Biology subjects

Kapur, V.

Publications and source records attributed to Kapur, V..

8 recordsLinked to original sources

bioRxiv2023

An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows

Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these referents do not capture the complete structural variation now known to be present in the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC0 from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC0 mapped more short sequencing reads and called more SNPs relative to the Comas et al. sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC0 provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent in H37Rv such as the TbD1 and RvD4496/RD7/RD713 regions in standard MTBC workflows without additional steps. The use of MTBC0 as an ancestral reference sequence into a standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC. Data SummaryThe MTBC0 sequence, is available in the online data supplement in FASTA format at https://github.com/lukebharrison/MTBC0. Included with the MTBC0 sequence in the data supplement are: the reference-free alignment of MTBC closed genomes in hierarchical alignment (HAL) format, control files for cactus, annotations for H37Rv and L8, a BED file of regions excluded from SNP calls lifted over onto MTBC0, as well as the scripts used to call SNPs and the phylogenetic trees generated in this article. All previously published sequence data is available at the NCBI nucleotide and SRA databases, accession number for sequences used in this manuscript are available in Supplementary Tables 1 and 2. Impact StatementThis article describes an imputed ancestral genomic sequence (MTBC0) at the base of the MTBC for use as a reference sequence for Mycobacterium tuberculosis genomic workflows. Widely used reference sequences are limited to the structural diversity present in H37Rv, a lineage 4 isolate. MTBC0 obviates this limitation by incorporating the structural variation present at the base of the Mycobacterium tuberculosis complex (MTBC) by encompassing a wide sample of human and animal lineages including newly discovered lineages (L8, M. orygis). Use of MTBC0 enables the mapping of more reads and calling of more SNPs and allows for the investigation of structural variation not present in the current used reference sequences within this important group of animal and human pathogens.

microbiology↗

bioRxiv2022

Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer

White-tailed deer (Odocoileus virginianus) are highly susceptible to infection by SARS-CoV-2, with multiple reports of widespread spillover of virus from humans to free-living deer. While the recently emerged SARS-CoV-2 B.1.1.529 Omicron variant of concern (VoC) has been shown to be notably more transmissible amongst humans, its ability to cause infection and spillover to non-human animals remains a challenge of concern. We found that 19 of the 131 (14.5%; 95% CI: 0.10-0.22) white-tailed deer opportunistically sampled on Staten Island, New York, between December 12, 2021, and January 31, 2022, were positive for SARS-CoV-2 specific serum antibodies using a surrogate virus neutralization assay, indicating prior exposure. The results also revealed strong evidence of age-dependence in antibody prevalence. A significantly ({chi}2, p < 0.001) greater proportion of yearling deer possessed neutralizing antibodies as compared with fawns (OR=12.7; 95% CI 4-37.5). Importantly, SARS-CoV-2 nucleic acid was detected in nasal swabs from seven of 68 (10.29%; 95% CI: 0.0-0.20) of the sampled deer, and whole-genome sequencing identified the SARS-CoV-2 Omicron VoC (B.1.1.529) is circulating amongst the white-tailed deer on Staten Island. Phylogenetic analyses revealed the deer Omicron sequences clustered closely with other, recently reported Omicron sequences recovered from infected humans in New York City and elsewhere, consistent with human to deer spillover. Interestingly, one individual deer was positive for viral RNA and had a high level of neutralizing antibodies, suggesting either rapid serological conversion during an ongoing infection or a "breakthrough" infection in a previously exposed animal. Together, our findings show that the SARS-CoV-2 B.1.1.529 Omicron VoC can infect white-tailed deer and highlights an urgent need for comprehensive surveillance of susceptible animal species to identify ecological transmission networks and better assess the potential risks of spillback to humans. Key FindingsThese studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for investigations on human-to-animal-to-human spillovers/spillbacks as well as on better defining the expanding host-range of SARS-CoV-2 in non-human animals and the environment.

microbiology↗

bioRxiv2021

Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)

Many animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission of the virus in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 may be circulating in deer, we tested 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between November 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%), and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive "One Health" approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2. One-Sentence SummarySARS-CoV-2 was detected in one-third of sampled white-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover and deer-to-deer transmission events.

microbiology↗

bioRxiv2021

Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.

synthetic biology↗

bioRxiv2020

Limited window for donation of convalescent plasma with high live-virus neutralizing antibodies for COVID-19 immunotherapy

The optimal timeframe for donating convalescent plasma to be used for COVID-19 immunotherapy is unknown. To address this important knowledge deficit, we determined in vitro live-virus neutralizing capacity and persistence of IgM and IgG antibody responses against the receptor-binding domain and S1 ectodomain of the SARS-CoV-2 spike glycoprotein in 540 convalescent plasma samples obtained from 175 COVID-19 plasma donors for up to 142 days post-symptom onset. Robust IgM, IgG, and viral neutralization responses to SARS-CoV-2 persist, in the aggregate, for at least 100 days post-symptom onset. However, a notable acceleration in decline in virus neutralization titers [≥]160, a value suitable for convalescent plasma therapy, was observed starting 60 days after first symptom onset. Together, these findings better define the optimal window for donating convalescent plasma useful for immunotherapy of COVID-19 patients and reveal important predictors of an ideal plasma donor, including age and COVID-19 disease severity score. One Sentence SummaryEvaluation of SARS-CoV-2 anti-spike protein IgM, IgG, and live-virus neutralizing titer profiles reveals that the optimal window for donating convalescent plasma for use in immunotherapy is within the first 60 days of symptom onset.

immunology↗

bioRxiv2020

Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma

Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer [≥]160 was 80% or greater with anti-RBD or anti-ECD titers of [≥]1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers [≥]160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of [≥]1:1350, and evidence of VN [≥]1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of [≥]1:1350 may provide critical information about protection against COVID-19 disease.

immunology↗

bioRxiv2019

Identifying age cohorts responsible for Peste des petits ruminants virus transmission among sheep, goats, and cattle in northern Tanzania

Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in global sheep and goat populations and leads to approximately $2 billion USD in global annual losses. PPRV is currently targeted by the Food and Agricultural Organization and World Animal Health Organization for global eradication by 2030. To better control this disease and inform eradication strategies, an improved understanding of how PPRV risk varies by age is needed. Our study used a piece-wise catalytic model to estimate the age-specific force of infection (FOI, per capita infection rate of susceptible hosts) among sheep, goats, and cattle from a cross-sectional serosurvey dataset collected in 2016 in Tanzania. Apparent seroprevalence rose with age, as would be expected if PPRV is a fully-immunizing infection, reaching 53.6%, 46.8%, and 11.6% (true seroprevalence: 52.7%, 52.8%, 39.2%) for sheep, goats, and cattle, respectively. Seroprevalence was significantly higher among pastoral animals than agropastoral animals across all ages, with pastoral sheep and goat seroprevalence approaching 70% and 80%, respectively, suggesting endemicity in pastoral settings. The best fitting piece-wise catalytic models included merged age groups: two age groups for sheep, three age groups for goats, and four age groups for cattle. However, the signal of these age heterogeneities was weak, with overlapping confidence intervals around force of infection estimates from most models with the exception of a significant FOI peak among 2.5-3.5 year old pastoral cattle. Pastoral animals had a higher force of infection overall, and across a wider range of ages than agropastoral animals. The subtle age-specific force of infection heterogeneities identified in this study among sheep, goats, and cattle suggest that targeting control efforts by age may not be as effective as targeting by other risk factors, such as management system type. Further research should investigate how specific husbandry practices affect PPRV transmission. Author SummaryAge differences in transmission are important for many infections, and can help target control programs. We used an age-structured serosurvey of Tanzanian sheep, goats, and cattle to explore peste des petits ruminants virus transmission. We estimated rate at which susceptibles acquire infection (force of infection) to determine which age group(s) had the highest transmission rates. We hypothesized that an age-varying model with multiple age groups would better fit the data than an age constant model and that the highest transmission rates would appear in the youngest age groups. Furthermore, we hypothesized evidence of immunity would increase with age. The data supported our hypothesis at the species level and the best fitting models merged age groups: two, three, and four age group models were best for sheep, goats, and cattle, respectively. The highest rates occurred among younger age groups and evidence of immunity rose with age for all species. In most models, confidence interval estimates overlapped, but there was a significant FOI peak among 2.3-3.5 year old pastoral cattle. Importantly, these data indicate that there is not sufficient evidence to support targeted control by age group, and that targeted control based on production system should be more effective.

ecology↗

bioRxiv2019

Zoonotic tuberculosis in India: looking beyond Mycobacterium bovis

BackgroundZoonotic tuberculosis (zTB) is the transmission of Mycobacterium tuberculosis complex (MTBC) subspecies from animals to humans. zTB is generally quantified by determining the proportion of human isolates that are Mycobacterium bovis. Although India has the worlds largest number of human TB cases and the largest cattle population, where bovine TB is endemic, the burden of zTB is unknown. MethodsTo obtain estimates of zTB in India, a PCR-based approach was applied to sub-speciate positive MGIT(R) cultures from 940 patients (548 pulmonary, 392 extrapulmonary disease) at a large referral hospital in India. Twenty-five isolates of interest were subject to whole genome sequencing (WGS) and compared with 715 publicly available MTBC sequences from South Asia. FindingsA conclusive identification was obtained for 939 samples; wildtype M. bovis was not identified (95% CI: 0 - 0.4%). There were 912 M. tuberculosis sensu stricto (97.0%, 95% CI: 95.7 - 98.0), 7 M. orygis (95% CI: 0.3 - 1.5%); 5 M. bovis BCG, and 15 non-tuberculous mycobacteria. WGS analysis of 715 MTBC sequences again identified no M. bovis (95% CI: 0 - 0.4%). Human and cattle MTBC isolates were interspersed within the M. orgyis and M. tuberculosis sensu stricto lineages. InterpretationM. bovis prevalence in humans is an inadequate proxy of zTB in India. The recovery of M. orygis from humans, together with the finding of M. tuberculosis in cattle, underscores the need for One Health investigations to assess the burden of zTB in countries with endemic bovine TB. FundingBill & Melinda Gates Foundation, Canadian Institutes for Health Research

microbiology↗