Genome sequencing of severe acute respiratory syndrome COVID-19 EF.1 variant strain obtained from a Moroccan patient

Here, we report the identification and coding-complete genome sequence of a severe acute respiratory syndrome COVID-19 (SARS-CoV-2) strain obtained from a Moroccan patient. The detected strain EF.1 belongs to the BQ1.1 subvariant of the BA.5 Omicron variant.

Editorial: The XBB.1.5 ('Kraken') Subvariant of Omicron SARS-CoV-2 and its Rapid Global Spread

In November 2021, the World Health Organization (WHO) first identified the Omicron variant of SARS-CoV-2, B.1.1.529, as a variant of concern (VOC). By early 2022, the Omicron variant and its five lineages, BA.1, BA.2, BA.3, BA.4. and BA.5, had become the predominant cause of COVID-19 in most countries. The Omicron XBB.1.5 subvariant is a sublineage of the XBB variant, a recombinant of two BA.2 sublineages, with the F486P mutation in the spike protein that increases infectivity due to increased binding affinity to the angiotensin-converting enzyme 2 (ACE2) receptor. On the week ending 21 January 2023, the XBB.1.5 subvariant caused 49.1% of cases of COVID-19 in the US. The rapid rise in the prevalence of this subvariant may be explained by immune escape to previous infection or vaccines, spike mutations in F486P, and increased affinity for the ACE2 receptor. Also, current booster vaccines may not provide adequate protection from infection from this subvariant, which has been named by the media as the 'Kraken' subvariant. This Editorial aims to present the current status of the XBB.1.5 subvariant of Omicron SARS-CoV-2 and the reasons for, and implications of, its rapid global spread.

Does the COVID-19 XBB Omicron subvariant signal the beginning of the end of the pandemic?

All pandemic viruses have eventually adapted to human hosts so that they become more transmissible and less virulent. The XBB Omicron subvariant is rapidly becoming the dominant strain of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Singapore from October 2022 and is one of several variants circulating globally with the potential to dominate autumn/winter waves in different countries. The XBB Omicron subvariant has demonstrated increased transmissibility through an apparent propensity for immune evasion. This is to be expected in the natural evolution of a virus in a population highly vaccinated with a vaccine targeting the spike protein of the original Wuhan strain of the virus. This review explores the important implications of the rising prevalence of the SARS-CoV-2 Omicron subvariant for public health in Singapore and beyond.

SARS-CoV-2 Omicron and its current known unknowns: A narrative review

The emergence of the SARS-CoV-2 Omicron variant (B.1.1.529) has created great global distress. This variant of concern shows multiple sublineages, importantly B.1.1.529.1 (BA.1), BA.1 + R346K (BA.1.1), and B.1.1.529.2 (BA.2), each with unique properties. However, little is known about this new variant, specifically its sub-variants. A narrative review was conducted to summarise the latest findings on transmissibility, clinical manifestations, diagnosis, and efficacy of current vaccines and treatments. Omicron has shown two times higher transmission rates than Delta and above ten times more infectious than other variants over a similar period. With more than 30 mutations in the spike protein's receptor-binding domain, there is reduced detection by conventional RT-PCR and rapid antigen tests. Moreover, the two-dose vaccine effectiveness against Delta and Omicron variants was found to be approximately 21%, suggesting an urgent need for a booster dose to prevent the possibility of breakthrough infections. However, the current vaccines remain highly efficacious against severe disease, hospitalisation, and mortality. Japanese preliminary lab data elucidated that the Omicron sublineage BA.2 shows a higher illness severity than BA.1. To date, the clinical management of Omicron remains unchanged, except for monoclonal antibodies. Thus far, only Bebtelovimab could sufficiently treat all three sub-variants of Omicron. Further studies are warranted to understand the complexity of Omicron and its sub-variants. Such research is necessary to improve the management and prevention of Omicron infection.

Vitamin D levels and clinical outcomes of SARS-CoV-2 Omicron subvariant BA.2 in children: A longitudinal cohort study

Objective

To investigate the picture between vitamin D levels and clinical outcomes of SARS-CoV-2 Omicron subvariant BA.2 in children.

Methods

A retrospective, longitudinal cohort study was performed. All included hospitalized cases were divided into the sufficient (sVD) and insufficient vitamin D (iVD) groups according to whether their serum 25-hydroxyvitamin D [25(OH)D] concentration was ≥30 ng/mL. Dynamic changes in clinical parameters were observed for seven time periods within 28 days after admission.

Results

Serum 25(OH)D concentrations were significantly negatively correlated with age in the included cases (r = −0.6; P < 0.001). Compared with the iVD group (n = 80), the sVD group (n = 36) had higher interleukin-6 (18.4 vs. 12.9; P = 0.003) within the first day; higher procalcitonin within the first (0.15 vs. 0.1; P = 0.03), 2–3 (0.14 vs. 0.07; P = 0.03), 4–5 (0.21 vs. 0.07; P = 0.02) days; more lymphocytes within the first (1.6 vs. 1.2; P = 0.02), 2–3 (3.7 vs. 2; P = 0.001), 4–5 (3.9 vs. 2.1; P = 0.01) and 6–7 (4.9 vs. 2.7; P = 0.02) days; notably, higher cycle threshold for N gene (30.6 vs 19.8; P = 0.03) or ORF1ab gene (31.4 vs 20.1; P = 0.03) within 2 to 3 days. Pneumonia lesions were found in eleven and six cases in the iVD and sVD groups, respectively, without significant difference on computed tomography at admission. Six out of eleven and five out of six had a repeat computed tomography after 1–2 weeks. Lesion improvement was more significant in the sVD group (P = 0.04).

Conclusions

Children with vitamin D insufficiency might have poorer clinical outcomes in Omicron subvariant BA.2 infection, especially in older pediatric patients. Further studies are needed to assess effectiveness of supplements in reducing the same.