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Researchers conducted a SARS-CoV-2 serosurvey on blood donors in New Zealand | Instant News


Various strategies are being used around the world to curb the ongoing coronavirus disease 2019 (COVID-19) pandemic. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new causative agent of COVID-19. The virus is highly contagious and is transmitted primarily by respiratory droplets from infected individuals.

New Zealand’s approach has reportedly been successful in reducing the incidence of COVID-19 effectively. In New Zealand, the first COVID-19 infection was reported on 26 February 2020. After a month from the first incident, the country implemented a strict 49 day lockdown. They follow difficult border controls, skillfully manage quarantine facilities for new arrivals, and also effectively manage isolation programs. As a result, New Zealand has remained largely free of COVID-19. However, it should be noted that at first, the diagnosis was limited reagent, rigorous PCR testing is not carried out. In addition, small community outbreaks and border intrusions were also reported.

Serological surveillance has been shown to be most effective and is used to determine the cumulative incidence and to assess the number of asymptomatic COVID-19 cases. In the current scenario, due to national lockdowns and limited movement, blood donors have been used as population guards in many settings. New research has been released in medRxiv* preprint server, which focuses on SARS-CoV-2 transmission and prevalence in New Zealand, via blood donor serosurvey.

In the current study, samples were obtained through a static collection center and a mobile collection service run by the Blood Service of New Zealand. Samples were collected from 3 December 2020 to 6 January 2021, from individuals aged between 16 and 88 years. In total, 9,806 samples were analyzed. From the 2018 New Zealand census, scientists determined a detailed overview of the participants’ demographics. Spatially speaking, the participants were most likely to come from sixteen districts, out of the twenty, represented by the health council. This study was also evaluated by the Health and Disability Ethics Committee.

The researchers found that compared with antibodies to the nucleocapsid protein (N), specific antibodies to the Spike protein (S) and receptor binding domain (RBD) were maintained several months after COVID-19. Because of this, protein S-based assays are used in serosurveys. In this study, the serological testing algorithm was optimized for specificity due to the low number of COVID-19 cases reported in New Zealand. Furthermore, optimization is important because the prevalence of seropositive individuals is low (0.04%). This decreases the positive predictive value of the serologic test and also decreases the specificity.

In this study, samples were initially filtered using 2-step ELISA. This test is based on a one-point dilution test against RBD, after which a titration is performed against the trimeric S protein. Blood samples above the cut-off were then assessed using two immunoassays, namely, EuroImmun SARS-CoV-2 IgG ELISA (EuroImmun AG, Lübeck, Germany) and cPass replacement Viral Neutralization Test (sVNT) (GenScript, New Jersey, USA) . Samples were considered seropositive only after obtaining positive results in both commercial tests. The sensitivity and specificity of this test were evaluated using a Receiver Operator Characteristic (ROC) curve, which is based on a previous analysis covering 413 pre-pandemic negatives, 99 confirmed cases of COVID-19 via PCR testing.

Investigators of this study have reported that among 9,806 samples studied, 18 were found to be positive for Spike IgG (EuroImmun) and antibodies that inhibit the RBD-hACE-2 (sVNT) interaction with a high degree of correlation (Pearson r 0.7993, p <0.0001). Furthermore, these 18 seropositive samples were analyzed using a multiplex bead-based assay. This test determines the reactivity of the antibody isotypes to the RBD, S, and N proteins, whose patterns are found to be similar to those of infections that occurred weeks or months earlier. Most of the samples showed high concentrations of RBD and S. IgG protein. However, very few samples reported the presence of N IgG, IgA, or IgM proteins against three antigens (S, N, and M).

The study reports that among 18 seropositive samples, six were associated with donors with previously confirmed COVID-19 infection. The other four seropositive samples were donors who had traveled to high-risk countries, such as the UK and Europe, in 2020. Thus, all four people were infected outside of New Zealand. The last eight seropositive samples came from seven different health districts, where the crude seroprevalence estimate was 0.082%. To estimate true prevalence, the Rogan-Gladen estimator was used with the CI Lang-Reiczigel method to assess the sensitivity of the test. In this study, it was estimated that the true seroprevalence was 0.103% (95% CI 0.09-0.12%). Furthermore, the research also revealed that during the study period, undiagnosed infections occurred.

Investigators from this study observed that the very low seroprevalence of SARS-CoV-2 infection in New Zealand indicates reduced community transmission. Similar incidents have also been reported in Australia. This study is the first report to provide serological evidence of the success of New Zealand’s strategy to control COVID-19 before the vaccination program.

* Important Notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as established information.

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Swiss research shows the SARS-CoV-2 cohort infection is rare in school classrooms | Instant News


The role played by school children in transmitting severe Coronavirus 2 (SARS-CoV-2) infection is a controversial issue in many countries. Although infection rates can be high in children, they rarely develop severe symptoms or health outcomes in the 2019 coronavirus disease (COVID-19). Despite this, schools in many countries were closed during the first wave of the pandemic to contain the transmission of the virus, which resulted in disruption of education for more than 1.5 billion students worldwide.

Analyzing longitudinal changes in SARS-CoV-2 seroprevalence and clustering in Zurich schoolchildren during the first and second waves of the pandemic

Researchers from Switzerland recently presented the results of a longitudinal cohort study they conducted in the city of Zurich. The main objectives of this prospective cohort study were to analyze longitudinal changes in SARS-CoV-2 seroprevalence and assess seropositive groupings of children in school classes from June to November 2020 in Zurich, Switzerland.

Switzerland was one of the countries most affected by the second wave of the SARS-CoV-2 pandemic during the fall of 2020 in Europe. Because schools in Switzerland remain open, they offer a moderate to high exposure environment for studying SARS-CoV-2 infection. Children were randomly selected from different schools and classes, stratified by district, and invited for SARS-CoV-2 serological testing. Parents of selected children completed questionnaires on health and questions related to sociodemography.

Research participants came from 275 classes in 55 schools. A total of 2,603 ​​children participated in the study in June-July 2020, and 2,552 children in October-November 2020. The age range of children was between 6 and 16 years. The main outcomes measured included SARS-CoV-2 seroprevalence in June-July and October-November 2020, seropositive grouping of children in classes, and presence of symptoms in children.

The seroprevalence of SARS-CoV-2 was 2.4% in summer and 4.5% in late fall

In June-July 2020, 74 seropositive children out of 2,496 children had serological results available. In October-November 2020 the number of seropositive children increased to 173 from 2,503 children. Overall, the seroprevalence of SARS-CoV-2 in summer was 2.4% and in late fall 4.5% in previously non-seropositive children. This resulted in a total of 7.8% of the children being seropositive. Seroprevalence varies across districts. In fall, it’s between 1.7 and 15.0%.

No significant differences were observed between lower, middle, and upper school levels or between children aged 6-9 years, 9-13 years, and 12-16 years. Of the 2,223 children tested in the summer and fall, 28/70 or 40% of previously seropositive children became seropositive, and 109 / 2,153 or 5% of previously seropositive children became seropositive. 22% of seronegative children and 29% of new seropositive children since summer showed symptoms. The ratio of children with SARS-CoV-2 infection to seropositive children was 1 in 8 between July and November 2020.

At least one child was detected in 47 of 55 schools and in 90 of 275 new seropositive classes. Of the 130 classes with high enrollment rates, no seropositive children were found in 73 or 56% of the classes; 1 or 2 seropositive children in 50 grades (38%), and at least 3 seropositive children in 7 classes (5%). In a stratified logistic regression model, the school level explains 8% and the grade level explains 24% the seropositive variant.

The findings indicated that the SARS-CoV-2 cohort infection was rare in school classrooms

With schools in Switzerland open since August 2020 and several prevention strategies in place, seropositive groupings of children occurred in only a few classes despite a spike in overall seroprevalence during the moderate to high period of SARS-CoV-2 transmission in the community. Whether these findings will differ from the emergence of a new SARS-CoV-2 variant and the dynamic community transmission rates is uncertain.

“Future testing rounds of this study will provide insights into classroom transmission over extended periods during dynamic levels of community transmission and the spread of the new SARS-CoV-2 variant.”

Journal reference:

  • Ulyte A, Radtke T, Abela IA, Haile SR, Berger C, Huber M et al. Longitudinal clustering and changes in SARS-CoV-2 seroprevalence in schoolchildren in the canton of Zurich, Switzerland: prospective cohort study of 55 BMJ 2021 schools; 372: n616 doi: 10.1136 / bmj.n616, https://www.bmj.com/content/372/bmj.n616

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The Brazilian COVID variant is 2.5 times more contagious than the ancestral strain | Instant News


In early January 2021, a new variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified from travelers returning from Brazil. This variant, referred to as “P.1”, likely appeared in early to late November 2020, and then spread throughout Manaus, the capital of the Brazilian state of Amazonas, during the following December.

Researchers from Brazil modeled infection rates from ‘susceptible’ to individuals ‘exposed’ to variant P.1, and found that the transmission rate of the new variant was x2.5 times higher than the ancestral strain first identified from Wuhan. . They also found that there was a low risk of reinfection in individuals who had been infected with the original wave 1 variant (6.4%).

Pre-printed versions of the research paper are available for full reading at medRxiv* server.

Expansion diagram of the Deterministic Compartment (SEAIHRD) Model of Vulnerability, Exposure, Infection, and Recovery (SEIR). S: Vulnerable, E: Exposure (pre-symptomatic), H: Inpatient (severely infected individual), I: Infected (symptomatic individual, not hospitalized), A: Asymptomatic. D: Died, R: Recovered. The compartments are divided into 3 age classes, not represented here for simplicity. The compartment without sub-index corresponds to the wild-type variant, the compartment with sub-index 2 corresponds to VOC P.1. A continuous line represents the flux between each compartment. The dotted line shows the path of infection. The three parameters set by the model are indicated by small arrows.

Renato Coutinho and colleagues obtained data on inpatient cases of Coronavirus disease 2019 (COVID-19) in Manaus using the Brazilian epidemiological syndrome surveillance system – SIVEP Gripe. Data for patients hospitalized between November 1st 2020 to 31 Januaryst 2021 was used to determine the rate of transmission and reinfection of variant P.1. In this three month period, the variant frequency has increased in Manaus from 0% of patients to 73%. The team also used the data that is now broadcast to calculate the time period from 31st Until January 15thth February, when the data was collected.

The investigators used a deterministic compartment model to observe infection rates across three categories: ‘hospitalized’, ‘infected’ (symptomatic but not hospitalized), and ‘asymptomatic’. Each category was then divided into three further plots according to age: ‘young’ (under 20 years), ‘adults’ (between 20 and 60 years), and ‘elderly’ (over 60 years). They compared the P.1 variant with the original variant to evaluate the rate of transmission and reinfection.

Their results are in agreement with findings from other studies that have estimated the transmissibility rate of P.1 to be higher than the original strain (x1.4-2.2).

Variant P.1 has been detected in at least 25 countries at present. Coutinho and colleagues note that P.1 transmission may be lower than they found if decreased immunity is an important aspect of COVID-19 and recognize that this study is somewhat limited by easy sampling and small sample sizes. However, they cautioned that serious mitigation measures and further immunological & pathogenicity studies are needed to fully understand the P.1 level.

* Important Notice

medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as defined information.

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The British SARS-CoV-2 variant will soon become dominant in Switzerland | Instant News


Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) variant B.1.1.7, also known as the UK variant, is spreading globally. With high contagion observed, it is and can spread faster than previous variants.

To date, the variant has reached many countries, with the United States reporting more than 3,000 cases.

Researchers at the Swiss Institute of Bioinformatics and other institutions estimate that the B.1.1.7 variant may have been dominant in Switzerland in March.

In the study, published in medRxiv* server, the researchers performed whole genome sequencing of SARS-CoV-2 samples obtained from large diagnostic laboratories each week for genome surveillance.

British variant

In December 2020, the United Kingdom (UK) variant, also called B.1.1.7, was reported to the World Health Organization (WHO).

Various variants were also reported at the same time as the appearance of variant B.1.1.7. These include the South African variant (B.1.351) and the Brazilian variant (P.1).

The B.1.1.7 variant spreads faster and more efficiently throughout the population than the previous strain. Although preliminary research suggests that the variant causes only mild to moderate illness, new evidence suggests that this variant may be associated with an increased risk of death.

Meanwhile, variant B.1.351 is likely to be more resistant to vaccines and some therapies against the 2019 coronavirus disease (COVID-19). The P.1 variant, on the other hand, appeared in early January and has already reached other countries, such as the US and Japan.

Learning

The researchers conducted whole genome sequencing based on samples from Violler AG, an extensive diagnostic laboratory that processes SARS-CoV-2 samples from all over Switzerland, to arrive at the research findings.

Each week, SARS-CoV-2 samples were randomly selected to be sequenced among all positive test samples in the laboratory. For each sample, the researcher knows the date of the test and the area where the test was carried out.

Furthermore, the team also used data from Dr.’s medical laboratory. Risch, who screened their samples for the 501Y mutation with a variant-specific polymerase chain reaction (PCR) assay. They conducted analysis for the seven economic regions.

The team calculated the British variant’s transmission fitness gain for two data sets. The first data set allowed researchers to obtain estimates for seven regions of the Swiss economy.

The study findings suggest that the logistic growth rate is around 0.09 to 0.10 per day for Switzerland. In March, B.1.1.7 will be dominant in Switzerland, based on Swiss data tracking the 501Y mutation.

Currently, most new infections may have been caused by variant B.1.1.7 since the case was confirmed 8 to 11 days after infection.

The team also points out that in the first half of January, the absolute number of British variants increased, while the absolute number of all other cases decreased.

Overall, the research shows a consistent signal for the superiority of the transmission of the British variant in Switzerland. The estimate coincides with tariffs from the UK, Denmark and Switzerland.

B.1.1.7 transmission rates appear to have slowed in February globally, which may be due to compliance with and adherence to mitigation measures against COVID-19.

About 4.9 percent of all cases confirmed during the study period were characterized by whole genome sequencing. The team plans to continue the sorting effort every week with all data going to GISAID.

This team aims to assist and facilitate the global response to SARS-CoV-2 and monitor the spread of the new variant.

To date, the number of cases worldwide has reached 117.60 million, with more than 2.61 million deaths. The United States reported 29 million cases and approximately 527,000 deaths.

* Important Notice

medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as defined information.

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Worse problems with the SARS-CoV-2 variant may be occurring | Instant News


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease (COVID-19), continues to spread globally.

With this spread, new variants and strains have emerged, posing a threat to the newly developed and distributed SARS-CoV-2 vaccine. efficacy.

Researchers at the Department of Integrative Biomedical Sciences, University of Cape Town, South Africa, found evidence of significant changes in the selective power acting on immunologically important SARS-CoV-2 genes, such as N and S. This likely coincided with their appearance. of the 501Y lineage.

In the study, published on a pre-print server medRxiv*, the team examined patterns of mutations that appeared in the SARS-CoV-2 genome during the pandemic.

SARS-CoV-2 mutation

Between December 2019 and October 2020, worldwide viral evolution involved new, highly vulnerable host populations. D614G (Asp614-to-Gly) mutation in viruses spike protein accelerate the spread of the virus.

From there, only a few mutations were epidemiologically significant without affecting the pathogenesis of SARS-CoV-2. However, these mutations are characterized by a mutation pattern of slow and selectively neutral random genetic drift.

Since October 2020, SARS-CoV-2 has mutated several times. Currently, three variants are actively spreading – the British variant is called B.1.1.7 with multiple mutations in fall 2020, the South African variant is called B.1.351, and the Brazilian variant is called P.1.

SARS-CoV-2 genome map showing location and amino acid changes encoding of what we consider here to be the signature mutations of the V1, V2 and V3 sequences. Genes represented with light blue blocks encode non-structural proteins and genes in orange encode structural proteins: S encode spike protein, E envelope protein, M matrix protein, and N nucleocapsid protein. Within the S-gene, the receptor-binding domain (RBD) is shown in darker color and the site where the S protein is cleaved into two subunits during priming for receptor binding and cell entry is indicated by a dotted vertical line.

The British variant spreads faster and easier than the other variants. In January 2021, scientists said that the variant may be associated with an increased risk of death compared to other variants of the virus. It has spread to many countries around the world.

Variant B.1.351 is known to be resistant to the effects of vaccines and therapy against COVID-19. Meanwhile, the P.1 variant appeared on travelers from Brazil in early January. This variant contains an additional set of mutations that can affect their ability to be recognized by antibodies.

In the study, variants B.1.17 or 501Y.V1 were referred to as V1, B.1.351 or 501Y.V2 variants were V2, and variants P.1 or 501Y.V3 were referred to as V3.

To date, research has shown that antibodies produced by vaccination with approved vaccines recognize this variant, but further investigations are ongoing.

Amino acid locations encoded by codons evolved under positive selection and / or encoding convergent amino acid changes between lineages mapped to the 3D Spike structure (PDB 7DF4 structure; 47).  Human ACE2 receptors are shown in light blue color.  Signature mutations are not represented unless concluded to be under positive selection.  Site pairs detected coexisting in different lineages are connected by purple lines.

Amino acid locations encoded by codons evolved under positive selection and / or encoding convergent amino acid changes between lineages mapped to the 3D Spike structure (PDB 7DF4 structure; 47). Human ACE2 receptors are shown in light blue color. Signature mutations are not represented unless concluded to be under positive selection. Site pairs detected coexisting in different lineages are connected by purple lines.

Learning

This study aims to determine the evolutionary capacity of SARS-CoV-2 to adapt to increased population immunity and infection control measures such as social distancing and vaccinations.

The researchers examined the mutation patterns that appeared in the SARS-CoV-2 genome during the pandemic.

The team used a series of phylogenetic-based natural selection analysis techniques to examine positive selection patterns in the protein-coding sequences of the three lineages.

The study findings suggest the emergence of the 501Y lineage is consistent with substantial global changes in positive selection signals. This implies a general change in the selective environment in which SARS-CoV-2 thrives.

They also found significant changes in the selective power acting on the SARS-CoV-2 gene. Furthermore, the team revealed that the adaptive evolution of the 501Y lineage unites between lineages. This study highlights the essence of surveillance on how members of the 501Y lineage develop similar stages to ensure their survival and persistence.

The sudden appearance of the 501Y lineage

The team explained that in the first months of the pandemic no mutations had appeared. This is the sluggish pace of virus evolution. The start of the pandemic was like the pinnacle of a virus’ fitness in its ability to infect and transmit between people.

However, since October 2020, the sudden appearance of the 501Y lineage has caused cases to skyrocket around the world. V1, V2, and V3 caused faster virus transmission, which has now reached 192 countries and regions.

“Given the number of infections that occurred in October, all of these individual mutations, and even all pairs of mutations that could potentially interact epistatically, would have emerged independently,” the investigators explain.

To date, the number of cases has reached more than 117 million and 2.59 million deaths. The United States reports the highest number of infections, exceeding 29 million. Other countries whose cases have skyrocketed include India with 11.22 million cases; Brazil 11 million cases, Russia 4.28 million cases, and Britain 4.23 million cases.

* Important Notice

medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as defined information.

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