Isolation and characterization of SARS-CoV-2 Beta variant from UAE travelers

Abstract

Background The emergence of SARS-CoV-2 variants in places where the virus is uncontained poses a global threat from the perspective of public health and vaccine efficacy. Travel has been important factor for the easy spread of SARS-CoV-2 variants worldwide. India has also observed the importation of SARS-CoV-2 variants through international travelers. Methods In this study, we have collected the oropharyngeal and nasopharyngeal swab specimens from 58 individuals with travel history from United Arab Emirates (UAE), East, West and South Africa, Qatar, Ukraine and Saudi Arabia arrived in India during February-March 2021. The clinical specimens were initially screened for SARS-CoV-2 using Real time RT-PCR. All the specimens were inoculated on to Vero CCL-81 cells for virus isolation. The viral isolates were further sequenced using Next-Generation Sequencing. Results All 58 cases were tested positive for SARS-CoV-2 using Real time RT-PCR. Four specimens showed progressive infectivity with fusion of the infected cells with neighboring cells leading to large mass of cells. Replication competent virus was confirmed from culture supernatant of the passage 2 using Real time RT-PCR. Two plaque purified SARS-CoV-2 isolates demonstrated high viral RNA load of 3.8-7.5 × 10 11 and 1.1-1.6 × 10 11 at passage 4 and 5 respectively. Nucleotide variations along with amino acid changes were also observed among these two isolates at passage 2 to 5. All four cases were male with no symptoms and co-morbidity. The sequence analysis has shown two different clusters, first cluster with nucleotide deletions in the ORF1ab and the spike, while second cluster with deletions in spike region. The viral isolates demonstrated 99.88-99.96% nucleotide identity with the representative sequences of Beta variant (B.1.351). Conclusion These findings suggest easier transmission of SARS-CoV-2 variants with human mobility through international travel. The isolated Beta variant would be useful to determine the protective efficacy of the currently available and upcoming COVID-19 vaccines in India.

Characterization of SARS-CoV-2 Escape Mutants to a Pair of Neutralizing Antibodies Targeting the RBD and the NTD

“…This escape variant also carries a S477N mutation within the RBD and a D215G mutation within the NTD. The S477N mutation has also been detected before in the TRES6 escape mutation ( Figure 1 E), whilst the D215G mutation has been observed in the Beta variant of concern [ 24 ].…”

“…Several different mutations have been identified in different VOC and virus variants that abrogate antibody binding of monoclonal antibodies interacting with the NTD. Here, for example, the Δ69–70 and ΔY144 mutations that are found amongst other NTD mutations in the Omicron and Alpha variants or the D215G, Δ242–244, and R246I NTD mutations identified in the Beta variant play an important role [ 21 , 22 , 23 , 24 ]. De novo mutations in SARS-CoV-2 do however not only arise in vivo but can also be observed in vitro [ 25 ].…”

SARS‐CoV‐2 variants and vulnerability at the global level

“… 47 In the RBD of spike protein, notable mutations include N501Y, K417N, and E484K, which can increase the protein's affinity for the human ACE2 receptor. 59 The E484K mutation may allow an individual to evade the immune system's response. 60 According to an in vitro test, all existing vaccines generate antibodies with decreased neutralizing activity against beta variants.…”

Recapping the Features of SARS-CoV-2 and Its Main Variants: Status and Future Paths

“…The Beta (B.1.351) variant emerged in South Africa in October 2020, being the most representative variant in this country until the onset of Omicron, and extended to 115 countries [ 79 ]. This variant presents nine mutations in the spike protein (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V).…”