Development of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern

AbstractTo support COVID-19 pandemic planning, we develop a model-inference system to estimate epidemiological properties of new SARS-CoV-2 variants of concern using case and mortality data while accounting for under-ascertainment, disease seasonality, non-pharmaceutical interventions, and mass-vaccination. Applying this system to study three variants of concern, we estimate that B.1.1.7 has a 46.6% (95% CI: 32.3–54.6%) transmissibility increase but nominal immune escape from protection induced by prior wild-type infection; B.1.351 has a 32.4% (95% CI: 14.6–48.0%) transmissibility increase and 61.3% (95% CI: 42.6–85.8%) immune escape; and P.1 has a 43.3% (95% CI: 30.3–65.3%) transmissibility increase and 52.5% (95% CI: 0–75.8%) immune escape. Model simulations indicate that B.1.351 and P.1 could outcompete B.1.1.7 and lead to increased infections. Our findings highlight the importance of preventing the spread of variants of concern, via continued preventive measures, prompt mass-vaccination, continued vaccine efficacy monitoring, and possible updating of vaccine formulations to ensure high efficacy.

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Author Correction: Development of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern

Nature Communications ◽

10.1038/s41467-021-27703-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Wan Yang ◽

Jeffrey Shaman

Keyword(s):

Inference System ◽

Model Inference ◽

Epidemiological Characteristics

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SARS-CoV-2 transmission dynamics in South Africa and epidemiological characteristics of the Omicron variant

10.1101/2021.12.19.21268073 ◽

2021 ◽

Author(s):

Wan Yang ◽

Jeffrey Shaman

Keyword(s):

South Africa ◽

Transmission Dynamics ◽

Gauteng Province ◽

Inference System ◽

South Africans ◽

Model Inference ◽

Population Immunity ◽

Novel Variant ◽

Nonpharmaceutical Interventions ◽

Epidemiological Characteristics

Within days of first detection, Omicron SARS-CoV-2 variant case numbers grew exponentially and spread globally. To better understand variant epidemiological characteristics, we utilize a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa and decompose novel variant transmissibility and immune erosion. Accounting for under-detection of infection, infection seasonality, nonpharmaceutical interventions, and vaccination, we estimate that the majority of South Africans had been infected by SARS-CoV-2 before the Omicron wave. Based on findings for Gauteng province, Omicron is estimated 100.3% (95% CI: 74.8 - 140.4%) more transmissible than the ancestral SARS-CoV-2 and 36.5% (95% CI: 20.9 - 60.1%) more transmissible than Delta; in addition, Omicron erodes 63.7% (95% CI: 52.9 - 73.9%) of the population immunity, accumulated from prior infections and vaccination, in Gauteng.

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129 Genomic Relationship Between PRRSV Wild-type Infection and PRRSV Vaccination for Antibody Response and Reproductive Performance

Journal of Animal Science ◽

10.1093/jas/skab054.032 ◽

2021 ◽

Vol 99 (Supplement_1) ◽

pp. 18-18

Author(s):

Leticia P Sanglard ◽

Felipe Hickmann ◽

Yijian Huang ◽

Kent A Gray ◽

Daniel Linhares ◽

...

Keyword(s):

Antibody Response ◽

Reproductive Performance ◽

Genetic Correlations ◽

Clinical Signs ◽

Respiratory Syndrome Virus ◽

Wild Type ◽

Large White ◽

Selection For ◽

Indicator Trait ◽

Type Infection

Abstract Immunoglobulin G antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) has been proposed as an indicator trait for improved reproductive performance in PRRSV-infected purebred sows and PRRSV-vaccinated crossbred gilts. In this study, we investigated the genetic correlations (rg) of S/P ratio following a PRRSV outbreak and PRRSV-vaccination with performance in non-exposed and PRRSV-exposed sows. PRRSV outbreak phase was defined based on previously described methodologies after the detection of typical clinical signs of PRRSV infection. 541 Landrace sows had S/P ratio measured at ~54 days after the beginning of the PRRSV outbreak (S/Poutbreak), and 906 Landrace x Large White naïve F1 gilts had S/P ratio measured at ~50 days after vaccination with a commercial modified live PRRSV vaccine (S/PVx). 711 and 428 Landrace sows had reproductive performance recorded before and during the PRRSV outbreak, respectively. 811 vaccinated F1 animals had farrowing performance for up to 3 parities. All animals were genotyped for ~28K SNPs. The estimate of rg of S/Poutbreakwith S/PVx was high (rg±SE = 0.72±0.18). Estimates of rg of S/Poutbreak with reproductive performance in F1 sows were low to moderate, ranging from 0.05±0.23 (number stillborn) to 0.30±0.20 (total number born). Estimates of rg of S/PVxwith reproductive performance in non-infected purebred sows were moderate and favorable with number born alive (0.50±0.23), but low (0 to -0.11±0.23) with litter mortality traits. Estimates of rg of S/PVx were moderate and negative (-0.47±0.18) with the number of mummies in PRRSV-infected purebred sows and low with other traits (-0.29±0.18 for total number born to 0.05±0.18 for number stillborn). These results indicate that selection for antibody response following a PRRSV outbreak collected in purebred sows and to PRRSV vaccination collected in commercial crossbred gilts may increase litter size of non-infected and PRRSV-exposed purebred and commercial crossbred sows.

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Molecular Typing ofNeisseria gonorrhoeaeIsolates by Opa-Typing and Ribotyping in New Delhi, India

International Journal of Microbiology ◽

10.1155/2009/934823 ◽

2009 ◽

Vol 2009 ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

Pejvak Khaki ◽

Preena Bhalla ◽

Ahmad Mir Fayaz ◽

Sohiela Moradi Bidhendi ◽

Majid Esmailzadeh ◽

...

Keyword(s):

Molecular Typing ◽

Preventive Measures ◽

Restriction Enzymes ◽

New Delhi ◽

Pcr Product ◽

Sexual Contacts ◽

High Level ◽

Epidemiological Characteristics ◽

Epidemiological Characterization

Control and preventive measures for gonococcal infections are based on precise epidemiological characteristics ofN. gonorrhoeaeisolates. In the present study the potential utility of opa-typing and ribotyping for molecular epidemiological study of consecutive gonococcal strains was determined. Sixty gonococcal isolates were subjected to ribotyping with two restriction enzymes,AvaII andHincII, and opa-typing withTaqI andHpaII for epidemiological characterization of gonococcal population. Ribotyping withAvaII yielded 6 ribotype patterns while twelve RFLP patterns were observed withHincII. Opa-typing of the 60 isolates revealed a total 54 opa-types, which 48 were unique and 6 formed clusters. Fifty-two opa-types were observed withTaqI-digested PCR product while opa-typing withHpaII demonstrated 54 opa-types. The opa-types from isolates that were epidemiologically unrelated were distinct, whereas those from the sexual contacts were identical. The results showed that opa-typing is highly useful for characterizing gonococcal strains from sexual contacts and has more discriminatory than ribotyping that could differentiate between gonococci of the same ribotype. The technique even with a single restriction enzyme has a high level of discrimination (99.9%) between epidemiologically unrelated isolates. In conclusion, the molecular methods such as opa-typing and ribotyping can be used for epidemiological characterization of gonococcal strains.

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Dynamic interactions of influenza viruses in Hong Kong during 1998-2018

10.1101/19008987 ◽

2019 ◽

Cited By ~ 1

Author(s):

Wan Yang ◽

Eric H. Y. Lau ◽

Benjamin J. Cowling

Keyword(s):

Hong Kong ◽

Influenza A ◽

Vaccine Development ◽

Immune Escape ◽

Influenza Viruses ◽

Influenza Surveillance ◽

Influenza Epidemic ◽

Inference System ◽

Population Immunity ◽

Cross Immunity

AbstractInfluenza epidemics cause substantial morbidity and mortality every year worldwide. Currently, two influenza A subtypes, A(H1N1) and A(H3N2), and type B viruses co-circulate in humans and infection with one type/subtype could provide cross-protection against the others. However, it remains unclear how such ecologic competition via cross-immunity and antigenic mutations that allow immune escape impact influenza epidemic dynamics at the population level. Here we develop a comprehensive model-inference system and apply it to study the evolutionary and epidemiological dynamics of the three influenza types/subtypes in Hong Kong, a city of global public health significance for influenza epidemic and pandemic control. Utilizing long-term influenza surveillance data since 1998, we are able to estimate the strength of cross-immunity between each virus-pairs, the timing and frequency of punctuated changes in population immunity in response to antigenic mutations in influenza viruses, and key epidemiological parameters over the last 20 years including the 2009 pandemic. We find evidence of cross-immunity in all types/subtypes, with strongest cross-immunity from A(H1N1) against A(H3N2). Our results also suggest that A(H3N2) may undergo antigenic mutations in both summers and winters and thus monitoring the virus in both seasons may be important for vaccine development. Overall, our study reveals intricate epidemiological interactions and underscores the importance of simultaneous monitoring of population immunity, incidence rates, and viral genetic and antigenic changes.

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Molecular Analysis and Genome Sequencing of SARS-Cov-2 during Second Wave 2021 Revealed Variant Diversity in India

Journal of Pure and Applied Microbiology ◽

10.22207/jpam.15.4.07 ◽

2021 ◽

Author(s):

Rupinder Bakshi ◽

Satinder Kaur ◽

Karashdeep Kaur ◽

Ramanpreet Kaur ◽

Jaspreet Kaur Boparai ◽

...

Keyword(s):

Genome Sequencing ◽

Immune Escape ◽

Age Group ◽

Wild Type ◽

Rt Pcr ◽

Dominant Trait ◽

Male Population ◽

Second Wave ◽

Rapid Emergence ◽

Critical Challenge

SARS-CoV-2 variants rapid emergence has posed critical challenge of higher transmission and immune escape causing serious threats to control the pandemic. The present study was carried out in confirmed cases of SARS-CoV-2 patients to elucidate the prevalence of SARS-CoV-2 variant strain. We performed RT-PCR using extracted RNA from the nasopharyngeal swabs of suspected Covid-19 patients. Confirmed positive cases with CT<25 were subjected to whole-genome sequencing to track the prevalence of the virus in the Malwa region of Punjab. The presence of B.1, B.1.1.7, B.1.351, B.1.617.1, B.1.617.2, AY.1 and other unidentified variants of SARS-CoV-2 was found in the studied population. Among all the variants, B.1.1.7 (UK variant) and B.1.617.2 (delta-Indian variant) was found to be the most dominant variant in the population and was found majorly in Patiala followed by Ludhiana, SBS Nagar, Mansa and Sangrur. In addition to this, sequencing results also observed that the dominant trait was more prevalent in male population and age group 21-40 years. The B.1.1.7 and B.1.617.2 variant of SARS-CoV-2 is replacing the wild type (Wuhan Strain) and emerging as the dominant variant in Punjab.

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An Evidence Base for School Health Policy during the COVID-19 Pandemic

Health Behavior and Policy Review ◽

10.14485/hbpr.8.1.4 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Saif Badran ◽

Omran Musa ◽

Somaya Al-maadeed ◽

Egon Toft ◽

Suhail Doi

Keyword(s):

Dose Response ◽

Case Fatality Rate ◽

School Health ◽

Meta Analysis ◽

Case Fatality ◽

Evidence Base ◽

Mortality Data ◽

Response Analysis ◽

Fatality Rate ◽

Epidemiological Characteristics

Objective: Children represent a small fraction of confirmed COVID-19 cases, with a low case fatality rate (CFR). In this paper, we lay out an evidence-based policy for reopening schools. Methods: We gathered age-specific COVID-19 case counts and identified mortality data for 14 countries. Dose-response meta-analysis was used to examine the relationship of the incremental case fatality rate (CFR) to age. In addition, an evidence-to-decision framework (EtD) was used to correlate the dose-response data with other epidemiological characteristics of COVID-19 in childhood. Results: In the dose-response analysis, we found that there was an almost negligible fatality below age 18. CFR rose little between ages 5 to 50 years. The confidence intervals were narrow, suggesting relative homogeneity across countries. Further data suggested decreased childhood transmission from respiratory droplets and a low viral load among children. Conclusions: Opening up schools and kindergartens is unlikely to impact COVID-19 case or mortality rates in both the child and adult populations. We outline a robust plan for schools that recommends that general principles not be micromanaged, with authority left to schools and monitored by public health authorities.

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Regulation and characterization of mutants of fixABCX in Rhizobium leguminosarum.

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-02-21-0037-r ◽

2021 ◽

Author(s):

Isabel Webb ◽

Jiabao Xu ◽

Carmen Sanchez-Cañizares ◽

Ramakrishnan Karunakaran ◽

Vinoy Ramachandran ◽

...

Keyword(s):

Nitrogen Fixation ◽

Rhizobium Leguminosarum ◽

Redox Balance ◽

Rna Seq ◽

Wild Type ◽

Transcription Start Sites ◽

Sym Plasmid ◽

Microaerobic Conditions ◽

Type Infection

Symbiosis between Rhizobium leguminosarum and Pisum sativum requires tight control of redox balance in order to maintain respiration under the microaerobic conditions required for nitrogenase, whilst still producing the eight electrons and sixteen molecules of ATP needed for nitrogen fixation. FixABCX, electron transfer flavoproteins essential for nitrogen fixation, are encoded on the Sym plasmid (pRL10), immediately upstream of nifA, which encodes the general transcriptional regulator of nitrogen fixation. There is a symbiotically-regulated NifA-dependent promoter upstream of fixA (PnifA1), as well as an additional basal constitutive promoter driving background expression of nifA (PnifA2). These were confirmed by 5’-end mapping of transcription start sites using differential (d) RNA-seq. Complementation of polar fixAB and fixX mutants (Fix- strains) confirmed expression of nifA from PnifA1 in symbiosis. Electron microscopy combined with single-cell Raman microspectroscopy characterization of fixAB mutants revealed previously unknown heterogeneity in bacteroid morphology within a single nodule. Two morphotypes of mutant fixAB bacteroids were observed. One was larger than wild-type bacteroids and contained high levels of polyhydroxy-3-butyrate, a complex energy/reductant storage product. A second bacteroid phenotype was morphologically and compositionally different and resembled wild-type infection thread cells. From these two characteristic fixAB mutant bacteroid morphotypes, inferences can be drawn on the metabolism of wild-type nitrogen-fixing bacteroids.

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Cryptococcus neoformans Evades Pulmonary Immunity by Modulating Xylose Precursor Transport

Infection and Immunity ◽

10.1128/iai.00288-20 ◽

2020 ◽

Vol 88 (8) ◽

Author(s):

Lucy X. Li ◽

Camaron R. Hole ◽

Javier Rangel-Moreno ◽

Shabaana A. Khader ◽

Tamara L. Doering

Keyword(s):

Cryptococcus Neoformans ◽

Mutant Strain ◽

Fungal Pathogen ◽

Wild Type ◽

Content Type ◽

Helper Cell Type ◽

Lymphoid Structures ◽

Type Infection

ABSTRACT Cryptococcus neoformans is a fungal pathogen that kills almost 200,000 people each year and is distinguished by abundant and unique surface glycan structures that are rich in xylose. A mutant strain of C. neoformans that cannot transport xylose precursors into the secretory compartment is severely attenuated in virulence in mice yet surprisingly is not cleared. We found that this strain failed to induce the nonprotective T helper cell type 2 (Th2) responses characteristic of wild-type infection, instead promoting sustained interleukin 12p40 (IL-12p40) induction and increased IL-17A (IL-17) production. It also stimulated dendritic cells to release high levels of proinflammatory cytokines, a behavior we linked to xylose expression. We further discovered that inducible bronchus-associated lymphoid tissue (iBALT) forms in response to infection with either wild-type cryptococci or the mutant strain with reduced surface xylose; although iBALT formation is slowed in the latter case, the tissue is better organized. Finally, our temporal studies suggest that lymphoid structures in the lung restrict the spread of mutant fungi for at least 18 weeks after infection, which is in contrast to ineffective control of the pathogen after infection with wild-type cells. These studies demonstrate the role of xylose in modulation of host response to a fungal pathogen and show that cryptococcal infection triggers iBALT formation.

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