RNA levels of the Delta variant were higher than that of the Omicron variants (Ct median 19.9 versus 23.85; p < 0.02). Anti-spike protein immunoglobulin-G and anti-N-protein immunoglobulin-G within 1 week post onset of Delta variant COVID-19 symptoms indicate prior SARS-CoV-2 infection. The Delta variant and Omicron BA.1 and BA.2 breakthrough infections in the Dhaka region, at 240 days post onset of COVID-19 symptoms, negatively correlated with the time interval between the second vaccine dose and serum sampling. The findings of lower anti-spike protein immunoglobulin-G reactivity after booster vaccination than after the second vaccine dose suggest that the booster vaccine is not necessarily beneficial in young Bangladeshi adults having a history of repeated SARS-CoV-2 infections.