The dynamic change of SARS-CoV-2 variants in Sierra Leone

Lin, Lei; Zhang, Juling; Rogers, James T.; Campbell, Allan; Zhao, Jian; Harding, Doris; Sahr, Foday; Liu, Yongjian; Wurie, Isata

doi:10.1016/j.meegid.2022.105208

Cited by 6 publications

(9 citation statements)

References 16 publications

(16 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The use of next-generation sequencing technology can be beneficial in several steps of an epidemic response [13], among them, pathogen identification [14], tracing the origins of the agent [15][16][17], and monitoring its spread [18][19][20][21][22][23] and evolution [17,24,25], as well as supporting development of diagnostic solutions and new therapeutic target discovery [26]. Even though there are different approaches to full-genome sequencing, the multiplex PCR amplicon method is currently one of the cheapest, while also proving to be superior to capture-based sequencing in the analysis of challenging samples [4].…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

Szargut

Cytacka

Serwin

et al. 2022

Viruses

View full text Add to dashboard Cite

The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.

show abstract

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

Szargut

Cytacka

Serwin

et al. 2022

Viruses

View full text Add to dashboard Cite

show abstract

“…In developing countries setting, conventional next‐generation sequences are commonly challenging and requires extensive bioinformatics expertise. Moreover, the Oxford MinION, a third‐generation nanopore‐based platform has been used in several LMICs including India, Bangladesh, Indonesia, and others for SARS‐CoV‐2 nationwide surveillance studies 31–38 . This study represents a pioneering genomic surveillance effort, involving systematic sampling in Mongolia for respiratory viral pathogens.…”

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

Erendereg,

Tumurbaatar,

Byambaa

et al. 2023

Immunity Inflam & Disease

View full text Add to dashboard Cite

BackgroundCoronavirus disease (COVID‐19) has had a significant impact globally, and extensive genomic research has been conducted on severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) lineage patterns and its variants. Mongolia's effective response resulted in low prevalence until vaccinations became available. However, due to the lack of systematically collected data and absence of whole genome sequencing capabilities, we conducted a two‐stepped, nationally representative molecular epidemiologic study of SARS‐CoV‐2 in Mongolia for 2020 and 2021.MethodsWe used retrospective analysis of stored biological samples from November 2020 to October 2021 and a variant‐specific real‐time reverse transcription polymerase chain reaction (RT‐PCR) test to detect SARS‐CoV‐2 variants, followed by whole genome sequencing by Nanopore technology. Samples were retrieved from different sites and stored at −70°C deep freezer, and tests were performed on samples with cycle threshold <30.ResultsOut of 4879 nucleic acid tests, 799 whole genome sequencing had been carried out. Among the stored samples of earlier local transmission, we found the 20B (B.1.1.46) variant predominated in the earlier local transmission period. A slower introduction and circulation of alpha and delta variants were observed compared to global dynamics in 2020 and 2021. Beta or Gamma variants were not detected between November 2020 and September 2021 in Mongolia.ConclusionsSARS‐CoV‐2 variants of concerns including alpha and delta were delayed in circulation potentially due to public health stringencies in Mongolia. We are sharing our initial experience with whole genome sequencing of SARS‐CoV‐2 from Mongolia, where sequencing data is sparse.

show abstract

“…This suggests that SARS-CoV-2's introduction led to local transmission events. A previous study showed that, in Sierra Leone, the second COVID-19 wave was mainly caused by the R1 lineage, while the third COVID-19 wave was dominated by the spread of the B.1.617.2 lineage (Delta variant), and further phylogenetic analysis revealed that multiple introductions of SARS-CoV-2 into Sierra Leone subsequently led to clusters and community transmission in the country ( 29 ). Similarly, most of Africa's COVID-19 cases that were considered to constitute the third wave of the pandemic were either imported cases or were triggered by imported COVID-19 cases ( 28 ).…”

Section: Discussionmentioning

confidence: 99%

Epidemiological Trends of Coronavirus Disease 2019 in Sierra Leone From March 2020 to October 2021

Liu

Gao²,

Xue³

et al. 2022

Front. Public Health

Self Cite

View full text Add to dashboard Cite

Coronavirus disease 2019 (COVID-19), a serious public health challenge the world over, has led to significant health concerns in Sierra Leone. In the present study, epidemic indices, such as the number of cases, positivity rate, reproduction rate (R0), case fatality rate (CFR), age, and sex, were used to characterize the epidemiological trends of COVID-19. As of October 31, 2021, a total of 6,398 cases and 121 related deaths had been confirmed. The total number of COVID-19 reverse transcription polymerase chain reaction (RT-PCR) tests conducted to October 31, 2021, was 249,534, and the average positivity rate was 2.56%. Three waves of COVID-19 were recorded, occurring during weeks 15–46 in 2020 (2,369 cases), week 47 in 2020 to week 16 in 2021 (1,665 cases), and weeks 17–43 in 2021 (2,364 cases), respectively. Remarkably, there was no increase in the numbers of confirmed COVID-19 cases despite rising test numbers throughout the three waves. Moreover, three high R0 values were observed before each wave. The number of positive cases significantly correlated with positive numbers of international arrivals (P < 0.01), deaths (P < 0.01), and the positivity rate of tested samples (P < 0.01). Moreover, all of the deaths occurred during the peak of the three waves. Our results indicate that there was a low level of COVID-19 epidemic in Sierra Leone and that COVID-19's introduction led to local transmission. It is vital to fight against the spread of SARS-CoV-2 from the source of origin by strengthening testing and management of people entering the country. Our findings will provide important clues for expanding sample screening and will contribute to the reasonable allocation of medical resources.

show abstract

The dynamic change of SARS-CoV-2 variants in Sierra Leone

Cited by 6 publications

References 16 publications

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

Epidemiological Trends of Coronavirus Disease 2019 in Sierra Leone From March 2020 to October 2021

Contact Info

Product

Resources

About