Monkeypox has spread unprecedentedly to nearly 100 countries and infected more than 51,000 people since 1 May 2022. This large-scale outbreak constituted a public health emergency of international concern (PHEIC), as declared by the World Health Organization. To better recognize and control this outbreak, we explore here through phylogenetic analysis the origins of MPXVs and their strains circulating in 2022, which remain unclear so far. Our results suggest that MPXVs possibly originated from some cowpox viruses and three lineages of MPXVs within Clade IIb circulated in 2022. Our results also suggest that two MPXVs respectively similar to the two MPXVs exported from Nigeria to the USA in 2021, ON676708/USA/2021 and ON676707/USA/2021, evolved into two lineages and sparked the large-scale outbreak in 2022, after their unknown evolutionary and epidemiological journeys possibly in Nigeria, the USA, or other countries before May 2022. This view does not stigmatize any country, because monkeypox is an endemic zoonosis in west Africa with wildlife reservoirs, and its large-scale outbreak in 2022 also resulted from the global decline of population immunity against smallpox due to the cease of vaccination against smallpox decades ago.

Hantaviridae currently encompasses seven genera and 53 species. Multiple hantaviruses such as Hantaan virus, Seoul virus, Dobrava-Belgrade virus, Puumala virus, Andes virus, and Sin Nombre virus are highly pathogenic to humans. They cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome or hantavirus pulmonary syndrome (HCPS/HPS) in many countries. Some hantaviruses infect wild or domestic animals without causing severe symptoms. Rodents, shrews, and bats are reservoirs of various mammalian hantaviruses. Recent years have witnessed significant advancements in the study of hantaviruses including genomics, taxonomy, evolution, replication, transmission, pathogenicity, control, and patient treatment. Additionally, new hantaviruses infecting bats, rodents, shrews, amphibians, and fish have been identified. This review compiles these advancements to aid researchers and the public in better recognizing this zoonotic virus family with global public health significance.

Few people in mainland China (MC) had been infected with COVID-19 before December 2022 due to the draconian zero-COVID policy of MC. The policy was terminated in early December 2022, and a tsunami-like epidemic of COVID-19 ensued soon. As elucidated below, the epidemic, which likely ended in January 2023, spread more rapidly and widely with a higher symptomatic rate than previously thought. The epidemic greatly enhanced the population immunity against COVID-19 in MC, which will accelerate the end of the pandemic (Figure 1) and reduce the emergence of risky variants of SARS-CoV-2 in China.We communicated on January 1−5, 2023 with 260 people who we knew before 2022 with the single question of how many percentages of their nearby acquaintances (i.e., those they have known for years and living around them) were infected with COVID-19 with obvious symptoms in December 2022). These 260 people were located at different places in 128 cities and 30 provinces or municipalities, and they were largely distributed as per the population density of MC. Among the 260 people, 195 lived in cities or towns, and 65 lived in the countryside. They stated that approximately 10%-100% (88.3 ± 12.5%) of their nearby acquaintances were infected with COVID-19 with fever and other obvious symptoms in December 2022. The rate in cities and towns, 88.3 ± 12.0%, was similar to the rate in the countryside, 88.4 ± 13.9%.The above data suggest that more than 85% of people in MC had a COVID-19 infection with obvious symptoms during the epidemic in December 2022. If 10% of COVID-9 cases during this epidemic were asymptomatic, more than 95% of people in MC were likely infected with COVID-19 during the epidemic. This is consistent with some official surveys, which showed that the epidemic spread very rapidly in various provinces or municipalities in December 2022. 1 The above data suggest that the COVID-19 epidemic spread more rapidly and prevalently, with a higher symptomatic rate than previously thought. This was comprehensible because COVID-19 has been highly contagious since early 2022 and MC adopted no strict restrictions to block the epidemic after November 2022. The cold weather during the epidemic and the natural decline of vaccination-induced immunity among the people in MC could account partially for the high infection rate and the high symptomatic rate of the epidemic. 2

Some nucleotide insertions or deletions (indels) in protein-coding open reading frames lead to frameshift mutations (FSMs) which can change amino acid sequences drastically. FSMs are widely distributed in the genomes of many organisms. However, few studies have been reported regarding frequencies of FSMs in microevolution or macroevolution. Many viruses evolve much more rapidly than cellular organisms, and they are hence suitable to investigate frequencies of FSMs in microevolution or macroevolution. In this report, we identified 667 FSMs in gene sequences of 13 virus families and each FSM changed approximately 11 amino acid residues on average. Of the FSMs, 89.21% were 2-indel compensatory FSMs, and the remaining were 1-, 3-, 4-, 5-indel FSMs. We found that FSMs usually occurred more frequently in the viruses of the same family with smaller sequence identities, and FSMs occurred in the sequences of with identities of 60.0−69.9% more frequently than in the sequences with identities of 90.0−99.9% or 80.0−89.9% by approximately 34.9 or 13.1 times on average. We also found FSMs occurred at different frequencies among genes in the same virus genome, among species in the same virus family, or among virus families (e.g., more frequently in Coronaviridae than in Orthomyxoviridae). These results suggest that FSMs are more frequent in the inter-species or macroevolution than in the intra-species or microevolution of viruses. They provide novel evidence for the hopeful monster hypothesis in evolutionary biology. They inspire researchers to investigate the roles, frequencies, features, and functions of FSMs in other viruses and cellular organisms.

The coronavirus disease 2019 (COVID-19) pandemic caused by the coronavirus severe acute respiratory syndrome coronavirus 2 remains risky worldwide. We elucidate here that good IDM (isolation, disinfection, and maintenance of health) is powerful to reduce COVID-19 deaths based on the striking differences in COVID-19 case fatality rates among various scenarios. IDM means keeping COVID-19 cases away from each other and from other people, disinfecting their living environments, and maintaining their health through good nutrition, rest, and treatment of symptoms and pre-existing diseases (not through specific antiviral therapy). Good IDM could reduce COVID-19 deaths by more than 85% in 2020 and more than 99% in 2022. This is consistent with the fact that good IDM can minimize co-infections and maintain body functions and the fact that COVID-19 has become less pathogenic (this fact was supported with three novel data in this report). Although IDM has been frequently implemented worldwide to some degree, IDM has not been highlighted sufficiently. Good IDM is relative, nonspecific, flexible, and feasible in many countries, and can reduce deaths of some other relatively mild infectious diseases. IDM, vaccines, and antivirals aid each other to reduce COVID-19 deaths.The IDM concept and strategy can aid people to improve their health behavior and fight against COVID-19 and future pandemics worldwide.

We found four striking differences in the COVID-19 case fatality rate (CFR). All of these striking differences suggest that, besides vaccination, good isolation of cases, disinfection of their living environments, and maintenance treatment (IDM) are highly effective is in mitigating COVID-19. This suggestion is crucial to the global control of the pandemic and consistent with the theoretical functions of IDM in minimizing co-infections with various other pathogens and maintaining human body functions. Accordingly, the risk for China to move away from its zero-COVID policy shall depend on China’s control measures. The CFR of COVID-19 in China can remain less than one tenth of that of influenza, namely that COVID-19 can remain “tiny influenza” in China, if the IDM measures are well implemented (e.g., staying at well-disinfected home with good rest for vast mild cases). Otherwise, the CFR of COVID-19 in China can be several times higher than that of influenza, namely that COVID-19 can be “giant influenza” in China. This analysis also clarifies that the COVID-19 CFR shall increase greatly if many asymptomatic or mild COVD cases are isolated together at temporary hospitals.

Human monkeypox, caused by monkeypox virus, has spread unprecedentedly to more than 100 countries since May 2022. Here we summarized the epidemiology of monkeypox through a literature review and elucidated the risks and elimination strategies of this outbreak mainly based on the summarized epidemiology. We demonstrated that monkeypox virus became more contagious and less virulent in 2022, which could result from the fact that the virus entered a special transmission network favoring close contacts (i.e., sexual behaviors of men who have sex with men outside Africa) and the possibility that the virus accumulated a few adaptive mutations. We gave the reasons to investigate whether cattle, goats, sheep, and pigs are susceptible to monkeypox virus and whether infection with monkeypox virus could be latent in some primates. We listed six potential scenarios for the future of the outbreak (e.g., the outbreak could lead to endemicity outside Africa with increased transmissibility or virulence). We also listed multiple factors aiding or impeding the elimination of the outbreak. We showed that the control measures strengthened worldwide after the World Health Organization declared the outbreak a public health emergency of international concern (PHEIC) could eliminate the outbreak in 2022. We clarified eight strategies, i.e., publicity and education, case isolation, vaccine stockpiling, risk-based vaccination or ring vaccination, importation quarantine, international collaboration, and laboratory management, for the elimination of the outbreak.

In recent years, the taxonomy of the families of Phenuiviridae, Nairoviridae, and Peribunyavidae in Bunyavirales was updated frequently, because many novel viruses in these families have been identified and the species demarcation criteria of these families have been changed. As per these criteria and sequence analysis, we found that the taxonomy of 19 species in these families should be revised. We presented six proposals for optimizing virus species taxonomy using the examples from these families. First, the species demarcation criteria for the same family (e.g., Peribunyavidae) should be unified. Second, the methods and parameters for the taxonomic calculation in the same order (e.g., Bunyavirales) should be unified. Third, virus species taxonomy should be based on phylogenetic relationships, rather than a cutoff value of sequence identities that is a self-contradictory demarcation criterion, although sequence identities aid virus taxonomy greatly. Fourth, virus species taxonomy should be based on the phylogenetic relationship of a key viral gene (e.g., the RdRp gene of Bunyavirales), which is important for the taxonomy of virus recombinants or reassortants. Fifth, a virus can be demarcated without a species before its biomedical significance has been revealed. Sixth, names of all viruses and virus species should be constituted exclusively with common characters (English letters and Arab numbers), to minimize difficulty in spelling and communication. These proposals are rational, flexible, and can accommodate all known viruses. They can also bridge the taxonomy history and the future demands due to their flexibility.