A quantitative evaluation of the impact of vaccine roll-out rate and coverage on reducing deaths: insights from the first 2 years of COVID-19 epidemic in Iran.

Background: Vaccination has played a pivotal role in reducing the burden of COVID-19. Despite numerous studies highlighting its benefits in reducing the risk of severe disease and death, we still lack a quantitative understanding of how varying vaccination roll-out rates influence COVID-19 mortality.

Methods: We developed a framework for estimating the number of avertable COVID-19 deaths (ACDs) by vaccination in Iran.

Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance.

Background: In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola.

The evolution of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion.

Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models.

The SARS-CoV-2 epidemic has been extended by the evolution of more transmissible viral variants. In autumn 2020, the B.1.

A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data.

The transmission dynamics and burden of SARS-CoV-2 in many regions of the world is still largely unknown due to the scarcity of epidemiological analyses and lack of testing to assess the prevalence of disease. In this work, we develop a quantitative framework based on excess mortality data to reconstruct SARS-CoV-2 transmission dynamics and assess the level of underreporting in infections and deaths. Using weekly all-cause mortality data from Iran, we are able to show a strong agreement between our attack rate estimates and seroprevalence measurements in each province and find significant heterogeneity in the level of exposure across the country with 11 provinces reaching near 100% attack rates.

Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza.

High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters.

Engaging Religious Institutions and Faith-Based Communities in Public Health Initiatives: A Case Study of the Romanian Orthodox Church During the COVID-19 Pandemic.

The success of public health interventions is highly dependent on the compliance of the general population. State authorities often implement policies without consulting representatives of faith-based communities, thereby overlooking potential implications of public health measures for these parts of society. Although ubiquitous, these challenges are more readily observable in highly religious states.

A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses.

Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent evolutionary histories of viruses but may severely underestimate their longer-term origins because of the inverse correlation between inferred rates of evolution and the timescale of their measurement. Here, we provide a predictive mechanistic model that readily explains the rate decay phenomenon over a wide range of timescales and recapitulates the ubiquitous power-law rate decay with a slope of -0.

Lessons for preparedness and reasons for concern from the early COVID-19 epidemic in Iran.

Introduction: Many countries with an early outbreak of SARS-CoV-2 struggled to gauge the size and start date of the epidemic mainly due to limited testing capacities and a large proportion of undetected asymptomatic and mild infections. Iran was among the first countries with a major outbreak outside China.

Methods: We constructed a globally representative sample of 802 genomes, including 46 samples from patients inside or with a travel history to Iran.

Excess deaths associated with the Iranian COVID-19 epidemic: A province-level analysis.

Objective: There has been no province-level data on the number of coronavirus disease 2019 (COVID-19)-related deaths in Iran since the start of the pandemic. This study was performed to estimate the number of COVID-19 deaths and population-level exposure per province using seasonal all-cause mortality data.

Methods: Time-series data were collected from the National Organization for Civil Registration on the seasonal all-cause mortality from spring 2015 to summer 2020 (from March 21, 2015 to September 21, 2020), in accordance with the Solar Hijri (SH) calendar, to estimate the expected number of seasonal deaths for each province using a piecewise linear regression model.

Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR.

BackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset.AimTo determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type.

Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method.

The transmission bottleneck is defined as the number of viral particles that transmit from one host to establish an infection in another. Genome sequence data have been used to evaluate the size of the transmission bottleneck between humans infected with the influenza virus; however, the methods used to make these estimates have some limitations. Specifically, viral allele frequencies, which form the basis of many calculations, may not fully capture a process which involves the transmission of entire viral genomes.

The expected time to cross extended fitness plateaus.

For a population to acquire a complex adaptation requiring multiple individually neutral mutations, it must cross a plateau in the fitness landscape. We consider plateaus involving three mutations, and show that large populations can cross them rapidly via lineages that acquire multiple mutations while remaining at low frequency, much faster than the ∝μ rate for simultaneous triple mutations. Plateau-crossing is fastest for very large populations.

On the role of topology in regulating transcriptional cascades.

We study the impact of topology on the response of a transcriptional cascade with certain circuit topologies to a constant and time-varying input signal. We systematically analyze the response of the output to activating and repressing cascades. We identify two types of responses for a linear cascade, namely the "Decaying mode", where the input signal becomes exceedingly weaker as it propagates, and the "Bistable mode", where the input signal can either be amplified or die out in the pathway.

Luria-Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution.

We re-examined data from the classic Luria-Delbrück fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms (as would happen for bacteria with CRISPR-Cas immunity). Analysis of the combined model was not performed in the original 1943 paper.