Molecular and serological investigation of the 2021 COVID-19 case surge in Mongolian vaccinees

A surge in Covid-19 cases in Mongolia in March 2021 resulted in a government-mandated shutdown. This shutdown was relaxed in May 2021 as case numbers decreased and nationwide vaccination rates using Sinopharm, Covishield/AstraZeneca, Sputnik V, and Pfizer/BioNTech vaccines exceeded 50% of the population. Case rates increased again in early June 2021 in both vaccinated and non-vaccinated individuals. To determine whether the surge was due to the emergence of Delta or another variant, or vaccine failure, a rapid, opportunistic investigation was conducted that comprised virus sequence analysis of nasal swab samples from breakthrough cases and antibody assays of plasma from healthy vaccinees. More than 90% of breakthrough infections during the second case surge were due to the Alpha variant. Spike protein ELISA and SARS-CoV-2 neutralization assays data revealed large differences in plasma titers of antibodies to SARS-CoV-2, with mRNA vaccines eliciting higher titers than adenovirus-vectored or killed virus vaccines.

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Performance of a SARS CoV-2 antibody ELISA based on simultaneous measurement of antibodies against the viral nucleoprotein and receptor-binding domain

European Journal of Clinical Microbiology & Infectious Diseases ◽

10.1007/s10096-021-04284-5 ◽

2021 ◽

Author(s):

Nina Reiners ◽

Carolin Schnurra ◽

Henning Trawinski ◽

Judith Kannenberg ◽

Thomas Hermsdorf ◽

...

Keyword(s):

Receptor Binding ◽

Simultaneous Measurement ◽

False Positives ◽

Binding Domain ◽

Diagnostic Sensitivity ◽

Spike Protein ◽

Receptor Binding Domain ◽

Simultaneous Testing ◽

Antibody Assays ◽

Antibody Elisa

AbstractSARS CoV-2 antibody assays measure antibodies against the viral nucleoprotein (NP) or spike protein. The study examined if testing of antibodies against both antigens increases the diagnostic sensitivity. Sera (N=98) from infected individuals were tested with ELISAs based on the NP, receptor-binding domain (RBD), or both proteins. The AUROCs were 0.958 (NP), 0.991 (RBD), and 0.992 (NP/RBD). The RBD- and NP/RBD-based ELISAs showed better performance than the NP-based assay. Simultaneous testing for antibodies against NP and RBD increased the number of true and false positives. If maximum diagnostic sensitivity is required, the NP/RBD-based ELISA is preferable. Otherwise, the RBD-based ELISA is sufficient.

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Genesis of Kirsten murine sarcoma virus: sequence analysis reveals recombination points and potential leukaemogenic determinant on parental leukaemia virus genome

Nucleic Acids Research ◽

10.1093/nar/12.17.6839 ◽

1984 ◽

Vol 12 (17) ◽

pp. 6839-6852 ◽

Cited By ~ 9

Author(s):

John D. Norton ◽

Jane Connor ◽

Roger J. Avery

Keyword(s):

Sequence Analysis ◽

Virus Genome ◽

Leukaemia Virus ◽

Murine Sarcoma Virus ◽

Sarcoma Virus ◽

Virus Sequence ◽

Murine Sarcoma

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Use of short tandem repeat fingerprinting to validate sample origins in hepatitis C virus molecular epidemiology studies

Journal of General Virology ◽

10.1099/vir.0.057828-0 ◽

2014 ◽

Vol 95 (1) ◽

pp. 66-70 ◽

Cited By ~ 2

Author(s):

Victoria C. Edwards ◽

C. Patrick McClure ◽

Richard J. P. Brown ◽

Emma Thompson ◽

William L. Irving ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Sequence Analysis ◽

Molecular Epidemiology ◽

Alternative Explanation ◽

Sequence Analyses ◽

Distinct Virus ◽

Virus Sequence ◽

Epidemiology Studies ◽

Short Tandem

Sequence analysis is used to define the molecular epidemiology and evolution of the hepatitis C virus. Whilst most studies have shown that individual patients harbour viruses that are derived from a limited number of highly related strains, some recent reports have shown that some patients can be co-infected with very distinct variants whose frequency can fluctuate greatly. Whilst co-infection with highly divergent strains is possible, an alternative explanation is that such data represent contamination or sample mix-up. In this study, we have shown that DNA fingerprinting techniques can accurately assess sample provenance and differentiate between samples that are truly exhibiting mixed infection from those that harbour distinct virus populations due to sample mix-up. We have argued that this approach should be adopted routinely in virus sequence analyses to validate sample provenance.

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High diversity in Delta variant across countries revealed via genome-wide analysis of SARS-CoV-2 beyond the Spike protein

10.1101/2021.09.01.458647 ◽

2021 ◽

Author(s):

Pritha Ghosh ◽

Rohit Suratekar ◽

Michiel J.M. Niesen ◽

Praveen Anand ◽

Gregory Donadio ◽

...

Keyword(s):

Amino Acid ◽

Spike Protein ◽

P Value ◽

Missense Mutations ◽

Systematic Analysis ◽

Viral Loads ◽

Amino Acid Mutations ◽

Mechanistic Basis ◽

Alpha Variant ◽

High Diversity

The highly contagious Delta variant of SARS-CoV-2 has emerged as the new dominant global strain, and reports of reduced effectiveness of COVID-19 vaccines against the Delta variant are highly concerning. While there has been extensive focus on understanding the amino acid mutations in the Delta variant's Spike protein, the mutational landscape of the rest of the SARS-CoV-2 proteome (25 proteins) remains poorly understood. To this end, we performed a systematic analysis of mutations in all the SARS-CoV-2 proteins from nearly 2 million SARS-CoV-2 genomes from 176 countries/territories. Six highly-prevalent missense mutations in the viral life cycle-associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, Gamma = 0.22%). Furthermore, we find that the Delta variant harbors a more diverse repertoire of mutations across countries compared to the previously dominant Alpha variant (cosine similarity: meanAlpha = 0.94, S.D.Alpha = 0.05; meanDelta = 0.86, S.D.Delta = 0.1; Cohen's dAlpha-Delta = 1.17, p-value < 0.001). Overall, our study underscores the high diversity of the Delta variant between countries and identifies a list of targetable amino acid mutations in the Delta variant's proteome for probing the mechanistic basis of pathogenic features such as high viral loads, high transmissibility, and reduced susceptibility against neutralization by vaccines.

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In-depth Sequence Analysis of SARS-CoV-2 Spike Protein Repudiates Mutation Mediated Adaptive Selection in the Virus

ACTA SCIENTIFIC MICROBIOLOGY ◽

10.31080/asmi.2020.03.0729 ◽

2020 ◽

Vol 3 (12) ◽

pp. 16-23

Author(s):

Pramita Chowdhury ◽

Bijurica Chakraborty ◽

Sanghamitra Sengupta

Keyword(s):

Sequence Analysis ◽

Spike Protein ◽

Adaptive Selection

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Serological follow-up of SARS-CoV-2 asymptomatic subjects

Scientific Reports ◽

10.1038/s41598-020-77125-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Gregorio Paolo Milani ◽

◽

Laura Dioni ◽

Chiara Favero ◽

Laura Cantone ◽

...

Keyword(s):

Blood Sample ◽

Nasal Swab ◽

Severe Pneumonia ◽

Spike Protein ◽

Serum Antibodies ◽

Follow Up Study ◽

Asymptomatic Subjects ◽

The University ◽

Structured Questionnaire

AbstractSARS-CoV-2 symptoms are non-specific and can range from asymptomatic presentation to severe pneumonia. Asymptomatic subjects carrying SARS-CoV-2 often remain undiagnosed and it is still debated whether they develop immunoglobulins (Ig) and how long they persist. The aim of this study was to investigate the development and persistence of antibodies against SARS-CoV-2 in asymptomatic subjects infected by the virus. This follow-up study was performed on the 31 asymptomatic subjects who presented a positive nasal swab or serology against SARS-CoV-2 (Ig against Spike-RBD) in the first part of the UNICORN study (March 2020) aimed at attesting previous or current contacts with the virus in the personnel of the University of Milan. Eight weeks after the first Ig measure, these subjects were invited to donate a second blood sample for testing serum antibodies (IgM, IgG and total antibodies) and to fill-in a structured questionnaire. About 80% of asymptomatic subjects did not present circulating immunoglobulins against SARS-CoV-2 after 8 weeks from a positive nasal swab against the virus. Moreover, in more than 40% of these subjects, no Ig against SARS-CoV-2 were detected at any time. Finally, about two third of subjects with immunoglobulins at baseline did not present IgG against SARS-CoV-2 after 8 weeks. The majority of subjects who developed an asymptomatic SARS-CoV-2 infection do not present antibodies against the RBD-spike protein after 8 weeks of follow-up. These data should be taken into account for the interpretation of the serological evidences on SARS-CoV-2 that are emerging nowadays.

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