Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats

Bats are the natural reservoir hosts for SARS-related coronavirus(SARSr-CoV)and other highly pathogenic microorganisms.Therefore,it is conceivable that an individual bat may harbor multiple microbes.However,there is limited knowledge on the overall co-circulation of microorganisms in bats.Here,we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts.Among these,76 individual samples were selected for further metagenomics analysis.We found a complex microenvironment characterized by the general cocirculation of microbes from two different sources:mammal-associated viruses or environment-associated microbes.The later includes commensal bacteria,enterobacteria-related phages,and insect or fungal viruses of food origin.Results showed that 25%(19/76)of the samples contained at least one another mammal-associated virus,notably alphacoronaviruses(13/76)such as AlphaCoV/YN2012,HKU2-related CoV and AlphaCoV/Rf-HuB2013,along with viruses from other families.Notably,we observed three viruses co-circulating within a single bat,comprising two coronavirus species and one picornavirus.Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats.Furthermore,we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples,some of which formed new evolutionary lineages.Collectively,our study reveals the complex microenvironment of bat microbiome,facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.

Characteristics of SARS-CoV-2 transmission in a medium-sized city with traditional communities during the early COVID-19 epidemic in China

The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-Co V-2 epidemics in several large cities or provinces of China. However,information regarding the early epidemics in small and medium-sized cities, where there are still traditionally large families and community culture is more strongly maintained and thus, transmission profiles may differ, is limited. In this study, we characterized 60 newly sequenced SARS-Co V-2 genomes from Anyang as a representative of small and medium-sized Chinese cities, compared them with more than 400 reference genomes from the early outbreak, and studied the SARS-Co V-2 transmission profiles. Genomic epidemiology revealed multiple SARS-Co V-2 introductions in Anyang and a large-scale expansion of the epidemic because of the large family size.Moreover, our study revealed two transmission patterns in a single outbreak, which were attributed to different social activities. We observed the complete dynamic process of single-nucleotide polymorphism development during community transmission and found that intrahost variant analysis was an effective approach to studying cluster infections. In summary, our study provided new SARS-Co V-2 transmission profiles representative of small and medium-sized Chinese cities as well as information on the evolution of SARS-Co V-2 strains during the early COVID-19 epidemic in China.

Genetic Mutation of SARS-CoV-2 during Consecutive Passages in Permissive Cells

Dear Editor,The ongoing COVID-19 disease,caused by severe acute respiratory syndrome coronavirus 2(SARS-Co V-2),has led to over 112 million confirmed cases and 2.4 million deaths in more than 220 countries as of 25 February 2021(WHO 2021).Hospital-admitted patients show clinical features including fever,dry cough,fatigue,dyspnea,lymphopenia,and pneumonia with radiological groundglass lung opacities(Huang et al.2020;Guan et al.2020).SARS-Co V-2 was quickly isolated and could be detected in clinical samples,such as nasopharyngeal swabs,sputum,alveolar lavage fluid,and feces,as well as occasionally in seminal fluid and tears among other sources(Bhat et al.2020;Li et al.2020),which means that it can infect a variety of human tissues and organs.