One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns.

The relative significance of graded immunizing and challenge doses in measuring the potency of vaccines; a study of mouse protection by typhoid vaccine

A study of the effect of graded immunizing doses of typhoid vaccine and graded challenge doses of S. typhosa in 5 per cent mucin on the degree of gradation of response (survival or death) elicited in successive groups of mice is reported. In the range of doses employed the effect of graded immunizing doses was markedly greater than was the effect of graded challenge doses. Statistically the difference exceeded the 0.1 per cent level of significance. It was concluded that the use of graded immunizing doses was preferable to the use of graded challenge doses as a basis for the immunological assay of typhoid vaccine, since with the former there was obtained (a) a greater significance of differences in response of groups given graded doses even with smaller fold increments in successive doses, (b) a greater slope of the dosage-response curve which permitted estimation of ED₅₀ values with smaller standard errors, and (c) an effect on response apparently less dependent on the sex of mice used.

Production of tolerance to the toxicity of Candida albicans by nonfungal materials

Hasenclever, H. F. (National Institute of Allergy and Infectious Diseases, Bethesda, Md.) and W. O. Mitchell. Production of tolerance to the toxicity of Candida albicans by nonfungal materials. J. Bacteriol. 84:1325-1329. 1962.-Tolerance in mice to the toxic manifestations of viable Candida albicans cells was elicited by injections of Salmonella enteritidis or S. typhosa lipopolysaccharides, or complete Freund's adjuvant. The greatest host stimulation occurred when the lipopolysaccharides were given 1 or 6 days before intravenous challenge. The highest level of tolerance produced by intraperitoneal preinfection with C. albicans was found when the yeast cells were injected 6 days before challenge. Older mice appeared to require larger amounts of endotoxin to demonstrate toxicity tolerance. Protection in mice that received both lipopolysaccharide injections and C. albicans intraperitoneal preinfection was slightly higher than in those mice given only the individual components.

A method for preparing smallpox vaccine on a large scale in cultured cells

A tissue culture system using chick embryo cells gave bacteria-free vaccinia virus suspensions of sufficient potency to use as a vaccine. Clinical trials with vaccines prepared by this method gave similar results to those with sheep lymph vaccine.

Allergic encephalomyelitis: rapid induction without the aid of adjuvants

Rapid production of allergic encephalomyelitis has heretofore required injection of nervous tissue emulsified in immunologic adjuvants. Adjuvants are not required if large doses of a potent nervous-tissue anttigen and a highly susceptible strain of rats are used. Susceptibility was increased in animals inoculated beforehand with pertussis vaccine.

EFFECT OF MITOCHONDRIAL STABILIZERS ON THE IMMUNOGENICITY OF THE PARTICULATE FRACTION ISOLATED FROM MYCOBACTERIUM TUBERCULOSIS

Youmans, Anne S. (Northwestern University Medical School, Chicago, Ill.), and Guy P. Youmans. Effect of mitochondrial stabilizers on the immunogenicity of the particulate fraction isolated from Mycobacterium tuberculosis. J. Bacteriol. 87:1346-1354. 1964.-A number of substances which have been used to stabilize mammalian mitochondrial preparations were tested to determine whether they would similarly affect the immunogenicity of a particulate fraction prepared from ruptured viable attenuated mycobacterial cells. The use of 0.44 m sucrose and the presence of 3 x 10(-2)m MgCl(2) during the preparatory processes markedly increased the immunogenicity of the particulate fraction. The increase was so great that immunogenic preparations were then consistently obtained which, in adequate dosage, were more immunogenic in CF-1 male mice than were viable attenuated mycobacterial cells. On the other hand, adenosine triphosphate (ATP), citrate, and polyvinylpyrrolidone when present during the preparatory processes reduced the immunogenicity. The addition of MgCl(2), ethylene-diaminetetraacetate, or ATP to the particulate fraction after it had been prepared did not increase its immunogenicity. When the particles were prepared in the 0.44 m sucrose buffer alone, incorporated in Freund's adjuvant, and injected intraperitoneally, immunogenicity was increased. However, this increase was not significantly greater than that obtained when the particles were prepared in the sucrose buffer containing MgCl(2). The immune state engendered in mice by the intraperitoneal injection of the particulate fraction persisted for at least 12 weeks.

IN VITRO MEASUREMENT OF THE POTENCY OF INACTIVATED FOOT-AND-MOUTH DISEASE VIRUS VACCINES

Inactivated vaccines have been prepared from one strain of FMD virus grown in guinea-pig pad epithelium, unweaned mice and cultured pig kidney and baby hamster kidney cells. The potencies of these vaccines in protecting guinea-pigs against challenge with inoculated infective virus of the same strain have been compared and related to the amounts of 25 mμ component present in the different virus suspensions. Although it was possible to obtain a relationship between the content of 25 mμ component and potency for an individual source of virus, this relationship does not hold for all the different sources of virus used. It is suggested that the reason for this failure is the partial masking of the 25 mμ component by a cell constituent present in some of the virus suspensions so that the component is incompletely estimated by the complement-fixation test.

EXPERIMENTAL VIABLE VACCINE AGAINST PULMONARY COCCIDIOIDOMYCOSIS IN MONKEYS

Converse, John L. (U.S. Army Biological Laboratories, Fort Detrick, Frederick, Md.), Merida W. Castleberry, and Ernest M. Snyder. Experimental viable vaccine against pulmonary coccidioidomycosis in monkeys. J. Bacteriol. 86:1041-1051. 1963.-Monkeys (Macaca mulatta) vaccinated by subcutaneous injection in the forearm with from 10 to 10(8) viable Coccidioides immitis arthrospores were protected against respiratory challenge with approximately 7000 viable arthrospores administered 6 months after vaccination. Protection was evident from: the healthy appearance throughout 4 months after respiratory challenge; negative chest X rays at 15, 30, 60, and 120 days; and only very minor histopathological pulmonary changes on autopsy at 120 days, with negative lung cultures in 80% of the animals. This was in striking contrast to the outward clinical appearance of control monkeys that were unvaccinated or had received nonviable arthrospore vaccines. These monkeys showed severe disease (loss of weight, accelerated respiration, severe coughing, general debilitation), positive X rays, massive pulmonary destruction, positive lung cultures, and death of five of nine animals. The appearance of spherules (very few in number, accompanied by very minor pathological changes) in the lungs of some of the "dissemination controls" (subcutaneous viable vaccination without respiratory challenge) indicated possible dissemination from the primary cutaneous infection, although oral transmission from the cutaneous lesions could not be ruled out.

COMPARATIVE STUDIES OF FRANCISELLA TULARENSIS AND FRANCISELLA NOVICIDA

Owen, C. R. (U.S. Public Health Service, Rocky Mountain Laboratory, Hamilton, Mont.), E. O. Buker, W. L. Jellison, D. B. Lackman, and J. F. Bell. Comparative studies of Francisella tularensis and Francisella novicida. J. Bacteriol. 87:676-683. 1964.-Comparative studies of various properties of Francisella tularensis (= Pasteurella tularensis) and F. novicida were performed. The two organisms are very similar morphologically. Growth of both was markedly enhanced by addition of cystine to media, but F. novicida is less fastidious than F. tularensis. The virulence of F. novicida for mice and cavies is lower than that of fresh isolates of F. tularensis. In complement-fixation tests, some cross-reaction occurred when rabbit antisera were used; complement-fixation tests with cavy antisera were specific. Agglutination tests with sera from both rabbits and cavies were specific. Nonliving vaccines of the two organisms (extracts, whole dead cells) conferred no cross-protection to mice; living attenuated vaccines conferred cross-protection which was more transitory than was specific protection. Passive cutaneous anaphylaxis (PCA) tests were highly specific. Absorption of antisera with homologous organisms removed all PCA reactivity, while absorption with heterologous organisms left it almost intact. Hemagglutination and hemagglutination-inhibition tests were specific. It was concluded that the two organisms are sufficiently similar to belong in the same genus but sufficiently different to be retained in separate species.

GAMMA GLOBULIN METABOLISM IN RABBITS DURING THE ANAMNESTIC RESPONSE

1. Gamma globulin metabolism and distribution were studied employing rabbit gamma globulin (RGG)I¹³¹ 24 times in 13 control rabbits. Similar studies were performed before and during the ananmestic response in 4 rabbits previously sensitized with a polyvalent pneumococcal vaccine. 2. During the ananmestic response, gamma-globulin levels increased from 1.0 to 6.0 gm/100 ml, and the gamma-globulin pool increased from 0.7 to 4.7 gm/kg. There was no change in the intravascular-extravascular partition of gamma globulin. 3. Gamma globulin degradation increased from 0.06 to 0.33 gm/kg/day during the 28 days of the immunization period while gamma globulin synthesis increased even further to average 0.47 gm/kg/day. Following the attainment of elevated gamma globulin levels the fractional rate of RGG-I¹³¹ turnover increased from 8.0 to 12.5 per cent/day. 4. No differences were noted in the metabolism of homologous or autologous gamma globulin regardless of the allotypic specificities.

RUNT DISEASE INDUCED IN NEONATAL MICE BY STERILE BACTERIAL VACCINES

A form of runt disease has been produced in neonatal CF-1 and ICR mice by the repeated injection of 10⁹ washed, autoclaved, saline-suspended staphylococci or streptococci. The most severely affected animals showed a marked decrease in lymphoid tissues and resembled grossly and microscopically animals suffering from the classical runt or wasting disease described by others. The timing of the initial antigenic stimulation was of importance, and animals started on their course of injections at an age of 48 hours or older showed no effect. There was a considerable variation in the severity of the disease within litters and from one litter to another. This variation could not be ascribed to a difference in susceptibility between sexes, since both male and female mice were observed to runt under appropriate conditions. Germ-free ICR mice were much more resistant to the runting phenomenon than conventional animals of the same strain, but could be induced to runt by injection of the staphylococcal vaccine suspended in homologous antiserum. The relationship of the runting phenomenon described here and classical runt disease or runting by adrenal hormones is discussed.

THE USE OF ACETYLETHYLENEIMINE IN THE PRODUCTION OF INACTIVATED FOOT-AND-MOUTH DISEASE VACCINES

Suspensions of FMD virus treated with 0·05% formalin at 26° C. for periods up to 144 hr. remained infective for cattle, although the infectivity could not be detected in the presence of aluminium hydroxide. Infectivity was detected in similar virus suspensions which had been treated with 0·05% AEI at 37° C. for 8 hr. but not in suspensions treated for 12 hr.

Vaccines prepared from these suspensions were antigenically potent and serum neutralization tests demonstrated the development and regression of serum antibody. The AEI vaccines were at least as potent as the corresponding formalin vaccines.