Evolutionary analysis of Omicron variant BF.7 and BA.5.2 pandemic in China

On December 7,2022,China adjusted public health control measures,there have been widespread of SARS-CoV-2 infections in Chinese mainland.As the number of infected people increased,the mutation probability of SARS-CoV-2 is also raised.Therefore,it is of great importance to monitor SARS-CoV-2 variants and its mutations in China.In this current study,665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants;to determine the composition of variants in China across different provinces;and analyze specific mutation frequency,focusing on 12 immune escape residues.The results showed that no new mutations were generated on the 12 immune escape residues.The evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites,officially named BF.7.14 by PANGO.This variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in China.The evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants,named BA.5.2.48 and BA.5.2.49 by PANGO,respectively.This variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic transmission.Finally,this study showed that current epidemic variants in China were already circulating in other countries,and there were no additional mutations on immune escape residues that could pose a threat to other countries.

“Mutation blacklist”and “mutation whitelist”of SARS-CoV-2

Over the past two years,scientists throughout the world have completed more than 6 million SARS-CoV-2 genome sequences.Today,the number of SARS-CoV-2 genomes exceeds the total number of all other viral genomes.These genomes are a record of the evolution of SARS-CoV-2 in the human host,and provide information on the emergence of mutations.In this study,analysis of these sequenced genomes identified 296,728 de novo mutations(DNMs),and found that six types of base substitutions reached saturation in the sequenced genome population.Based on this analysis,a“mutation blacklist”of SARS-CoV-2 was compiled.The loci on the“mutation blacklist”are highly conserved,and these mutations likely have detrimental effects on virus survival,replication,and transmission.This information is valuable for SARS-CoV-2 research on gene function,vaccine design,and drug development.Through association analysis of DNMs and viral transmission rates,we identified 185 DNMs that positively correlated with the SARS-CoV-2 transmission rate,and these DNMs where classified as the“mutation whitelist”of SARS-CoV-2.The mutations on the“mutation whitelist”are beneficial for SARS-CoV-2 transmission and could therefore be used to evaluate the transmissibility of new variants.The occurrence of mutations and the evolution of viruses are dynamic processes.To more effectively monitor the mutations and variants of SARS-CoV-2,we built a SARS-CoV-2 mutation and variant monitoring and pre-warning system(MVMPS),which can monitor the occurrence and development of mutations and variants of SARSCoV-2,as well as provide pre-warning for the prevention and control of SARS-CoV-2(https://www.omicx.cn/).Additionally,this system could be used in real-time to update the“mutation whitelist”and“mutation blacklist”of SARS-CoV-2.

All five COVID-19 outbreaks during epidemic period of 2020/2021 in China were instigated by asymptomatic or pre-symptomatic individuals

Introduction:The significance of asymptomatic or pre-asymptomatic individuals in driving the COVID-19 epidemic in China or other countries remains uncertain.Method:We collected and analyzed all the epidemiologic and virological diagnostic details of the infected individuals released by public health authorities and reiterated every episode of outbreak on a timeline.All individuals associated with the five outbreaks had tested positive for SARS-CoV-2 infection.Results:In this study,all five COVID-19 outbreaks reported in China since October 2020 were analyzed.The Kashgar outbreak in Xinjiang province came into light for the first time on October 22,2020.However,it was initiated before October 11,2020,by a local asymptomatic import and export worker,who was infected at the working place.Subsequently,his wife caught the infection,which led to 430 more infections reported in the outbreak.The Beijing outbreak with 41 cases was noticed for the first time on December 22,2020.However,our analysis revealed that it was initiated by an asymptomatic individual from Indonesia on December 10,2020.The Shenyang outbreak,with 38 cases,noticed for the first time on December 23,2020,was initiated by a pre-symptomatic individual from South Korea on December 13,2020.Conclusion:The asymptomatic or pre-symptomatic individuals during the asymptomatic period were unsuspectingly infected by SARS-CoV-2,and unintentionally transmitted the virus to a large number of people.These findings suggest that early detection of asymptomatic or pre-symptomatic individuals is of critical importance in preventing future outbreaks or epidemics.

Genomic Characterization of a New Coronavirus from Migratory Birds in Jiangxi Province of China

Dear Editor,The emergence of COVID-19 since December 2019 has attracted great attention around the world and reminds the powerful pathogenic potential of viruses(Zhou et al.2020).The subfamily Orthocoronavirinae of the family Coronaviridae contains four genera Alphacoronavirus,Betacoronavirus,Gammacoronavirus,and Deltacoronavirus,which are the largest group of positive-sense,non-segmented,single-stranded,enveloped RNA viruses(Woo et al.2012;Shi et al.2016).The genus Gammacoronavirus currently has five species(https://talk.ictvonline.org/taxonomy/),which are primarily spread through birds(Woo et al.2012).

Beta-and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China

Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses(SARS-Co V, MERS-Co V and SARS-Co V-2).Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world's high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus(beta-Co V) genome and a novel delta-coronavirus(delta-Co V) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-Co V shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-Co V(Mt Co V) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-Co V showed highest amino acid identity to Sparrow coronavirus HKU17(73.1%). Interestingly, our results identified a novel host(Montifringilla taczanowskii) for the novel delta-Co V and the potential cross-species transmission. The most recent common ancestor(t MRCA) of Mt Co Vs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-Co Vs and deltaCo Vs, and also provides a new perspective of the coronavirus hosts.

Novel pegiviruses infecting wild birds and rodents

Pegivirus(family Flaviviridae)is a genus of small enveloped RNA viruses that mainly causes blood infections in various mammals including human.Herein,we carried out an extensive survey of pegiviruses from a wide range of wild animals mainly sampled in the Qinghai-Tibet Plateau of China.Three novel pegiviruses,namely Passer montanus pegivirus,Leucosticte brandti pegivirus and Montifringilla taczanowskii pegivirus,were identified from different wild birds,and one new rodent pegivirus,namely Phaiomys leucurus pegivirus,was identified from Blyth's vole.Interestingly,the pegiviruses of non-mammalian origin discovered in this study substantially broaden the host range of Pegivirus to avian species.Co-evolutionary analysis showed virus-host co-divergence over long evolutionary timescales,and indicated that pegiviruses largely followed a virus-host co-divergence relationship.Overall,this work extends the biodiversity of the Pegivirus genus to those infecting wild birds and hence revises the host range and evolutionary history of genus Pegivirus.

Massive‐scale genomic analysis reveals SARS‐CoV‐2 mutation characteristics and evolutionary trends

The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 pandemic.In this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 genomes.All possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation efficiency.As a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation frequency.Furthermore,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons usage.In addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐2.Finally,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.

Food-trade-associated COVID-19 outbreak from a contaminated wholesale food supermarket in Beijing

The re-emerging outbreak of COVID-19 in Beijing,China,in the summer of 2020 originated from a SARSCoV-2-infested wholesale food supermarket.We postulated that the Xinfadi market outbreak has links with food-trade activities.Our Susceptible to the disease,Infectious,and Recovered coupled Agent Based Modelling(SIR-ABM)analysis for studying the diffusion of SARS-CoV-2 particles suggested that the trade-distancing strategy effectively reduces the reproduction number(R0).The retail shop closure strategy reduced the number of visitors to the market by nearly half.In addition,the buy-local policy option reduced the infection by more than 70%in total.Therefore,retail closures and buy-local policies could serve as significantly effective strategies that have the potential to reduce the size of the outbreak and prevent probable outbreaks in the future.