Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province,China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)with unknown origin spread rapidly to 222 countries,areas or territories.To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong,60 specimens of SARS-CoV-2 were used to perform whole genome sequencing,and genomics,amino acid variation and Spike protein structure modeling analyses.Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species,with no evolution to other coronaviruses.There were one to seven nucleotide variations(SNVs)in each genome and all SNVs were distributed in various fragments of the genome.The Spike protein bound with human receptor,an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling.Our study clarifed the characteristics of SARS-CoV-2 genomic evolution,variation and Spike protein structure in the early phase of local cases in Guangdong,which provided reference for generating prevention and control strategies and tracing the source of new outbreaks.

Comprehensive narrative review of real-world COVID-19 vaccines:viewpoints and opportunities

Currently,people all over the world have been affected by coronavirus disease 2019(COVID-19).Fighting against COVID-19 is the top priority for all the countries and nations.The development of a safe and effective COVID-19 vaccine is considered the optimal way of ending the pandemic.Three hundred and 44 vaccines were in development,with 149 undergoing clinical research and 35 authorized for emergency use as to March 15 of 2022.Many studies have shown the effective role of COVID-19 vaccines in preventing SARS-CoV-2 infections as well as serious and fatal COVID-19 cases.However,tough challenges have arisen regarding COVID-19 vaccines,including long-term immunity,emerging COVID-19 variants,and vaccine inequalities.A systematic review was performed of recent COVID-19 vaccine studies,with a focus on vaccine type,efficacy and effectiveness,and protection against SARS-CoV-2 variants,breakthrough infections,safety,deployment and vaccine strategies used in the real-world.Ultimately,there is a need to establish a unified evaluation standard of vaccine effectiveness,monitor vaccine safety and effectiveness,along with the virological characteristics of SARS-CoV-2 variants;and determine the most useful booster schedule.These aspects must be coordinated to ensure timely responses to beneficial or detrimental situations.In the future,global efforts should be directed toward effective and immediate vaccine allocations,improving vaccine coverage,SARS-CoV-2 new variants tracking,and vaccine booster development.

Characterizing a large outbreak of dengue fever in Guangdong Province, China

Background:Dengue cases have been reported each year for the past 25 years in Guangdong Province,China with a recorded historical peak in 2014.This study aims to describe the epidemiological characteristics of this large outbreak in order to better understand its epidemic factors and to inform control strategies.Methods:Data for clinically diagnosed and laboratory-confirmed dengue fever cases in 2014 were extracted from the China Notifiable Infectious Disease Reporting System.We analyzed the incidence and characteristics of imported and indigenous cases in terms of population,temporal and spatial distributions.Results:A total of 45224 dengue fever cases and 6 deaths were notified in Guangdong Province in 2014,with an incidence of 47.3 per 100000 people.The elderly(65+years)represented 11.7%of total indigenous cases with the highest incidence(72.3 per 100000).Household workers and the unemployed accounted for 23.1%of indigenous cases.The majority of indigenous cases occurred in the 37th to 44th week of 2014(September and October)and almost all(20 of 21)prefecture-level cities in Guangdong were affected.Compared to the non-Pearl River Delta Region,the Pearl River Delta Region accounted for the majority of dengue cases and reported cases earlier in 2014.Dengue virus serotypes 1(DENV-1),2(DENV-2)and 3(DENV-3)were detected and DENV-1 was predominant(88.4%).Conclusions:Dengue fever is a serious public health problem and is emerging as a continuous threat in Guangdong Province.There is an urgent need to enhance dengue surveillance and control,especially for the high-risk populations in high-risk areas.

Malaria Surveillance of Entry People During the COVID-19 Epidemic—Guangdong Province,China,October 2020–May 2021

Summary What is already known about this topic?Malaria control was affected by the coronavirus disease 2019(COVID-19)pandemic.This study conducted active case finding for key flights and key populations to determine malaria transmission.What is added by this report?Surveillance for malaria was conducted for entry personnel coming from areas affected by malaria.It is estimated that at least 100,000 tests were conducted in Guangdong Province.

First Human Infection with Avian Influenza H9N2—Guangdong Province,China,2020

A case of avian influenza H9N2 was detected in a human in Zhuhai City,Guangdong Province through routine influenza surveillance on March 30,2020.The patient was a 3-year-old child who developed fever and cough on March 22.A pharyngeal swab was collected on March 23,and the novel coronavirus nucleic acid test was negative.On March 26,the pharyngeal swab was sent to Zhuhai CDC for influenza virus tests and was found to be H9 influenza A positive,and on March 30,Guangdong Provincial CDC reexamined the pharyngeal swabs as positive for influenza A(H9N2).

The collaboration between infectious disease modeling and public health decision-making based on the COVID-19

Public health decision-making may have great uncertainty especially in dealing with emerging infectious diseases,so it is necessary to establish a collaborative mechanism among modelers,epidemiologists,and public health decision-makers to reduce the uncertainty as much as possible.We searched the relevant studies on transmission dynamics modeling of infectious diseases,SARS,MERS,and COVID-19 as of March 1,2021 based on PubMed.We compared the key health decision-making time points of SARS,MERS,and COVID-19 prevention and control,and the publication time points of modeling research,to reveal the collaboration between infectious disease modeling and public health decision-making in the context of the COVID-19 pandemic.Searching with infectious disease and mathematical model as keywords,there were 166,81 and 1289 studies on the modeling of infectious disease transmission dynamics of SARS,MERS,and COVID-19 were retrieved respectively.Based on the modeling application framework of public health practice proposed in the current study,the collaboration among modelers,epidemiologists and public health decision-makers should be strengthened in the future.

Dengue Fever Outbreaks Caused by Varied Serotype Dengue Virus--Guangdong Province,China,2019

What is already known about this topic?Dengue fever(DF)outbreaks affect hundreds of millions of people worldwide and have increased significantly in Guangdong Province in 2019.What is added by this report?This paper described briefly DF outbreaks were attributed to several types of dengue virus(DENV)including DENV-1,DENV-2,and DENV-3 in 2019 in Guangdong,tracked the sources of viruses through phylogenetic analysis and epidemiological investigation,and primarily revealed the epidemiological links among the outbreaks.What are the implications for public health practice?The introduction of DENV from DF endemic areas increased pressure on the prevention and control of DF in Guangdong.Early detection of suspected cases and typing and genotyping of circulating viruses should be prioritized and enhanced to promptly assess the likelihood of local transmission,of introduction,and of subsequent sustained local transmission of the virus to implement optimal prevention and control strategies and measures.

Facilitating fine-grained intra-urban dengue forecasting by integrating urban environments measured from street-view images

Background:Dengue fever(DF)is a mosquito-borne infectious disease that has threatened tropical and subtropical regions in recent decades.An early and targeted warning of a dengue epidemic is important for vector control.Current studies have primarily determined weather conditions to be the main factor for dengue forecasting,thereby neglecting that environmental suitability for mosquito breeding is also an important factor,especially in fine-grained intra-urban settings.Considering that street-view images are promising for depicting physical environments,this study proposes a framework for facilitating fine-grained intra-urban dengue forecasting by integrating the urban environments measured from street-view images.