Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy)

Impact of in vitro SARS-CoV-2 infection on breast cancer cells

The pandemic of coronavirus disease 19 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), had severe repercussions for breast cancer patients. Increasing evidence indicates that SARS-CoV-2 infection may directly impact breast cancer biology, but the effects of SARS-CoV-2 on breast tumor cells are still unknown. Here, we analyzed the molecular events occurring in the MCF7, MDA-MB-231 and HCC1937 breast cancer cell lines, representative of the luminal A, basal B/claudin-low and basal A subtypes, respectively, upon SARS-CoV-2 infection. Viral replication was monitored over time, and gene expression profiling was conducted. We found that MCF7 cells were the most permissive to viral replication. Treatment of MCF7 cells with Tamoxifen reduced the SARS-CoV-2 replication rate, suggesting an involvement of the estrogen receptor in sustaining virus replication in malignant cells. Interestingly, a metagene signature based on genes upregulated by SARS-CoV-2 infection in all three cell lines distinguished a subgroup of premenopausal luminal A breast cancer patients with a poor prognosis. As SARS-CoV-2 still spreads among the population, it is essential to understand the impact of SARS-CoV-2 infection on breast cancer, particularly in premenopausal patients diagnosed with the luminal A subtype, and to assess the long-term impact of COVID-19 on breast cancer outcomes.

Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy

We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) of the whole viral genome and Sanger sequencing of the spike coding region. Phylogenetic analysis classified viral isolates and traced their evolutionary relationships. Clusters were identified using 70% cut-off. Sequencing methods yielded comparable results in terms of variant classification. In 2020 and 2021, we identified several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), and Delta (4/67). In 2022, only Omicron and its sub-lineage variants were observed (37/67). SARS-CoV-2 isolates were screened to detect naturally occurring resistance in genomic regions, the target of new therapies, comparing them to the Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron isolates carried the G15S 3CLpro substitution responsible for reduced susceptibility to protease inhibitors. On the other hand, Omicron isolates carried unusual substitutions A1803V, D1809N, and A949T on PLpro, and the D216N on 3CLpro. Finally, the P323L substitution on RdRp coding regions was not associated with the mutational pattern related to polymerase inhibitor resistance. This study highlights the importance of continuous genomic surveillance to monitor SARS-CoV-2 evolution in the general population, as well as in restricted communities.

Clinical and laboratory features of SARS-CoV-2 variants across multiple rounds of pandemic waves in hospitalized children in an Iranian referral hospital

BACKGROUND

Since the onset of the COVID-19 pandemic, SARS-CoV-2 has evolved into independent new forms, variants of concern (VOCs). While epidemiological data showed increased transmissibility of VOCs, their impact on clinical outcomes is less clear. This study aimed to investigate the differences between the clinical and laboratory features of children infected with VOCs.

METHODS

This study included all cases with SARS-CoV-2-positive nasopharyngeal swabs obtained from patients referred to Children's Medical Center (CMC), an Iranian referral hospital, between July 2021 and March 2022. The inclusion criteria for this study included all patients, regardless of age, who had a positive test anywhere in the hospital setting. Exclusion criteria for the study included those whose data was obtained from non-hospital outpatient settings, or referred from another hospital. The SARS-CoV-2 genome area encoding the S1 domain was amplified and sequenced. The type of variant in each sample was identified based on the mutations in the S1 gene. Demographic characteristics, clinical data, and laboratory findings were collected from the patient's medical records.

RESULTS

This study included 87 pediatric cases with confirmed COVID-19, with a median age of 3.5 years (IQR: 1-8.12). Data from sequencing reveals the type of variants as 5 (5.7%) alpha, 53 (60.9%) Delta, and 29 (33.3%) Omicron. The incidence of seizure was higher in patients with Alpha and Omicron infection compared to the Delta group. A higher incidence of diarrhea was reported in Alpha-infected patients, and a higher risk of disease severity, distress, and myalgia was associated with Delta infection.

CONCLUSION

Laboratory parameters did not mostly differ among the patients infected with Alpha, Delta, and Omicron. However, these variants may manifest different clinical features. Further studies with larger sample sizes are required to fully understand the clinical manifestations of each variant.

Identification of SARS CoV-2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

BACKGROUND

Five variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) have been globally recorded including Alpha, Beta, Gamma, Delta, and Omicron. The Omicron variant has outcompeted the other variants including the Delta variant. Molecular screenings of VOCs are important for surveillance, treatment, and vaccination programs. This study aimed to identify VOCs by using rapid inexpensive methods and partial sequencing of the virus's spike gene.

METHODS

Mutation-specific rRT PCR probes were used for both D614G and K417N mutations to potentially discriminate between Delta and Omicron variants. These were followed by sequencing of a fragment of spike gene (748 nucleotides), which covers the most notable VOC mutations in the receptor binding domain of SARS CoV-2.

RESULTS

Rapid methods showed that out of 24 SARS CoV-2 positive samples, 19 carried the N417 mutation, which is present in the Omicron variant. Furthermore, 3 samples carried K417 wildtype, which is present in the Delta variant. Additionally, 2 samples containing both K417 and N417 suggested mixed infections between the two variants. The D614G mutation was present in all samples. Among the 4 samples sequenced, 3 samples carried 13 mutations, which are present in Omicron BA.1. The fourth sample contained the two common mutations (T478K and L452R) present in Delta, in addition to two more rare mutations (F456L and F490S), which are not commonly seen in Delta. Our data suggested that both Omicron variant BA.1 and a novel Delta variant might have circulated in this region that needs further investigations.

Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level

Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.

SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods

Since the beginning of COVID-19 pandemic the Real Time sharing of genome sequences of circulating virus supported the diagnostics and surveillance of SARS-CoV-2 and its transmission dynamics. SARS-CoV-2 straightaway showed its tendency to mutate and adapt to the host, culminating in the emergence of variants; so it immediately became of crucial importance to be able to detect them quickly but also to be able to monitor in depth the changes on the whole genome to early identify the new possibly emerging variants. In this scenario, this manuscript aims to provide an overview of the existing methods for the identification of SARS-CoV-2 variants (from rapid method based on identification of one or more specific mutations to Whole Genome sequencing approach-WGS), taking into account limitations, advantages and applications of them in the field of diagnosis and surveillance of SARS-CoV-2.

Textiles Functionalized with Copper Oxides: A Sustainable Option for Prevention of COVID-19

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and healthcare-associated infections (HAIs) represent severe problems in health centers and public areas. Polyester/cotton (PES/CO) blend fabrics have been functionalized with copper oxides on an industrial scale. For functionalization, the impregnation dyeing technique was applied. The functionalized samples were tested virologically against SARS-CoV-2 and human coronavirus (229E) according to ISO 18184-2019 and microbiologically against Escherichia coli (ATCC 25922) bacteria according to ASTM E2149-2013. The results show that the fabric functionalized with copper oxides inactivated both viruses after 30 min of exposure, presenting excellent virucidal activity against 229E and SARS-CoV-2, respectively. Furthermore, its inactivation efficiency for SARS-CoV-2 was 99.93% and 99.96% in 30 min and 60 min exposure, respectively. The fabric inhibited bacterial growth by more than 99% before and after 10 and 20 washes. In conclusion, 265 m of PES/CO fabric (wide 1.7 m) was functionalized in situ on an industrial scale with copper oxide nanoparticles. The functionalized fabric presented virucidal and bactericidal properties against SARS-CoV-2 and Escherichia coli.

Excess Mortality on Italian Small Islands during the SARS-CoV-2 Pandemic: An Ecological Study

Small islands have been considered at an advantage when dealing with infectious diseases, including COVID-19, but the evidence is still lacking. Crude mortality rates (CMRs) and excess mortality rates (EMRs) were calculated for 35 municipalities on the Italian small islands for 2020 and 2021, and the corresponding estimates were compared to those of the parent provinces and the national estimates. Notification rates for COVID-19 were retrieved, but detailed data at the municipality level were not available. A relatively low CMR (1.069 per 100 per year, 95% confidence interval [95% CI] 0.983−1.164) was identified in 2020, compared to 1.180, 95% CI 1.098−1.269 for 2021. EMRs of small islands ranged between −25.6% and +15.6% in 2020, and between −13.0% and +20.9% in 2021, with an average gain of +0.3% (95% CI −5.3 to +5.8) for the entirety of the assessed timeframe, and no substantial differences between 2020 and 2021 (pooled estimates of −4.1%, 95% CI −12.3 to 4.1 vs. 4.6%, 95% CI −3.1 to 12.4; p = 0.143). When dealing with COVID-19 notification rates, during the first wave, parent provinces of Italian small islands exhibited substantially lower estimates than those at the national level. Even though subsequent stages of the pandemic (i.e., second, third, and fourth waves) saw a drastic increase in the number of confirmed cases and CMR, estimates from small islands remained generally lower than those from parent provinces and the national level. In regression analysis, notification rates and mortality in the parent provinces were the main effectors of EMRs in the small islands (β = 0.469 and β = 22.768, p < 0.001 and p = 0.007, respectively). Contrarily, the management of incident cases in hospital infrastructures and ICUs was characterized as a negative predictor for EMR (β = −11.208, p = 0.008, and −59.700, p = 0.003, respectively). In summary, the study suggests a potential role of small geographical and population size in strengthening the effect of restrictive measures toward countering the spread and mortality rate of COVID-19.