Responding to an outbreak of a novel coronavirus [agent of coronavirus disease 2019 (COVID-19)] in December 2019, China banned travel to and from Wuhan city on 23 January 2020 and implemented a national emergency response. We investigated the spread and control of COVID-19 using a data set that included case reports, human movement, and public health interventions. The Wuhan shutdown was associated with the delayed arrival of COVID-19 in other cities by 2.91 days. Cities that implemented control measures preemptively reported fewer cases on average (13.0) in the first week of their outbreaks compared with cities that started control later (20.6). Suspending intracity public transport, closing entertainment venues, and banning public gatherings were associated with reductions in case incidence. The national emergency response appears to have delayed the growth and limited the size of the COVID-19 epidemic in China, averting hundreds of thousands of cases by 19 February (day 50).

The proposed pulmonary inflammation load score was higher in patients with severe COVID-19 in comparison with patient with mild disease. The optimal inflammation load score threshold for identifying severe patients was 19.5, with 83.3% sensitivity and 94% specificity. Summary statement The chest CT severity score could be used to rapidly identify patients with severe forms of COVID-19. Background: Quantitative and semi-quantitative indicators to evaluate the severity of lung inflammation in Coronavirus Disease 2019 (COVID-19) could provide an objective approach to rapidly identify patients in need of hospital admission. Purpose: To evaluate the value of chest computed tomography severity score (CT-SS) in differentiating clinical forms of COVID-19. Materials and Methods: Inclusion of 102 patients with COVID-19 confirmed by positive real-time reverse transcriptase polymerase chain reaction on throat swabs underwent chest CT (53 men and 49 women, 15-79 years old, 84 cases with mild and 18 cases with severe disease). The CT-SS was defined by summing up individual scores from 20 lung regions; scores of 0, 1, and 2 were respectively assigned for each region if parenchymal opacification involved 0%, less than 50%, or equal or more than 50% of each region (theoretical range of CT-SS from 0 to 40). The clinical and laboratory data were collected, and patients were clinically subdivided according to disease severity by the Chinese National Health Commission guidelines. Results: The posterior segment of upper lobe (left, 68/102; right, 68/102), superior segment of lower lobe (left, 79/102; right, 79/102), lateral basal segment (left, 79/102; right, 70/102) and posterior basal segment of lower lobe (left, 81/102; right, 83/102) were the most frequently involved sites in COVID-19. Lung opacification mainly involved the lower lobes, in comparison with middle-upper lobes. No significant differences in distribution of the disease were seen between right and left lungs. The individual scores of in each lung, as well as the total CT-SS were higher in severe COVID-19 when compared with mild cases (P＜ 0.05. The optimal CT-SS threshold for identifying severe COVID-19 was 19.5 (area under curve, 0.892), with 83.3% sensitivity and 94% specificity. Conclusion: CT-SS could be used to quickly and objectively evaluate the severity of pulmonary involvement in COVID-19 patients.

The human gut microbiota is a reservoir of antibiotic resistance genes, but little is known about their diversity and richness within the gut. Here we analyse the antibiotic resistance genes of gut microbiota from 162 individuals. We identify a total of 1,093 antibiotic resistance genes and find that Chinese individuals harbour the highest number and abundance of antibiotic resistance genes, followed by Danish and Spanish individuals. Single-nucleotide polymorphism-based analysis indicates that antibiotic resistance genes from the two European populations are more closely related while the Chinese ones are clustered separately. We also confirm high abundance of tetracycline resistance genes with this large cohort study. Our study provides a broad view of antibiotic resistance genes in the human gut microbiota.

The genetic diversity of Yersinia pestis, the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of Y. pestis strains that were isolated in China and elsewhere. These SNPs define the genealogy of Y. pestis since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.infectious disease | molecular clock | phylogenomics | NGS | molecular epidemiology

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species.