Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Letter Virology

Mutational and phylogenetic analyses of the two lineages of the Omicron variant

Swagata Majumdar et al.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Letter Virology

Emergence of Omicron third lineage BA.3 and its importance

Perumal A. Desingu et al.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Virology

Sequence analysis of the emerging SARS-CoV-2 variant Omicron in South Africa

Lulan Wang et al.

Summary: The discovery of the Omicron variant has sparked global concerns about its mutations, transmission, and immune escape properties. Current research suggests that the variant may impact viral infectivity and host immunity, and it may evolve from clade 20B.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Review Virology

The emergence and epidemic characteristics of the highly mutated SARS-CoV-2 Omicron variant

Dandan Tian et al.

Summary: The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Botswana in November 2021 and has since become the dominant strain in many countries. With a high number of mutations, it presents new challenges for preventing and controlling COVID-19. This review aims to provide a scientific reference by analyzing and summarizing the biological characteristics, epidemic features, immune escape, and vaccine reactivity of the Omicron variant.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Medicine, General & Internal

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

Nicole Wolter et al.

Summary: According to data analysis from South Africa, individuals infected with the omicron variant have a lower likelihood of hospitalization compared to those infected with non-omicron variants. Furthermore, individuals infected with the omicron variant have a lower odds of severe disease compared to individuals infected with the earlier delta variant.

LANCET (2022)

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Article Multidisciplinary Sciences

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana et al.

Summary: The SARS-CoV-2 epidemic in southern Africa has experienced three distinct waves, driven by different variants. The recently identified Omicron variant has rapidly spread in South Africa and to numerous countries, raising global concern.

NATURE (2022)

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Article Environmental Sciences

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

Fuqing Wu et al.

Summary: This research shows that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and infer early viral shedding dynamics for newly infected individuals, which are difficult to capture in clinical investigations.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

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Article Environmental Sciences

SARS-CoV-2 wastewater surveillance data can predict hospitalizations and ICU admissions

Aikaterini Galani et al.

Summary: This study in Greece measured the SARS-CoV-2 RNA load in raw wastewater as an early indicator of COVID-19 cases, hospitalizations, and ICU admissions, showing predictive leads of 5 to 9 days. Modeling techniques were used to establish relationships between RNA load in wastewater and pandemic health indicators, demonstrating the potential of combining clinical and environmental surveillance data to study and predict COVID-19 dynamics.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

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Article Multidisciplinary Sciences

Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology

Rabia Johnson et al.

Summary: This study used wastewater-based epidemiology to track the geographical distribution of SARS-CoV-2 variants in wastewater treatment plants in South Africa. The findings showed that the Delta variant became the predominant variant during the third wave, with signature mutations possibly increasing its viral infectivity.

SCIENTIFIC REPORTS (2022)

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Article Public, Environmental & Occupational Health

Trends in Disease Severity and Health Care Utilization During the Early Omicron Variant Period Compared with Previous SARS-CoV-2 High Transmission Periods — United States, December 2020–January 2022

A. Danielle Iuliano et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2022)

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Article Biochemistry & Molecular Biology

mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits similar B cell expansion, neutralizing responses, and protection from Omicron

Matthew Gagne et al.

Summary: This study shows that both mRNA-1273 and mRNA-Omicron generate comparable immunity and protection after booster doses, and are able to neutralize the Omicron variant.

CELL (2022)

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Review Environmental Sciences

Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic

Rekha Khandia et al.

Summary: Since December 2019, SARS-CoV-2 has been rapidly evolving and mutating, leading to various variants with different levels of infectivity and lethality. The most recent variant of concern is Omicron (B.1.1.529), which has raised concerns about its ability to evade pre-existing immunity and overcome antibody-based therapies. Several theories have been proposed to explain the high number of mutations in Omicron. To successfully handle the ongoing pandemic, a multifaceted approach including rapid diagnosis, genome analysis, vaccination, and updated medical facilities is needed.

ENVIRONMENTAL RESEARCH (2022)

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Meeting Abstract Infectious Diseases

Estimating SARS-CoV-2 prevalence from large-scale wastewater surveillance: insights from combined analysis of 44 sites in England

M. Morvan et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2022)

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Article Medicine, General & Internal

Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observational study from the ZOE COVID Study

Cristina Menni et al.

Summary: This study investigated the differences in symptom prevalence, risk of hospital admission, and symptom duration between omicron and delta variants of the SARS-CoV-2 virus. The study found that loss of smell was less common in omicron infections, sore throat was more common, and the rate of hospital admission was lower.

LANCET (2022)

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Article Multidisciplinary Sciences

COVID-19: How Omicron overtook Delta in three charts

Smriti Mallapaty

NATURE (2022)

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Article Multidisciplinary Sciences

Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa

Juliet R. C. Pulliam et al.

Summary: This study provides two methods for monitoring reinfection trends in routine surveillance data. The results suggest immune evasion by the Omicron variant in previously infected individuals in South Africa, and there has been an increase in the risk of having a third infection since mid-November 2021.

SCIENCE (2022)

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Article Virology

Estimation of Serial Interval and Reproduction Number to Quantify the Transmissibility of SARS-CoV-2 Omicron Variant in South Korea

Dasom Kim et al.

Summary: This study aimed to report the early estimates of the serial interval distribution and reproduction number for the omicron variant in South Korea. The findings showed that the omicron variant had a significantly shorter serial interval in child infectors compared to adult infectors. The mean reproduction number for the omicron variant during the first local outbreak was estimated to be 1.72. Adherence to strict public health measures, especially in children, is recommended to reduce the transmission risk of the highly transmissible omicron variant in the community.

VIRUSES-BASEL (2022)

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Article Multidisciplinary Sciences

Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

Rebecca J. Rockett et al.

Summary: The study reveals the co-infection of SARS-CoV-2 variants Omicron and Delta in two patients with chronic kidney disease, highlighting the importance of integrated genomic surveillance in vulnerable populations.

NATURE COMMUNICATIONS (2022)

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Article Public, Environmental & Occupational Health

Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa

Chengzhuo Tong et al.

Summary: This study proposes a province-level geographic prediction model to explore the spatiotemporal spread of Omicron in South Africa. The results suggest that the spread of Omicron varied at different stages and implementing lockdown measures and vaccination can effectively control its spread.

TRAVEL MEDICINE AND INFECTIOUS DISEASE (2022)

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Article Virology

Omicron (BA.1) and sub-variants (BA.1.1, BA.2, and BA.3) of SARS-CoV-2 spike infectivity and pathogenicity: A comparative sequence and structural-based computational assessment

Suresh Kumar et al.

Summary: This study used computational tools to evaluate the infectivity, transmission, and pathogenicity of the Omicron variant and its sub-variants. The research found that the Omicron and sub-variants have multiple mutations in the receptor-binding domain, increasing their affinity for human ACE2 and potential for transmission. However, mutations in the spike protein's N-terminal domain may result in less impact on the lower respiratory tract. Some mutations in the sub-variants of Omicron seemed to restore the binding effectiveness to ACE2.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Environmental Sciences

Managing an evolving pandemic: Cryptic circulation of the Delta variant during the Omicron rise

Karin Yaniv et al.

Summary: This paper discusses the spread of the new variant of concern, Omicron, and its impact on the Delta variant. Wastewater testing revealed the cryptic circulation of the Delta variant. The use of wastewater-based epidemiology is recommended for pandemic containment.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

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Article Environmental Sciences

SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ??.1 transition patterns in the absence of conventional surveillance evidence

Taxiarchis Chassalevris et al.

Summary: Wastewater-based variant surveillance provides valuable supplementary practice to conventional SARS-CoV-2 surveillance, offering timely and cost-effective information on virus prevalence.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

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Article Environmental Sciences

Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities

Femi F. Oloye et al.

Summary: Monitoring the communal incidence of COVID-19 is important for decision-making, but relying on a single method may lead to inaccurate results. Wastewater surveillance provides unbiased data that can predict COVID-19 situations in smaller communities.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

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Article Environmental Sciences

Comparing Rates of Change in SARS-CoV-2 Wastewater Load and Clinical Cases in 19 Sewersheds Across Four Major Metropolitan Areas in the United States

Mitham Al-Faliti et al.

Summary: This study tested various data processing approaches on wastewater surveillance data sets and found that a specific method led to strong correlations between wastewater and clinical case counts. The study also identified a sensitivity threshold for wastewater data that can help determine significant changes. The findings provide guidance for data processing and utilization of wastewater surveillance data.

ACS ES&T WATER (2022)

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Review Water Resources

SARS-CoV-2 known and unknowns, implications for the water sector and wastewater-based epidemiology to support national responses worldwide: early review of global experiences with the COVID-19 pandemic

Kelly Hill et al.

Summary: Wastewater surveillance of pathogens is a useful tool to assess the effectiveness of disease monitoring, providing a sensitive and rapid indicator of infection rate changes. Models can be used to back-calculate wastewater prevalence to population prevalence, as well as help design wastewater sampling strategies.

WATER QUALITY RESEARCH JOURNAL (2021)

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Article Environmental Sciences

COVID-19 containment on a college campus via wastewater-based epidemiology, targeted clinical testing and an intervention

Walter Q. Betancourt et al.

Summary: Wastewater-based epidemiology has shown potential as an early-warning tool for detecting the presence of COVID-19 in communities. By utilizing wastewater testing, infected individuals were identified and isolated, thereby preventing potential disease transmission.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

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Article Environmental Sciences

Spatial and Temporal Trends of SARS-CoV-2 RNA from Wastewater Treatment Plants over 6 Weeks in Cape Town, South Africa

Renee Street et al.

Summary: A study in Cape Town monitored SARS-CoV-2 RNA in wastewater during the peak of the COVID-19 epidemic, finding that the viral RNA signal peaked in the early stage and then gradually declined. The decrease in detected viral RNA in wastewater was associated with a reduction in newly identified COVID-19 cases in the city.

INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH (2021)

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Article Environmental Sciences

Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds

Jennifer Weidhaas et al.

Summary: The study found that SARS-CoV-2 RNA can be detected in wastewater, and highlighted the utility of wastewater epidemiology in assisting public health responses to COVID-19.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

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Article Medicine, General & Internal

Qualitative and quantitative detection of SARS-CoV-2 RNA in untreated wastewater in Western Cape Province, South Africa

R. Johnson et al.

Summary: Recent studies have shown that detecting SARS-CoV-2 genetic material in wastewater could help track virus dissemination in communities. Establishing a wastewater-based system in South Africa to monitor COVID-19 transmission is viable and could facilitate rapid identification of hotspots for interventions.

SAMJ SOUTH AFRICAN MEDICAL JOURNAL (2021)

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Article Environmental Sciences

First detection of SARS-CoV-2 in untreated wastewaters in Italy

Giuseppina La Rosa et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2020)

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Article Public, Environmental & Occupational Health

Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France

Julie Trottier et al.

ONE HEALTH (2020)

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Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

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