Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1.

COVID-19 results from SARS-CoV-2, which mutates frequently, challenging current treatments. Therefore, it is critical to develop new therapeutic drugs against this disease. This study explores the interaction between SARS-CoV-2 3CLpro and RetroMAD1, a well-characterized coronavirus protein and potential drug target, using in-silico methods. The analysis through the HDOCK server showed stable complex formation with a binding energy of -12.3, the lowest among reference drugs. The RetroMAD1-3CLpro complex underwent a 100 ns molecular dynamics simulation (MDS) in an explicit solvation system, generating various trajectories, including RMSD, RMSF, hydrogen bonding, radius of gyration, and ligand binding energy. MDS results confirmed intact interactions within the RetroMAD1-3CLpro complex during simulations. In vitro experiments validated RetroMAD1's ability to inhibit 3CLpro enzyme activity and prevent SARS-CoV-2 infection in human bronchial cells. RetroMAD1 exhibited antiviral efficacy comparable to Remdesivir without cytotoxicity at effective concentrations. These results suggest RetroMAD1 as a potential drug candidate against SARS-CoV-2, warranting further in vivo and clinical studies to assess its efficiency.

Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia.

SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with CT value < 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p <0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted.

COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang.

SARS-CoV-2 is a very transmissible and pathogenic coronavirus which detected in Malaysia in January 2020. Nevertheless, the sample from Malaysia is still under-sequenced. Hence lacking clarity of the circulating strain in Malaysia leads to a deadlock in understanding the virus infectivity. This study aimed to investigate the genome identity of circulating COVID-19 strains in Pahang and understand disease epidemiology during the pandemic. This study leveraged high-throughput sequencing analysis for the whole genome sequencing and implemented bioinformatic technique for the analysis. Here we reported that the virus with D614G mutation in Spike protein circulates in a few Malaysia states before the Sivagangga cluster announced in Kedah in July 2020. This mutated virus includes our virus sample isolated in April 2020 from an asymptomatic patient in Pahang. Based on the phylogenetic analysis, we discovered the origin of our sample Pahang/IIUM91 was not related to Sivagangga cluster. Here, we have generated 3D structure model of Pahang/IIUM91 Spike protein. D614G mutation in Pahang/IIUM91 Spike protein increases viral stability and flexibility, hence render higher infectivity. Collectively, our results suggest for the establishment of a complete SARS-CoV-2 genome database in Malaysia. Hence, more research should be established to learn the behaviour of this virus.

Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia.

Here, we report the nearly complete genome sequences of nine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the D614G mutation. These viruses were detected from various infected individuals with different levels of severity from Pahang, Malaysia. In addition, this study described the presence of lineage B.1.351 as a type of variant of concern (VOC) and lineages B.1.466.2 and B.1.524 as local variants.

Streptococcus salivarius K12 inhibits Candida albicans aggregation, biofilm formation and dimorphism.

Candida albicans causes candidiasis, particularly in immunocompromised patients. Streptococcus salivarius K12 (K12) is a probiotic isolated from a healthy oral cavity. The study aimed to determine the effect of K12 on C. albicans aggregation, biofilm formation and dimorphism. C. albicans ATCC MYA-4901, acquired immunodeficiency syndrome (AIDS) isolate (ALC2), and oral cancer isolate (ALC3) and K12 were used in the study. All C. albicans strains and K12 were grown in yeast peptone dextrose agar and brain heart infusion agar, respectively, prior to aggregation, biofilm and dimorphism assays. Auto-aggregation of C. albicans MYA-4901 and ALC2 was categorised as high, while the co-aggregation of the strains was low in the presence of K12. C. albicans total cell count decreased significantly when co-cultured with K12 compared with monocultured C. albicans biofilm (p < 0.05). Inhibition of yeast-to-hyphae transition was also observed when co-cultured with K12. In conclusion, K12 inhibits C. albicans aggregation, biofilm formation and dimorphism.