Emergence of SARS-CoV-2 variant of interest B.1.525 (Eta) in Bangladesh.

In the present study, we report the complete genome of five Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Bangladesh harboring mutations at Spike protein (E484K, Q677H, D614G, A67V, Q52R, Y144del, H69del, V70del, F888L) assigned to the B.1.525 lineage (Variant of interest). Mutations are also found in viral structural proteins other than spike region (E_L21F, M_I82F, N_A12G and N_T208I) and other mutations (NSP3_T1189I, NSP6_S106del, NSP6_F108del, NSP6_G107del, NSP12_P323F) from all of five B.1.525 SARS-CoV-2 variants of Bangladesh. We have also found four unique mutations from two of SARS-CoV-2 B.1.525 variant of Bangladesh. Among the four unique mutations two mutations (NS7a_L96H, NS7a_Y97D) obtained from strain BCSIR-NILMRC-718, one (NSP3_A1430V) from BCSIR-NILMRC-738 and two mutation including one spike protein mutation (NSP2_L444I, Spike_I68 M) present in BCSIR-AFIP-10 strain. The identification of new mutations will contribute to characterizing SARS-CoV-2, to continue tracking its spread and better understanding its biological and clinical features to take medical countermeasures and vaccines.

Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant of interest in Brazil: Case report.

The appearance of new variants of SARS-CoV-2 has recently challenged public health authorities with respect to tracking transmission and mitigating the impact in the evolving pandemic across countries. B.1.525 is considered a variant under investigation since it carries specific genetic signatures present in P.1, B.1.1.7, and B.1.351. Here we report genomic evidence of the first likely imported case of the SARS-CoV-2 B.1.525 variant, isolated in a traveler returning from Nigeria.

Optimization and validation of RT-LAMP assay for diagnosis of SARS-CoV2 including the globally dominant Delta variant.

BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 pandemic, has infected more than 179 million people worldwide. Testing of infected individuals is crucial for identification and isolation, thereby preventing further spread of the disease. Presently, Taqman™ Reverse Transcription Real Time PCR is considered gold standard, and is the most common technique used for molecular testing of COVID-19, though it requires sophisticated equipments, expertise and is also relatively expensive. OBJECTIVE: Development and optimization of an alternate molecular testing method for the diagnosis of COVID-19, through a two step Reverse Transcription Loop-mediated isothermal AMPlification (RT-LAMP). RESULTS: Primers for LAMP were carefully designed for discrimination from other closely related human pathogenic coronaviruses. Care was also taken that primer binding sites are present in conserved regions of SARS-CoV2. Our analysis shows that the primer binding sites are well conserved in all the variants of concern (VOC) and variants of interest (VOI), notified by World Health Organization (WHO). These lineages include B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427/B.1.429, P.2, B.1.525, P.3, B.1.526 and B.1.617.1. Various DNA polymerases with strand displacement activity were evaluated and conditions were optimized for LAMP amplification and visualization. Different LAMP primer sets were also evaluated using synthetic templates as well as patient samples. CONCLUSION: In a double blind study, the RT-LAMP assay was validated on more than 150 patient samples at two different sites. The RT-LAMP assay appeared to be 89.2% accurate when compared to the Taqman™ rt-RT-PCR assay.

Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria.

The emergence of new SARS-CoV-2 variants with enhanced transmissibility or decreased susceptibility to immune responses is a major threat to global efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Disparities in viral genomic surveillance capabilities and efforts have resulted in gaps in our understanding of the viral population dynamics across the globe. Nigeria, despite having the largest population of any nation in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. Here we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria in January 2021. Most isolates belonged to either the B.1.1.7 Alpha "variant of concern" or the B.1.525 Eta lineage, which is currently considered a "variant of interest" containing multiple spike protein mutations previously associated with enhanced transmissibility and possible immune escape. Nigeria has the highest reported frequency of the B.1.525 lineage globally with phylogenetic characteristics consistent with a recent monophyletic origin and rapid expansion. Spike protein from the B.1.525 lineage displayed both increased infectivity and decreased neutralization by convalescent sera compared to Spike proteins from other clades. These results, along with indications that the virus is outpacing the B.1.1.7 lineage in Nigeria, suggest that the B.1.525 lineage represents another "variant of concern" and further underline the importance of genomic surveillance in undersampled regions across the globe.