A follow up study of cycle threshold values of SARS-CoV-2 in Hunan Province,China

Since the epidemic of the severe acute respiratory syndrome coronavirus 2(SARS-COV-2),many governments have used reverse transcription polymerase chain reaction(RT-PCR)to detect the virus.However,there are fewer measures of CT values information based on RT-PCR results,and the relationship between CT values and factors from consecutive tests is not clear enough.So in this study,we analyzed the connection between CT values and the factors based on cohort data from Delta variant of SARS-CoV-2 in Hunan Province.Previous studies have showed that the mean age of the cases was 33.34 years(±18.72 years),with a female predominance(55.03%,n=71),and the greatest proportion of clinical symptoms were of the common type(60.47%,n=78).There were statistical differences between the N and ORF1ab genes in the CT values for the cases.Based on the analysis of the association between CT values and the factors,the lowest CT values were obtained for the unvaccinated,older and clinically symptomatic group at 3e10 days,the maximum peak of viral load occurred.Therefore,it is recommended to use patient information to focus on older,clinically symptomatic,unvaccinated patients and to intervene promptly upon admission.

Contact pattern,current immune barrier,and pathogen virulence determines the optimal strategy of further vaccination

Background:The current outbreak of novel coronavirus disease 2019 has caused a seriousdisease burden worldwide.Vaccines are an important factor to sustain the epidemic.Although with a relatively high-vaccination worldwide,the decay of vaccine efficacy andthe arising of new variants lead us to the challenge of maintaining a sufficient immunebarrier to protect the population.Method:A case-contact tracking data in Hunan,China,is used to estimate the contactpattern of cases for scenarios including school,workspace,etc,rather than ordinary susceptible population.Based on the estimated vaccine coverage and efficacy,a multi-groupvaccinated-exposed-presymptomatic-symptomatic-asymptomatic-removed model(VEFIAR)with 8 age groups,with each partitioned into 4 vaccination status groups isdeveloped.The optimal dose-wise vaccinating strategy is optimized based on the currentlyestimated immunity barrier of coverage and efficacy,using the greedy algorithm thatminimizes the cumulative cases,population size of hospitalization and fatality respectivelyin a certain future interval.Parameters of Delta and Omicron variants are used respectivelyin the optimization.Results:The estimated contact matrices of cases showed a concentration on middle ages,and has compatible magnitudes compared to estimations from contact surveys in otherstudies.The VEFIAR model is numerically stable.The optimal controled vaccination strategy requires immediate vaccination on the un-vaccinated high-contact population of age30e39 to reduce the cumulative cases,and is stable with different basic reproductionnumbers(R_(0)).As for minimizing hospitalization and fatality,the optimized strategy requires vaccination on the un-vaccinated of both aged 30e39 of high contact frequencyand the vulnerable older.Conclusion:The objective of reducing transmission requires vaccination in age groups ofthe highest contact frequency,with more priority for un-vaccinated than un-fully or fullyvaccinated.The objective of reducing total hospitalization and fatality requires not only toreduce transmission but also to protect the vulnerable older.The priority changes byvaccination progress.For any region,if the local contact pattern is available,then with thevaccination coverage,efficacy,and disease characteristics of relative risks in heterogeneouspopulations,the optimal dose-wise vaccinating process will be obtained and gives hintsfor decision-making.

Transmission Dynamics and Epidemiological Characteristics of the SARS-CoV-2 Delta Variant ― Hunan Province, China, 2021

Monitoring changes in the epidemiologic features between different severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants is key to understanding the evolution of viral fitness in the host population.Here,we analyzed a successfully contained local outbreak of the Delta variant that took place in Hunan,China,in July–August,2021.Detailed data on SARS-CoV-2 infections and their contacts were collected during the outbreak.By leveraging these data,we estimated key epidemiological parameters,including the incubation period,serial interval,and generation time.We constructed a generalized linear mixed-effects model(GLMM)to quantify risk factors for Delta infection and transmission.Between July 28 and August 15,2021,a total of 129 infections and their 2,118 close contacts were identified during the outbreak in Hunan Province.

Genetic Variation of Multiple Serotypes of Enteroviruses Associated with Hand, Foot and Mouth Disease in Southern China

Enteroviruses(EVs)species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand,foot and mouth disease(HFMD)in China.Mild infections are common in children;however,HFMD can also cause severe illness that affects the central nervous system.To molecularly characterize EVs,a prospective HFMD virological surveillance program was performed in China between 2013 and 2016.Throat swabs,rectal swabs and stool samples were collected from suspected HFMD patients at participating hospitals.EVs were detected using generic real-time and nested reverse transcription-polymerase chain reactions(RT-PCRs).Then,the complete VP1 regions of enterovirus A71(EV-A71),coxsackievirus A16(CVA16)and CVA6 were sequenced to analyze amino acid changes and construct a viral molecular phylogeny.Of the 2836 enrolled HFMD patients,2,517(89%)were EV positive.The most frequently detected EVs were CVA16(32.5%,819),CVA6(31.2%,785),and EV-A71(20.4%,514).The subgenogroups CVA16B1 b,CVA6D3 a and EV-A71C4 a were predominant in China and recombination was not observed in the VP1 region.Sequence analysis revealed amino acid variations at the 30,29 and 44 positions in the VP1 region of EV-A71,CVA16 and CVA6(compared to the respective prototype strains Br Cr,G10 and Gdula),respectively.Furthermore,in 21 of 24(87.5%)identified EV-A71 samples,a known amino acid substitution(D31 N)that may enhance neurovirulence was detected.Our study provides insights about the genetic characteristics of common HFMD-associated EVs.However,the emergence and virulence of the described mutations require further investigation.