SARS-CoV-2 Sequence Analysis during COVID-19 Case Surge, Liberia, 2021

Shobayo, Bode I.; Mishra, Mitali; Sameroff, Stephen; Petrosov, Alexandra; Ng, James; Gokden, Alper; Macauley, J. W.; Jain, Komal; Renken, Courtney; Duworko, James Tanu; Badio, Moses; Jallah, Wilhemina; Hensley, Lisa E.; Briese, Thomas; Lipkin, W. Ian; Mishra, Nischay

doi:10.3201/eid2712.211818

Cited by 6 publications

(4 citation statements)

References 5 publications

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“…The capital city of Monrovia (Montserrado County) and Kakata (Margibi County) are highly populated regions with dense regions of commerce. Urban areas have been reported to be more inundated with SARS-CoV-2 circulation in Liberia and Sierra Leone [20,23]. The results of the MIA assay were able to recapitulate these findings in Liberia.…”

Section: Discussionmentioning

confidence: 70%

“…Our study was conducted at University of Liberia's Fendall laboratory on samples collected before the major vaccine rollout in Liberia during the summer of 2021. At this time, Liberia and Sierra Leone surged in COVID-19 cases as the Delta variant was detected in the region [20,21]. However, this study did not test for reactivity against Delta variant spike protein as this antigen was unavailable at the time.…”

Section: Discussionmentioning

confidence: 95%

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A Serological Multiplexed Immunoassay (MIA) Detects Antibody Reactivity to SARS-CoV-2 and Other Viral Pathogens in Liberia and Is Configurable as a Multiplexed Inhibition Test (MINT)

Haun,

To,

Williams

et al. 2024

Immuno

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The SARS-CoV-2 pandemic ignited global efforts to rapidly develop testing, therapeutics, and vaccines. However, the rewards of these efforts were slow to reach many low- to middle-income countries (LMIC) across the African continent and globally. Therefore, two bead-based multiplexed serological assays were developed to determine SARS-CoV-2 exposure across four counties in Liberia. This study was conducted during the summer of 2021 on 189 samples collected throughout Grand Bassa, Bong, Margibi, and Montserrado counties. Our multiplexed immunoassay (MIA) detected elevated exposure to SARS-CoV-2 and multiple variant antigens. Additionally, we detected evidence of exposure to Dengue virus serotype 2, Chikungunya virus, and the seasonal coronavirus NL63. Our multiplexed inhibition test (MINT) was developed from the MIA to observe antibody-mediated inhibition of SARS-CoV-2 spike protein binding to its cognate cellular receptor ACE-2. We detected inhibitory antibodies in the tested Liberian samples, which were collectively consistent with a convalescent serological profile. These complementary assays serve to supplement existing serological testing needs and may enhance the technical capacity of scientifically underrepresented regions globally.

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Section: Discussionmentioning

confidence: 70%

Section: Discussionmentioning

confidence: 95%

A Serological Multiplexed Immunoassay (MIA) Detects Antibody Reactivity to SARS-CoV-2 and Other Viral Pathogens in Liberia and Is Configurable as a Multiplexed Inhibition Test (MINT)

Haun,

To,

Williams

et al. 2024

Immuno

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“…Near complete SARS-CoV-2 genomic sequences (>99% genome recovery) recovered from Pt 1, Pt 6, and Pt 7 were submitted to the GISAID database (accession ID: EPI_ISL_4298277 to EPI_ISL_4298281). The SARS-CoV-2 genome sequences of different variants of concerns, additional Alpha and Delta variant sequences recovered from immunocompetent individuals from recently published studies [ 24 , 25 ], and the viral genomes recovered from the immunocompromised patients in this study were compared for their genomic variability ( Figure 2 A). The genome recovered from Pt 1 represented the 20A variant with characteristic F4V, L212V, L452R, D614G, A672V, and P681H spike aa substitutions.…”

Section: Resultsmentioning

confidence: 99%

“…( A ) Nucleotide alignment of surface glycoprotein gene recovered from Pt 1, Pt 6, and Pt 7 showing non-synonymous nucleotide mutations compared against other SARS-CoV-2 variants of concern (VOCs) and the consensus Alpha and Delta sequences from previous studies. •Consensus Alpha variant sequence was generated from alignment of 88 individual SARS-CoV-2 Alpha variant genomic sequences recovered from 88 patients [ 24 ], and consensus Delta variant sequence was generated from alignment of 44 individual SARS-CoV-2 Delta variant genomic sequences recovered from 44 patients [ 25 ] using Geneious R10 software. ( B ) Twenty-four nucleotide deletions were observed in the surface glycoprotein of the virus recovered from Pt 1-Swab, Pt 1 Swab-VC, and Pt 6 swab; ( C ) Eight amino acid deletions from 138–145 positions were observed in the protein alignment; ( D ) Time-point growth curve for SARS-CoV-2 VOCs (WA1, Alpha, Beta, Gamma, and Omicron) and Pt 1_VC from 0 to 144 h in vitro.…”

Section: Figurementioning

confidence: 99%

A Short Series of Case Reports of COVID-19 in Immunocompromised Patients

Mishra

Zahra

Chauhan

et al. 2022

Viruses

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Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.

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