Epidemiology


Last updated: 2021 Sep 13
Total hit(s): 22
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G-variant of the SARS-CoV-2 was highly prevalent in Brazil and the use of a SEIR model that could be used to predict future outbreaks in infected countries was highlighted in the study. The spread of COVID-19 in Brazil was taken as the first case study, where 2 lineages of SARS-CoV-2 and time-varying reproduction number were considered. Prediction of the second outbreak at end of 2020 was due to the release of NPIs across Brazil. The importance of NPIs, continuous genomic surveillance to monitor SARS-CoV-2 mutations in the development of immunological interventions was highlighted.
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PMID
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Date of Publishing: 2020 Dec 10
Title The Impact of SARS-CoV-2 Variant to COVID-19 Epidemic in Brazil
Date of Entry 2021 Sep 13


The disease outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with those with wild-type strains were compared. B.1.617.2 infection was associated with lower PCR Ct values and longer viral shedding. B.1.617.2 infection was associated with higher chances of oxygen requirement, ICU admission or death. There were a number of vaccine breakthrough infections in the cohort, all patients infected with VOC, post-vaccination suffered from mild disease.
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PMID
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Date of Publishing: 2021 Jun 07
Title Clinical and Virological Features of SARS-CoV-2 Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.315 (Beta), and B.1.617.2 (Delta)
Date of Entry 2021 Sep 13


SARS-CoV-2 Delta variant presented the highest risk among the currently circulating strains, even in vaccinated individuals. Two Indian patients transmitted the Delta variant to 5 wedding guests in Houston, USA. The observations in the study indicate cases of vaccine breakthrough since there was no history of vaccine failure in the infected individuals.
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PMID
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Date of Publishing: 2021 Jul 04
Title Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections
Date of Entry 2021 Aug 6


Delta variant, identified in India, was reported to be 60% more infectious than the wild type SARS-CoV-2. Lockdown measures and unfavourable weather conditions, rather than population immunity, were responsible for low infection rates. Delta variant was able to evade immunity from previous wild type infection during the first and second wave (for about 45.8% of the time).
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PMID
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Date of Publishing: 2021 Jun 25
Title COVID-19 pandemic dynamics in India and impact of the SARS-CoV-2 Delta (B.1.617.2) variant
Date of Entry 18_28_50 Jul


SARS-CoV-2 Epsilon variant (B.1.427/B.1.429) found in California showed a 20% higher transmissibility and higher viral RNA loads being detected in patients compared to non-variants. No significant difference was found in Ct values between hospitalized patients and outpatients infected with B.1.427/B.1.429 variant or even non-variants.
33991487
(Cell)
PMID
33991487
Date of Publishing: 2021 Jun 24
Title Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Author(s) nameDeng X, Garcia-Knight MA et al.
Journal Cell
Impact factor
27.35
Citation count: 6
Date of Entry 18_28_50 Jul


B.1.526 variant has surged rapidly across the New York state in mid-April, and now it can be found in all 50 states of the US as well as in other numerous countries. During the initial days of infection, B.1.526 variant increased rapidly in the population until B.1.1.7 variant showed its dominance with an estimated growth rate of 5.3% per day. B.1.1.7 variant had an overall fitness advantage of 12-15% than its competitor B.1.526. Hence, B.1.1.7 variant slowed down the growth of the B.1.526 variant. Cases of the B.1.526 variant started to decline rapidly in areas where the B.1.1.7 variant was reported.
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PMID
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Date of Publishing: 2021 Jun 12
Title A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
Date of Entry 18_28_50 Jul


The transmission of the SARS-CoV-2 Alpha variant (B.1.1.7) was exclusive to the US where the majority of COVID-19 transmission routes were contributed by California, Washington, and Ohio as compared to the other states. Super spreader events can be one of the possible reasons of sudden rise in cases.
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PMID
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Date of Publishing: 2021 May 18
Title Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations
Date of Entry 18_28_50 Jul


The emergence of N440K variant in several parts of India has been reported during the second wave of the pandemic. It has been concluded that the N440K variant has higher transmissibility rate than the other two prevalent strains (A2a and A3i) when they were compared on the basis of replicative fitness and infectivity. To get a thorough understanding of the penetration of N440K in the Indian population, whole genome sequencing of the viral samples should be carried out.
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PMID
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Date of Publishing: 2021 Apr 30
Title N440K variant of SARS-CoV-2 has Higher Infectious Fitness
Date of Entry 18_28_50 Jul


First case of SARS-CoV-2 Alpha variant was detected In Japan on January 6, 2021, which was imported from UK with 60% higher infectiousness than the original strain. Possibility of a community outbreak was not unlikely in Japan 2 months after the detection of the first variant case, but could not be confirmed.
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PMID
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Date of Publishing: 2021 Apr 17
Title Estimating SARS-CoV-2 variant strain infectiousness in Japan as of March 28, 2021
Date of Entry 18_28_50 Jul


The spread of Alpha variant in Switzerland increased due to its higher transmission fitness which was 43-52% more than that of the older circulating strains. Reproductive number for the Alpha variant was always above 1 while the non-Alpha strain showed a Ro below 1. The growth model predicted that there would be a rise in case numbers if the B.1.1.7 variant becomes predominant during the month of March in Switzerland. However, the model was not inclusive of the effects of lockdown measures, vaccination and infection-induced imuunity.
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PMID
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Date of Publishing: 2021 Apr 16
Title Quantification of spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
Date of Entry 18_28_50 Jul


3 regions in England reported a higher number of cases (34.6%) with the SARS-CoV-2 Alpha variant. However, the Alpha variant did not show higher transmission during lockdowns. But the prevalence of the Alpha variant in the samples increased over the study period (from 79% to 96%) due to failure in the detection of the spike gene target in RT-PCR tests. There is no need of changing the criteria for symptomatic COVID-19 testing.
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PMID
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Date of Publishing: 2021 Apr 12
Title Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study
Date of Entry 18_28_50 Jul


It was observed that the SARS-CoV-2 named CAL.20C (B.1.427/B.1.429) variant originated in California and progressively spread to other US states and 29 other countries. The progressive geographical spread of the B.1.427/B.1.429 VOC from California to other US states and countries were found to be consistent with the other recent findings of their increased transmissibility relative to currently circulating strains.
33821281
(bioRxiv)
PMID
33821281
Date of Publishing: 2021 Apr 1
Title SARS-CoV-2 immune evasion by variant B.1.427/B.1.429
Author(s) nameMcCallum M, Bassi J et al.
Journal bioRxiv
Impact factor
Its not a journal
Citation count: 1
Date of Entry 18_28_50 Jul


The increased prevalence of the SARS-CoV-2 Epsilon variant (B.1.427/B.1.429) in San Fransico had a higher rate of transmissibility than other variants that resulted in increased secondary household infections. Limitations : There were several limitations of the study; being done on a random basis without differentiatial selection of variants, improper classification of index cases and incomplete coverage of household tests
33688689
(medRxiv)
PMID
33688689
Date of Publishing: 2021 Mar 3
Title Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco
Author(s) namePeng J, Mann SA et al.
Journal medRxiv
Impact factor
Cant find
Citation count: 1
Date of Entry 18_28_50 Jul


Mathematical modelling studies showed that the frequency of emergence of new variants was fairly common in infected individuals. Most of these variants do not survive. The predominant variants are associated with higher infectiousness and super-spreader events soon after they are introduced in the general population. 1. The reason for predominance of certain variants is unknown. 2. Approximate outbreak sizes for introduction of new variations and secondary infections from a person infected with a new variant could not be predicted.
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PMID
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Date of Publishing: 2021 Mar 24
Title Early super-spreader events are a likely determinant of novel SARS-CoV-2 variant predominance
Date of Entry 18_28_50 Jul


The rapid spread and rise in the 20E (EU1) variant cases were due to increased summer travelers from Spain and the lack of effective screening/restrictions despite having no transmission advantage over the circulating strains. Spain was likely to be the origin of 20E (EU1) introductions in most countries. A higher incidence of non-20E (EU1) variants towards the end of summer in Belgium might explain the low incidence of the 20E (EU1) variant in some countries (Belgium, France, Czech Republic).
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PMID
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Date of Publishing: 2021 Mar 24
Title Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Date of Entry 18_28_50 Jul


3 imported cases were reported from London to Madrid, Spain. One of these cases initiated a household transmission to 3 other individuals. In addition, 2 cases were identified without epidemiological association to the UK strain, indicating independent introduction. Sequence deposited at GISAID: EPI_ISL_756271, 756272, 756273 and 756274
33685741
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PMID
33685741
Date of Publishing: 2021 Feb 19
Title First confirmation of importation and transmission in Spain of the newly identified SARS-CoV-2 B.1.1.7 variant
Date of Entry 18_28_50 Jul


The SARS-CoV-2 Alpha variant (B.1.1.7) emerged around October,2020 in UK. It had a rapid epidemic growth and higher transmissibility relative to other variants and was declared as the Variant of Concern(VOC). The study was important to control the spread of a highly transmissible variant. Limitations : - data analyzed did not entirely represent SARS-CoV-2 infections, - the analysis was on relatively simple data using simple parsimonious assumptions, - the spatiotemporal correlation intrinsic in infectious disease data was not explicitly modelled.
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PMID
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Date of Publishing: 2021 Jan 04
Title Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking B.1.1.7 in England: Insights from linking epidemiological and genetic data.
Date of Entry 18_28_50 Jul


The SARS-CoV-2 Alpha variant (501Y.V2), prevalent in early Sept and mid-Nov, and the Beta variant (501Y.V2), circulating since late Sept, was 10% and 75% more transmissible than the 501N lineage, respectively. The proportion of 501Y Variant 2 has been spreading rapidly, in the South East, East of England and London regions since Nov suggesting a transmission advantage over the 501N lineage. Only a small number of 501Y Variant 2 has been identified elsewhere (e.g., in Denmark) - origin unclear, and the 501Y variant lineages in Australia and spain are devoid of the deletions.
33413740
(Euro Surveill)
PMID
33413740
Date of Publishing: 2021 Jan
Title Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020
Author(s) nameLeung K, Shum MH et al.
Journal Euro Surveill
Impact factor
7.37
Citation count: 4
Date of Entry 18_28_50 Jul


The analysis of the growth during the english chanel lockdown( Nov 5 and Dec 2 2020) revealed that the SARS-CoV-2 Alpha variant (B.1.1.7) spread widely (R>1) and increased during lockdown, while other lineages declined(R<1), suggesting a strong transmissibility advantage over previous circulating lineages. Limitation - dense PCR testing but relatively low genomic surveillance data; Geographic coverage is very uneven with some countries sequencing at higher rates than others
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PMID
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Date of Publishing: 2020 Dec 30
Title Lineage-specific growth of SARS-CoV-2 B.1.1.7 during the English national lockdown
Date of Entry 18_28_50 Jul


The dynamic tracking of the SARS-CoV-2 shows that the D614G variant was predominant in Europe and North America but not in China. In the absence of positive selection pressure due to anti-viral drugs, human population genetics could be a possible reason for evolution of the virus. It is not clear how the ACE2 expression score correlates with fold changes in ACE2 expression in different populations. It is also unclear which threshold of ACE2 expression score is required to provide enough driving force for SARS-CoV-2 selection.The SARS-CoV-2 D614G mutation notably did not increase the binding affinity with ACE2
33374416
(Genes (Basel))
PMID
33374416
Date of Publishing: 2020 Dec 24
Title Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation
Author(s) nameHuang SW, Miller SO et al.
Journal Genes (Basel)
Impact factor
3.759
Citation count: 1
Date of Entry 18_28_50 Jul


The SARS-CoV-2 Beta variant (501Y.V2) emerged in the Nelson Mandela Bay of South Africa between July and August, which was associated with a greater number of cases by early November when compared to the three main older circulating strains. The Beta variant was the dominant circulating strain in Eastern and Western Cape, owing to the rapid surge in SARS-CoV-2 infections.
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PMID
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Date of Publishing: 2020 Dec 22
Title Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
Date of Entry 18_28_50 Jul


A novel SARS-CoV-2 variant called the Y839 variant was reported in Portugal, which rapidly spread throughout the country by the end of April. This novel variant was imported from Italy and was more prevalent in the northern (22%) and central regions (59%) of Portugal. The new variant Y839 was selectively advantageous over other known circulating strains which led to its dissemination in 12 other countries comprising 4 continents. Moreover, the mean ct values for variant Y839 (22.7) was more than the ct value for variant D839 (22.6) which indicated a lower viral load relating to higher infectivity in the sample than the ancestral variant (D839).
33131453
(Emerg Microbes Infect)
PMID
33131453
Date of Publishing: 2020 Dec
Title Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal.
Author(s) nameBorges V, Isidro J et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 1
Date of Entry 18_28_50 Jul