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Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad.

ABSTRACT: In view of the rapidly progressing COVID-19 pandemic, our aim was to isolate and characterize SARS-CoV-2 from Indian patients. SARS-CoV-2 was isolated from nasopharyngeal swabs collected from the two members of a family without any history of (H/O) travel abroad. Both the virus isolates (8003 and 8004) showed CPE on day 3 post-inoculation, viral antigens by immunofluorescence assay and produced distinct, clear and uniform plaques. Infectious virus titers were 5?×?10⁶ and 4?×?10⁶ Pfu/ml by plaque assay and 10^7.5 and 10⁷ by CPE-based TCID50/ml, respectively. Phylogenetic analysis grouped our isolates with the Italian strains. On comparison with Wuhan strain, 3 unique mutations were identified in nsp3 (A1812D), exonuclease (P1821S) of Orf1ab and spike protein (Q677H) regions, respectively. Both the viruses grouped with Italian strains of SARS-CoV-2 suggesting possible source being the virus imported from Italy. These fully characterized virus isolates will be useful in developing neutralization/virological assays for the evaluation of vaccines/antivirals.

SUBMITTER: Shrivastava S

PROVIDER: S-EPMC7938031 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe 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.MethodsIn 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.ResultsAll 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 × 1011 and 1.1-1.6 × 1011 at passage 4 and 5 respectively. Nucleotide variations along with amino acid changes were also observed among these two isolates at passage 2-5. 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).ConclusionThese 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.

Project description:Rationale for the review: Air travel may be associated with viruses spread via infected passengers and potentially through in-flight transmission. Given the novelty of the SARS-CoV-2 virus, transmission associated with air travel is based on transmission dynamics of other respiratory viruses. Our objective was to provide a rapid summary and evaluation of relevant data on SARS-CoV-2 transmission aboard aircraft, report policy implications, and highlight research gaps requiring urgent attention.MethodsWe searched four electronic databases (1 February 2020 to 27 January 2021) and included studies on SARS-CoV-2 transmission aboard aircraft. We assessed study quality based on five criteria and reported important findings.Key findingsWe included 18 studies on in-flight SARS-CoV-2 transmission (130 unique flights) and two studies on wastewater from aircraft. The quality of evidence from most published studies was low. Two wastewater studies reported PCR-positive samples with high Cycle threshold values (33-39). Index case definition was heterogeneous across studies. The proportion of contacts traced ranged from 0.68% to 100%. Authors traced 2800/19729 passengers, 140/180 crew members, and 8/8 medical staff. Altogether, 273 index cases were reported, with 64 secondary cases. Three studies, each investigating one flight, reported no secondary cases. Secondary attack rate among studies following up > 80% of passengers and crew (including data on ten flights) varied between 0-8.2%. The studies reported on the possibility of SARS-CoV-2 transmission from asymptomatic, pre-symptomatic, and symptomatic individuals. Two studies performed viral cultures with ten positive results. Genomic sequencing and phylogenetic analysis were performed in individuals from four flights.ConclusionCurrent evidence suggests SARS-CoV-2 can be transmitted during aircraft travel, but published data do not permit any conclusive assessment of likelihood and extent. The variation in design and methodology restricts the comparison of findings across studies. Standardized guidelines for conducting and reporting future studies of transmission on aircraft should be developed.

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Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad.

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