Genomic surveillance of SARS-CoV-2 in mainland China after ending the zero-COVID policy, December 2022-January 2023.
Ontology highlight
ABSTRACT:
SUBMITTER: Liu P
PROVIDER: S-EPMC9977122 | biostudies-literature | 2023 Apr
REPOSITORIES: biostudies-literature
Publications
Genomic surveillance of SARS-CoV-2 in mainland China after ending the zero-COVID policy, December 2022-January 2023.
The Journal of infection 20230301 4
Similar Datasets
Project description:ImportanceRespiratory pathogens cause high rates of morbidity and mortality globally and have high pandemic potential. During the SARS-CoV-2 pandemic, influenza surveillance was significantly interrupted because of resources being diverted to SARS-CoV-2 testing and sequencing. Based on recommendations from the World Health Organization, the Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 testing and genomic sequencing into the influenza surveillance program. We describe the results of influenza and SARS-CoV-2 testing of samples collected from 16 sentinel surveillance sites located throughout Uganda as well as SARS-CoV-2 testing and sequencing in other health centers. The surveillance system showed that both SARS-CoV-2 and influenza can be monitored in communities at the national level. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will help facilitate the timely release of SARS-CoV-2 information for COVID-19 pandemic mitigation and provide important information regarding the persistent threat of influenza.
| S-EPMC10715035 | biostudies-literature
Project description:Data on reinfection in large Asian populations are limited. In this study, we aimed to evaluate the reinfection rate, disease severity, and time interval between the infections in the symptomatic and asymptomatic populations which are firstl infected with BA.2 Omicron Variant. We retrospectively included adult patients with COVID-19 discharged from four designated hospitals between 27 April 2021 and 30 November 2022, who were interviewed via telephone from 29 January to 1 March 2023. Univariable and multivariable analyses were used to explore risk factors associated with reinfection. A total of 16,558 patients were followed up, during the telephone survey of an average of 310.0 days, 1610 (9.72%) participants self-reported reinfection. The mean time range of reinfection was 257.9 days. The risks for reinfection were analysed using multivariable logistic regression. Patients with severe first infection were at higher risk for reinfection (aORs, 2.50; P < 0.001). The male (aORs,0.82; P < 0.001), the elderly (aORs, 0.44; P < 0.001), and patients with full vaccination (aORs, 0.67; P < 0.001) or booster (aORs, 0.63; P < 0.001) had the lower risk of reinfection. Patients over 60 years of age (aORs,9.02; P = 0.006) and those with ≥2 comorbidities (aORs,11.51; P = 0.016). were at higher risk for severe reinfection. The number of clinical manifestations of reinfection increases in people with severe first infection (aORs, 2.82; P = 0.023). The overall reinfection rate was 9.72%, and the reinfection rate of Omicron-to-Omicron subvariants was 9.50% at one year. The severity of Omicron-Omicron reinfection decreased. Data from our clinical study may provide clinical evidence and bolster response preparedness for future COVID-19 reinfection waves.
| S-EPMC10849001 | biostudies-literature
Project description:ImportanceSeveral pharmacotherapies have been authorized to treat nonhospitalized persons with symptomatic COVID-19. Longitudinal information on the use of these therapies is needed.ObjectiveTo analyze trends and factors associated with prescription of outpatient COVID-19 pharmacotherapies within the Veterans Health Administration (VHA).Design, setting, and participantsThis cohort study evaluated nonhospitalized veterans in VHA care who tested positive for SARS-CoV-2 from January 2022 through January 2023 using VHA and linked Community Care and Medicare databases.ExposuresDemographic characteristics, underlying medical conditions, COVID-19 vaccination, and regional and local systems of care, including Veterans Integrated Services Networks (VISNs).Main outcomes and measuresMonthly receipt of any COVID-19 pharmacotherapy (nirmatrelvir-ritonavir, molnupiravir, sotrovimab, or bebtelovimab) was described. Multivariable logistic regression was used to identify factors independently associated with receipt of any vs no COVID-19 pharmacotherapy.ResultsAmong 285 710 veterans (median [IQR] age, 63.1 [49.9-73.7] years; 247 358 males [86.6%]; 28 444 Hispanic [10.0%]; 61 269 Black [21.4%] and 198 863 White [69.6%]) who tested positive for SARS-CoV-2 between January 2022 and January 2023, the proportion receiving any pharmacotherapy increased from 3285 of 102 343 veterans (3.2%) in January 2022 to 5180 of 21 688 veterans (23.9%) in August 2022. The proportion declined to 2194 of 10 551 veterans (20.8%) by January 2023. Across VISNs, the range in proportion of patients who tested positive who received nirmatrelvir-ritonavir or molnupiravir during January 2023 was 41 of 692 veterans (5.9%) to 106 of 494 veterans (21.4%) and 2.1% to 120 of 1074 veterans (11.1%), respectively. Veterans receiving any treatment were more likely to be older (adjusted odds ratio [aOR] for ages 65-74 vs 50-64 years, 1.18; 95% CI, 1.14-1.22; aOR for ages ≥75 vs 50-64 years, 1.19; 95% CI, 1.15-1.23) and have a higher Charlson Comorbidity Index score (aOR for CCI ≥6 vs 0, 1.52; 95% CI, 1.44-1.59). Compared with White veterans, Black veterans (aOR, 1.06; 95% CI, 1.02-1.09) were more likely to receive treatment, and compared with non-Hispanic veterans, Hispanic veterans (aOR 1.06; 95% CI, 1.01-1.11) were more likely to receive treatment.Conclusions and relevanceThis study found that prescription of outpatient COVID-19 pharmacotherapies in the VHA peaked in August 2022 and declined thereafter. There were large regional differences in patterns of nirmatrelvir-ritonavir and molnupiravir use.
| S-EPMC10472184 | biostudies-literature
Project description:China announced a slight easing of its zero-COVID rules on November 11, 2022, and then a major relaxation on December 7, 2022. We estimate that the ensuing wave of SARS-CoV-2 infections caused 1.41 million deaths in China during December 2022-February 2023, substantially higher than that reported through official channels.
| S-EPMC10521589 | biostudies-literature
Project description:ImportanceIn China, the implementation of stringent mitigation measures kept COVID-19 incidence and excess mortality low during the first years of the pandemic. However, China's decision to end its dynamic zero COVID policy (a proactive strategy that deploys mass testing and strict quarantine measures to stamp out any outbreak before it can spread) in December 2022 resulted in a surge in COVID-19 incidence and hospitalizations. Despite worldwide attention given to this event, the actual impact of this sudden shift in policy on population mortality has not been empirically estimated.ObjectiveTo assess the association of the sudden shift in China's dynamic zero COVID policy with mortality using empirical and syndromic surveillance data.Design, setting, and participantsThis cohort study analyzed published obituary data from 3 universities in China (2 in Beijing and 1 in Heilongjiang) and search engine data from the Baidu index (BI; weighted frequency of unique searches for a given keyword relative to the total search volume on the Baidu search engine) in each region of China from January 1, 2016, to January 31, 2023. Using an interrupted time-series design, analyses estimated the relative change in mortality among individuals 30 years and older in the universities and the change in BI for mortality-related terms in each region of China from December 2022 to January 2023. Analysis revealed a strong correlation between Baidu searches for mortality-related keywords and actual mortality burden. Using this correlation, the relative increase in mortality in Beijing and Heilongjiang was extrapolated to the rest of China, and region-specific excess mortality was calculated by multiplying the proportional increase in mortality by the number of expected deaths. Data analysis was performed from February 10, 2023, to March 5, 2023.ExposureThe end to the dynamic zero COVID policy in December 2022 in China.Main outcomes and measuresMonthly all-cause mortality by region.ResultsAn estimated 1.87 million (95% CI, 0.71 million-4.43 million; 1.33 per 1000 population) excess deaths occurred among individuals 30 years and older in China during the first 2 months after the end of the zero COVID policy. Excess deaths predominantly occurred among older individuals and were observed across all provinces in mainland China except Tibet.Conclusions and relevanceIn this cohort study of the population in China, the sudden lifting of the zero COVID policy was associated with significant increases in all-cause mortality. These findings provide valuable insights for policy makers and public health experts and are important for understanding how the sudden propagation of COVID-19 across a population may be associated with population mortality.
| S-EPMC10450565 | biostudies-literature
Project description:COVID-19 is an acute respiratory infectious disease caused by SARS-CoV-2. It was first reported in Wuhan, China in December 2019 and rapidly spread globally in early 2020, triggering a global pandemic. In December 2022, China adjusted the dynamic COVID-zero strategy that lasted for three years. The number of positive cases in China increased rapidly in the short term. Weihai was also affected during this period. We conducted genomic surveillance of SARS-CoV-2 variants in Weihai during this period, hoping to understand the changes in the genomic characteristics of SARS-CoV-2 before and after the adjustment of the epidemic policy. In this study,we collected SARS-CoV-2 positive samples from March 2022 to March 2023 in Weihai and performed SARS-CoV-2 whole genome sequencing on these samples using next-generation sequencing technology. we obtained a total of 704 SARS-CoV-2 whole genome sequences, and selected 581 high-quality sequences for further analysis. The analysis results showed that from March 2022 to November 2022, before the adjustment of epidemic policy, the COVID-19 cases in Weihai were mainly from four local clusters,which were caused by four variants, including BA.2,BA.1.1,P.1.15 and BA.5.2.1. Phylogenetic analysis showed that: In the same cluster,the sequences between each other were highly homologous, and the whole genome sequence were almost identical. After December 2022, the epidemic policy was adjusted, BF.7 and BA.5.2 became the dominant variants in Weihai, consistent with the main domestic strains in China during the same period. Phylodynamic analysis showed that BF.7 and BA.5.2 had a large amount of genetic diversities in December, and the effective population size of BF.7 and BA.5.2 also showed explosive growth in December. In conclusion, we reported the composition and dynamic trend of SARS-CoV-2 variants in Weihai from March 2022 to March 2023. We found that there have been significant changes in the variants and expansion patterns of SARS-CoV-2 before and after the adjustment of epidemic policies. But the dominant variants in Weihai were the same as the SARS-CoV-2 variants circulating globally at the same time and we found no persistently dominant variants or new lineages during this period.
| S-EPMC10682769 | biostudies-literature
Project description:This article documents the public availability of (i) transcriptome sequence data and assembly for the rostrum dace (Leuciscus burdigalensis) naturally infected by a copepod ectoparasite (Tracheliastes polycolpus) and (ii) SNPs identified and validated from RAD sequencing for the Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing.
| S-EPMC4491430 | biostudies-literature
Project description:With numbers of COVID-19 cases having substantially increased at the end of 2022 in China, some countries have started or expanded testing and genomic surveillance of travellers. We report screening results in Italy in late December 2022 of 556 flight passengers in provenance from two Chinese provinces. Among these passengers, 126 (22.7%) tested SARS-CoV-2 positive. Whole genome sequencing of 61 passengers' positive samples revealed Omicron variants, notably sub-lineages BA.5.2.48, BF.7.14 and BQ.1.1, in line with data released from China.
| S-EPMC9837854 | biostudies-literature
Project description:Analysis of genomic variability of pathogens associated with heightened public health concerns is an opportunity to track transmission routes of the disease and helps to develop more effective vaccines and specific diagnostic tests. We present the findings of a detailed genomic analysis of the genomic variability of the SARS-CoV-2 Omicron variant that spread in Russia between 8 December 2021 and 30 January 2022. We performed phylogenetic analysis of Omicron viral isolates collected in Moscow (n = 589) and downloaded from GISAID (n = 397), and identified that the BA.1 lineage was predominant in Russia during this period. The BA.2 lineage was also identified early in December 2021. We identified three cases of BA.1/BA.2 coinfections and one case of Delta/Omicron coinfection. A comparative genomic analysis of SARS-CoV-2 viral variants that spread in other countries allowed us to identify possible cases of transmission. We also found that some mutations that are quite rare in the Global Omicron dataset have a higher incidence rate, and identified genetic markers that could be associated with ways of Omicron transmission in Russia. We give the genomic variability of single nucleotide variations across the genome and give a characteristic of haplotype variability of Omicron strains in both Russia and around the world, and we also identify them.
| S-EPMC9786029 | biostudies-literature
Project description:BackgroundThe emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata.ResultsIn total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related.ConclusionThe global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.
| S-EPMC10257533 | biostudies-literature